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Information on EC 6.3.1.19 - prokaryotic ubiquitin-like protein ligase
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EC Tree
6.3.1.19 prokaryotic ubiquitin-like protein ligaseIUBMB Comments
The enzyme has been characterized from the bacteria Mycobacterium tuberculosis and Corynebacterium glutamicum. It catalyses the ligation of the prokaryotic ubiquitin-like protein (Pup) to a target protein by forming a bond between an epsilon-amino group of a lysine residue of the target protein and the gamma-carboxylate of the C-terminal glutamate of the ubiquitin-like protein (Pup). The attachment of Pup, also known as Pupylation, marks proteins for proteasomal degradation.
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Word Map
- 6.3.1.19
- mycobacterium
- tuberculosis
-
depupylation
-
pup-proteasome
- actinobacteria
- depupylase
-
deamidation
- ligases
- deamidase
- smegmatis
-
ubiquitin-proteasome
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tcmsp
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cytoscape
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isopeptide
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genecards
- nitrospirae
- drug development
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Reaction Schemes
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[prokaryotic ubiquitin-like protein]-L-glutamate
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N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Synonyms
pup ligase, proteasome accessory factor a, ubiquitin-like protein ligase, prokaryotic ubiquitin-like protein ligase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PafA
proteasome accessory factor A
Pup ligase
Pup-protein ligase
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Rv2097c
ubiquitin-like protein ligase
PafA
Micrococcus luteus ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230
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PafA
ambiguous
Pup ligase
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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Pup ligase
Micrococcus luteus ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230
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Pup ligase
Renibacterium salmoninarum ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
PafA catalyzes a two-step reaction by forming a gamma-glutamyl phosphate-mixed anhydride intermediate on the C-terminal glutamate of PupE by hydrolyzing ATP, followed by attaching it to nucleophilic substrates by catalyzing the formation of isopeptide bonds between PupE C-terminal glutamate gamma-carboxylate and the side chain of protein substrate lysine residues, mechanism of PafA self-pupylation, overview. K320 is the major target residue for the pupylation of PafA. During the self-pupylation of PafA, the attachment of the first Pup to PafA is catalyzed by the other PafA molecule through an intermolecular reaction, while the formation of the polymeric Pup chain is carried out in an intramolecular manner through the internal ligase activity of the already pupylated PafA. Among the three lysine residues, K7, K31 and K61, in Mycobacterium smegmatis Pup, K7 and K31 are involved in the formation of the poly-Pup chain in PafA poly-pupylation. Poly-pupylation of PafA can be reversibly regulated by depupylase Dop
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Bifidobacterium adolescentis ATCC 15703 / DSM 20083 / NCTC 11814 / E194a
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Acidothermus cellulolyticus ATCC 43068 / 11B
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Mycobacterium tuberculosis ATCC 25618 / H37Rv
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Renibacterium salmoninarum ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Kocuria rhizophila ATCC 9341 / DSM 348 / NBRC 103217 / DC2201
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Salinispora tropica ATCC BAA-916 / DSM 44818 / CNB-440
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Mycolicibacterium smegmatis ATCC 700084 / mc2155
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
PafA catalyzes a two-step reaction by forming a gamma-glutamyl phosphate-mixed anhydride intermediate on the C-terminal glutamate of PupE by hydrolyzing ATP, followed by attaching it to nucleophilic substrates by catalyzing the formation of isopeptide bonds between PupE C-terminal glutamate gamma-carboxylate and the side chain of protein substrate lysine residues, mechanism of PafA self-pupylation, overview. K320 is the major target residue for the pupylation of PafA. During the self-pupylation of PafA, the attachment of the first Pup to PafA is catalyzed by the other PafA molecule through an intermolecular reaction, while the formation of the polymeric Pup chain is carried out in an intramolecular manner through the internal ligase activity of the already pupylated PafA. Among the three lysine residues, K7, K31 and K61, in Mycobacterium smegmatis Pup, K7 and K31 are involved in the formation of the poly-Pup chain in PafA poly-pupylation. Poly-pupylation of PafA can be reversibly regulated by depupylase Dop
Mycolicibacterium smegmatis ATCC 700084 / mc2155
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Rhodococcus erythropolis PR4 / NBRC 100887
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine = ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
reaction mechanisms of ligation to substrates and cleavage from pupylated substrates, overview. Pup passes a process of disorder-to-order transition
Micrococcus luteus ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
[prokaryotic ubiquitin-like protein]:[protein]-L-lysine
The enzyme has been characterized from the bacteria Mycobacterium tuberculosis and Corynebacterium glutamicum. It catalyses the ligation of the prokaryotic ubiquitin-like protein (Pup) to a target protein by forming a bond between an epsilon-amino group of a lysine residue of the target protein and the gamma-carboxylate of the C-terminal glutamate of the ubiquitin-like protein (Pup). The attachment of Pup, also known as Pupylation, marks proteins for proteasomal degradation.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [adenylate kinase-His6]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[adenylate kinase-His6]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [FabD]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[FabD]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [IdeR]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[IdeR]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [inositol 1-phosphate synthetase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[inositol 1-phosphate synthetase]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [Log]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[Log]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [malonyl Co-A acyl carrier protein transacylase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[malonyl Co-A acyl carrier protein transacylase]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [myo-inositol-1-phosphate synthetase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[myo-inositol-1-phosphate synthetase]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[PanB]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [phosphoenolpyruvate-protein phosphotransferase I]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[phosphoenolpyruvate-protein phosphotransferase I]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [prokaryotic ubiquitin-like protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[prokaryotic ubiquitin-like protein]-L-lysine
in addition to the lysine at position 61, Pup (prokaryotic ubiquitin-like protein) presents two more lysines, one at position 7 and another at position 31. Pup can be pupylated on different lysines
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [proteasome-interacting ATPase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[proteasome-interacting ATPase]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein PanB]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-[[prokaryotic ubiquitin-like protein]-L-glutamate]-[[protein]-L-lysine]
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [adenylate kinase-His6]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[adenylate kinase-His6]-L-lysine
adenylate kinase from Escherichia coli is pupylated
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [adenylate kinase-His6]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[adenylate kinase-His6]-L-lysine
adenylate kinase from Escherichia coli is pupylated
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [FabD]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[FabD]-L-lysine
FabD from Mycobacterium tuberculosis is pupylated on a preferred Lys173
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [FabD]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[FabD]-L-lysine
Mycobacterium tuberculosis ATCC 25618 / H37Rv
FabD from Mycobacterium tuberculosis is pupylated on a preferred Lys173
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [IdeR]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[IdeR]-L-lysine
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [IdeR]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[IdeR]-L-lysine
Mycobacterium smegmatis recombinant His6-tagged IdeR is a model substrate for in vitro studies
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [IdeR]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[IdeR]-L-lysine
Mycolicibacterium smegmatis ATCC 700084 / mc2155
Mycobacterium smegmatis recombinant His6-tagged IdeR is a model substrate for in vitro studies
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [IdeR]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[IdeR]-L-lysine
Mycolicibacterium smegmatis ATCC 700084 / mc2155
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [inositol 1-phosphate synthetase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[inositol 1-phosphate synthetase]-L-lysine
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [inositol 1-phosphate synthetase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[inositol 1-phosphate synthetase]-L-lysine
Mycobacterium tuberculosis ATCC 25618 / H37Rv
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [Log]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[Log]-L-lysine
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [Log]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[Log]-L-lysine
Mycobacterium tuberculosis ATCC 25618 / H37Rv
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [malonyl Co-A acyl carrier protein transacylase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[malonyl Co-A acyl carrier protein transacylase]-L-lysine
Lys173 is the predominant modified residue in malonyl Co-A acyl carrier protein transacylase (FabD) purified from Escherichia coli. Lys122 and Lys181 are also identified as pupylation targets. At least three lysines in Mtb FabD can be pupylated in Escherichia coli. It also seems that only one residue per FabD polypeptide is pupylated at one time
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [malonyl Co-A acyl carrier protein transacylase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[malonyl Co-A acyl carrier protein transacylase]-L-lysine
Lys173 is the predominant modified residue in malonyl Co-A acyl carrier protein transacylase (FabD) purified from Escherichia coli. Lys122 and Lys181 are also identified as pupylation targets. At least three lysines in Mtb FabD can be pupylated in Escherichia coli. It also seems that only one residue per FabD polypeptide is pupylated at one time
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [myo-inositol-1-phosphate synthetase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[myo-inositol-1-phosphate synthetase]-L-lysine
expression of Mycobacterium tuberculosis ino1, pafA and pupGlu, results in pupylated myo-inositol-1-phosphate synthetase (Ino1) in Escherichia coli
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [myo-inositol-1-phosphate synthetase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[myo-inositol-1-phosphate synthetase]-L-lysine
expression of Mycobacterium tuberculosis ino1, pafA and pupGlu, results in pupylated myo-inositol-1-phosphate synthetase (Ino1) in Escherichia coli
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[PanB]-L-lysine
Mycobacterium tuberculosis PanB is a model substrate of PafA, in silico docking analysis reveals interaction via PafA residue arginine 207
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[PanB]-L-lysine
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Mycobacterium tuberculosis PanB is a model substrate of PafA, in silico docking analysis reveals interaction via PafA residue arginine 207
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[PanB]-L-lysine
PanB from Mycobacterium tuberculosis is pupylated at a single lysine residue, K212, formation of a covalent MtbPup-MtbPanB conjugate
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[PanB]-L-lysine
Mycobacterium tuberculosis ATCC 25618 / H37Rv
PanB from Mycobacterium tuberculosis is pupylated at a single lysine residue, K212, formation of a covalent MtbPup-MtbPanB conjugate
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[PanB]-L-lysine
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[PanB]-L-lysine
PanB is a model substrate of PafA
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[PanB]-L-lysine
Mycolicibacterium smegmatis ATCC 700084 / mc2155
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-
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [phosphoenolpyruvate-protein phosphotransferase I]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[phosphoenolpyruvate-protein phosphotransferase I]-L-lysine
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [phosphoenolpyruvate-protein phosphotransferase I]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[phosphoenolpyruvate-protein phosphotransferase I]-L-lysine
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?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [proteasome-interacting ATPase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[proteasome-interacting ATPase]-L-lysine
pupylation of proteasome-interacting ATPase (Mpa) occurs predominantly on one target lysine. Pupylation at this position prevents interaction of Mpa/prokaryotic ubiquitin-like protein(Pup) with the proteasome core. Ultimately, pupylation leads to deoligomerization of the Mpa hexamer driven by the unfolding activity of Mpa, thereby rendering Mpa-Pup fully inactive
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [proteasome-interacting ATPase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[proteasome-interacting ATPase]-L-lysine
pupylation of proteasome-interacting ATPase (Mpa) occurs predominantly at Lys591
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [proteasome-interacting ATPase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[proteasome-interacting ATPase]-L-lysine
pupylation of proteasome-interacting ATPase (Mpa) occurs predominantly on one target lysine. Pupylation at this position prevents interaction of Mpa/prokaryotic ubiquitin-like protein(Pup) with the proteasome core. Ultimately, pupylation leads to deoligomerization of the Mpa hexamer driven by the unfolding activity of Mpa, thereby rendering Mpa-Pup fully inactive
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [proteasome-interacting ATPase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[proteasome-interacting ATPase]-L-lysine
pupylation of proteasome-interacting ATPase (Mpa) occurs predominantly at Lys591
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein PanB]-L-lysine
a pupylation product with a molecular mass approximately 7 kDa heavier than PanB suggests that each PanB monomer is singly pupylated by PafA. PanB is pupylated primarily on either one of two lysines, namely Lys34 or Lys36. Pupylation on Lys137 is also detected, although less frequently
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein PanB]-L-lysine
the C-terminal glutamate of Pup-GGE is coupled to the protein substrate PanB lysine residue via the side-chain carboxylate
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein PanB]-L-lysine
[protein PanB]-L-lysine shows a 3 orders of magnitude stronger affinity than free lysine
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein PanB]-L-lysine
the C-terminal glutamate of Pup-GGE is coupled to the protein substrate PanB lysine residue via the side-chain carboxylate
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein PanB]-L-lysine
[protein PanB]-L-lysine shows a 3 orders of magnitude stronger affinity than free lysine
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein PanB]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein PanB]-L-lysine
a pupylation product with a molecular mass approximately 7 kDa heavier than PanB suggests that each PanB monomer is singly pupylated by PafA. PanB is pupylated primarily on either one of two lysines, namely Lys34 or Lys36. Pupylation on Lys137 is also detected, although less frequently
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Acidothermus cellulolyticus ATCC 43068 / 11B
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Acidothermus cellulolyticus ATCC 43068 / 11B
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Bifidobacterium adolescentis ATCC 15703 / DSM 20083 / NCTC 11814 / E194a
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Bifidobacterium adolescentis ATCC 15703 / DSM 20083 / NCTC 11814 / E194a
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Mycobacterium smegmatis Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
the Mycobacterium smegmatis Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Kocuria rhizophila ATCC 9341 / DSM 348 / NBRC 103217 / DC2201
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Kocuria rhizophila ATCC 9341 / DSM 348 / NBRC 103217 / DC2201
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Micrococcus luteus ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Micrococcus luteus ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
key enzyme in the Pup tagging (i.e. pupylation) system. Protein pupylation can be regulated at the enzyme level via an allosteric mechanism
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
no activity with ATPgammaS
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
PafA is an allosteric enzyme that binds its target substrates cooperatively. In contrast, binding of deamidated Pup (Pup-L-glutamate) by PafA follows simple kinetics and is, therefore, not involved in the allosteric transitions of PafA. Pup and target substrate binding by PafA are independent events
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Pup is linked to substrate proteins by the formation of an isopeptide bond between the side-chain carboxylate of glutamate64 and a lysine side chain of the substrate protein
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the C-terminal 26 amino acid sequence of the prokaryotic ubiquitin-like protein (Pup) is the minimal ligase recognition motif in Mycobacterium tuberculosis. Specific hydrophobic residues within this sequence that are known to be important for the interactions of Pup with proteasomes are also critical for the activation of Pup by PafA
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the enzyme catalyzes a two-step reaction mechanism proceeding through a gamma-glutamyl phosphate-mixed anhydride intermediate that is formed on the C-terminal glutamate of the prokaryotic ubiquitin-like protein (Pup) before transfer of Pup to the substrate acceptor lysine. Phosphorylated [prokaryotic ubiquitin-like protein]-L-glutamate and ADP are retained on the enzyme in a stable fashion following activation
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA. The enzyme turns over one molecule of ATP to ADP per conjugation cycle, suggesting that PafA activates Pup by phosphorylation of its C-terminal glutamate. The formation of this intermediate occurs even in the absence of substrate and is shown to be the rate-limiting step of the PafA catalyzed reaction. After activation, the phosphorylated Pup and ADP remain bound to PafA, awaiting the nucleophilic attack of the substrate lysine, which finally results in the formation of the isopeptide bond. The C-terminal residue of the ligation-competent PupE features two carboxylates, the C-terminal alpha-carboxylate and the gamma-carboxylate of the glutamyl side chain, both of which could in principle be used for Pup-attachment. NMR-experiments using the pupylated proteasomal substrate PanB show that only the gamma-carboxylate is used to form the isopeptide bond between Pup and the target
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA. The enzyme turns over one molecule of ATP to ADP per conjugation cycle, suggesting that PafA activates Pup by phosphorylation of its C-terminal glutamate. The formation of this intermediate occurs even in the absence of substrate and is shown to be the rate-limiting step of the PafA catalyzed reaction. After activation, the phosphorylated Pup and ADP remain bound to PafA, awaiting the nucleophilic attack of the substrate lysine, which finally results in the formation of the isopeptide bond. The C-terminal residue of the ligation-competent PupE features two carboxylates, the C-terminal alpha-carboxylate and the gamma-carboxylate of the glutamyl side chain, both of which could in principle be used for Pup-attachment. NMR-experiments using the pupylated proteasomal substrate PanB show that only the gamma-carboxylate is used to form the isopeptide bond between Pup and the target
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Pup is linked to substrate proteins by the formation of an isopeptide bond between the side-chain carboxylate of glutamate64 and a lysine side chain of the substrate protein
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-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the C-terminal 26 amino acid sequence of the prokaryotic ubiquitin-like protein (Pup) is the minimal ligase recognition motif in Mycobacterium tuberculosis. Specific hydrophobic residues within this sequence that are known to be important for the interactions of Pup with proteasomes are also critical for the activation of Pup by PafA
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the enzyme catalyzes a two-step reaction mechanism proceeding through a gamma-glutamyl phosphate-mixed anhydride intermediate that is formed on the C-terminal glutamate of the prokaryotic ubiquitin-like protein (Pup) before transfer of Pup to the substrate acceptor lysine. Phosphorylated [prokaryotic ubiquitin-like protein]-L-glutamate and ADP are retained on the enzyme in a stable fashion following activation
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
key enzyme in the Pup tagging (i.e. pupylation) system. Protein pupylation can be regulated at the enzyme level via an allosteric mechanism
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
PafA is an allosteric enzyme that binds its target substrates cooperatively. In contrast, binding of deamidated Pup (Pup-L-glutamate) by PafA follows simple kinetics and is, therefore, not involved in the allosteric transitions of PafA. Pup and target substrate binding by PafA are independent events
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
no activity with ATPgammaS
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycobacterium tuberculosis ATCC 25618 / H37Rv
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup product of the Dop reaction presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycolicibacterium smegmatis ATCC 700084 / mc2155
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycolicibacterium smegmatis ATCC 700084 / mc2155
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycolicibacterium smegmatis ATCC 700084 / mc2155
the Pup product of the Dop reaction presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Renibacterium salmoninarum ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Renibacterium salmoninarum ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Rhodococcus erythropolis PR4 / NBRC 100887
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Rhodococcus erythropolis PR4 / NBRC 100887
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Salinispora tropica ATCC BAA-916 / DSM 44818 / CNB-440
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Salinispora tropica ATCC BAA-916 / DSM 44818 / CNB-440
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
the Pup variant used presents a glutamate at its C-terminus (PupE) and, as such, can be readily conjugated to target proteins by PafA, PupE is covalently attached to the protein via a GGL bridge, overview. The isopeptide bond to the lysine residue of the target protein occurs via the side-chain carboxylate
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-[[prokaryotic ubiquitin-like protein]-L-glutamate]-[[protein]-L-lysine]
pupylation targets the substrates for degradation by the proteasome
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-[[prokaryotic ubiquitin-like protein]-L-glutamate]-[[protein]-L-lysine]
pupylation targets the substrates for degradation by the proteasome
-
-
?
additional information
?
-
PafA substrate docking study, overview. PafA can use ammoniumions as targets for pupylation. The reaction catalyzed is in fact the conversion of PupE C-terminal glutamate into a glutamine, that is, PupE amidation. The docking of a small molecule like ammonium in the PafA active site cannot be supported by auxiliary interactions. PafA residue R207 stabilizes the interaction of the enzyme with PanB, the R207A mutant amidates PupE and the wild-type variant
-
-
?
additional information
?
-
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
PafA substrate docking study, overview. PafA can use ammoniumions as targets for pupylation. The reaction catalyzed is in fact the conversion of PupE C-terminal glutamate into a glutamine, that is, PupE amidation. The docking of a small molecule like ammonium in the PafA active site cannot be supported by auxiliary interactions. PafA residue R207 stabilizes the interaction of the enzyme with PanB, the R207A mutant amidates PupE and the wild-type variant
-
-
?
additional information
?
-
PafA can move Pup from one proteasome substrate, inositol 1-phosphate synthetase (Ino1), to two different proteins, malonyl coenzyme A (CoA)-acyl carrier protein transacylase (FabD) and lonely guy (Log). Mutagenesis of substrate FabD Lys173 to Ala results in reduced transfer of Pup from Pup-Ino1 in the transpupylation reaction. Pup-Ino1 is a better Pup donor than Pup-FabD, and transpupylation requires ATP. PafA needs depupylase activity to transfer Pup between proteins. Pupylation is a two-step reaction in which PafA uses ATP to phosphorylate a carboxylate on the C terminus of Pup, which is then attacked by the amino group of a lysine side chain
-
-
?
additional information
?
-
-
PafA can move Pup from one proteasome substrate, inositol 1-phosphate synthetase (Ino1), to two different proteins, malonyl coenzyme A (CoA)-acyl carrier protein transacylase (FabD) and lonely guy (Log). Mutagenesis of substrate FabD Lys173 to Ala results in reduced transfer of Pup from Pup-Ino1 in the transpupylation reaction. Pup-Ino1 is a better Pup donor than Pup-FabD, and transpupylation requires ATP. PafA needs depupylase activity to transfer Pup between proteins. Pupylation is a two-step reaction in which PafA uses ATP to phosphorylate a carboxylate on the C terminus of Pup, which is then attacked by the amino group of a lysine side chain
-
-
?
additional information
?
-
the prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins. When linked to the proteasomal substrates FabD and PanB, Pup is unstructured and retains the ability to interact with its different binding partners. This suggests that it is not the conformation of Pup attached to these two substrates which determines their delivery to the proteasome, but the availability of the degradation complex and the depupylase. Structure analysis of Pup coupled to the PanB decamer, overview
-
-
?
additional information
?
-
-
the prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins. When linked to the proteasomal substrates FabD and PanB, Pup is unstructured and retains the ability to interact with its different binding partners. This suggests that it is not the conformation of Pup attached to these two substrates which determines their delivery to the proteasome, but the availability of the degradation complex and the depupylase. Structure analysis of Pup coupled to the PanB decamer, overview
-
-
?
additional information
?
-
Mycobacterium tuberculosis ATCC 25618 / H37Rv
the prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins. When linked to the proteasomal substrates FabD and PanB, Pup is unstructured and retains the ability to interact with its different binding partners. This suggests that it is not the conformation of Pup attached to these two substrates which determines their delivery to the proteasome, but the availability of the degradation complex and the depupylase. Structure analysis of Pup coupled to the PanB decamer, overview
-
-
?
additional information
?
-
Mycobacterium tuberculosis ATCC 25618 / H37Rv
PafA can move Pup from one proteasome substrate, inositol 1-phosphate synthetase (Ino1), to two different proteins, malonyl coenzyme A (CoA)-acyl carrier protein transacylase (FabD) and lonely guy (Log). Mutagenesis of substrate FabD Lys173 to Ala results in reduced transfer of Pup from Pup-Ino1 in the transpupylation reaction. Pup-Ino1 is a better Pup donor than Pup-FabD, and transpupylation requires ATP. PafA needs depupylase activity to transfer Pup between proteins. Pupylation is a two-step reaction in which PafA uses ATP to phosphorylate a carboxylate on the C terminus of Pup, which is then attacked by the amino group of a lysine side chain
-
-
?
additional information
?
-
PafA can pupylate itself, extra-pupylation by PafA can also occur, mostly in the form of poly-pupylation. Unlike in the eukaryotic UPS where poly-ubiquitylation is seen, in vivo targets of the Pup-proteasome system are found almost exclusively to be monopupylated, except for PafA itself. Poly-pupylation occurs via pupylation of an already pupylated target, rather than by conjugation of pre-formed poly-Pup chains
-
-
?
additional information
?
-
PafA binds IdeR with low affinity, compared to PanB, a model substrate whose affinity for PafA is about 10fold higher
-
-
?
additional information
?
-
PafA can catalyze the poly-pupylation of itself, poly-pupylation of PafA. One common pupylation substrate is protein PanB. PafA self-pupylation is suppressed when PanB is added at high concentrations. Unlike the pattern of poly-pupylated PafA, only mono-pupylated PanB and a few di-pupylated PanB (Pup2-PanB) can be detected in the reaction system
-
-
?
additional information
?
-
Mycolicibacterium smegmatis ATCC 700084 / mc2155
PafA can pupylate itself, extra-pupylation by PafA can also occur, mostly in the form of poly-pupylation. Unlike in the eukaryotic UPS where poly-ubiquitylation is seen, in vivo targets of the Pup-proteasome system are found almost exclusively to be monopupylated, except for PafA itself. Poly-pupylation occurs via pupylation of an already pupylated target, rather than by conjugation of pre-formed poly-Pup chains
-
-
?
additional information
?
-
Mycolicibacterium smegmatis ATCC 700084 / mc2155
PafA binds IdeR with low affinity, compared to PanB, a model substrate whose affinity for PafA is about 10fold higher
-
-
?
additional information
?
-
Mycolicibacterium smegmatis ATCC 700084 / mc2155
PafA can catalyze the poly-pupylation of itself, poly-pupylation of PafA. One common pupylation substrate is protein PanB. PafA self-pupylation is suppressed when PanB is added at high concentrations. Unlike the pattern of poly-pupylated PafA, only mono-pupylated PanB and a few di-pupylated PanB (Pup2-PanB) can be detected in the reaction system
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?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [proteasome-interacting ATPase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[proteasome-interacting ATPase]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-[[prokaryotic ubiquitin-like protein]-L-glutamate]-[[protein]-L-lysine]
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [proteasome-interacting ATPase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[proteasome-interacting ATPase]-L-lysine
pupylation of proteasome-interacting ATPase (Mpa) occurs predominantly on one target lysine. Pupylation at this position prevents interaction of Mpa/prokaryotic ubiquitin-like protein(Pup) with the proteasome core. Ultimately, pupylation leads to deoligomerization of the Mpa hexamer driven by the unfolding activity of Mpa, thereby rendering Mpa-Pup fully inactive
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [proteasome-interacting ATPase]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[proteasome-interacting ATPase]-L-lysine
pupylation of proteasome-interacting ATPase (Mpa) occurs predominantly on one target lysine. Pupylation at this position prevents interaction of Mpa/prokaryotic ubiquitin-like protein(Pup) with the proteasome core. Ultimately, pupylation leads to deoligomerization of the Mpa hexamer driven by the unfolding activity of Mpa, thereby rendering Mpa-Pup fully inactive
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Acidothermus cellulolyticus ATCC 43068 / 11B
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Bifidobacterium adolescentis ATCC 15703 / DSM 20083 / NCTC 11814 / E194a
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Kocuria rhizophila ATCC 9341 / DSM 348 / NBRC 103217 / DC2201
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Micrococcus luteus ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
key enzyme in the Pup tagging (i.e. pupylation) system. Protein pupylation can be regulated at the enzyme level via an allosteric mechanism
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond. Pup proteins are small, ranging from 60 to 70 residues in length with Gly-Gly-Glu or Gly-Gly-Gln as C-terminal residues. Deamidation of the C-terminal glutamine of Pup by the deamidase of Pup (Dop) renders Pup competent for conjugation to substrates, which is then carried out by the Pup-ligase PafA
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
key enzyme in the Pup tagging (i.e. pupylation) system. Protein pupylation can be regulated at the enzyme level via an allosteric mechanism
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Renibacterium salmoninarum ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Rhodococcus erythropolis PR4 / NBRC 100887
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Salinispora tropica ATCC BAA-916 / DSM 44818 / CNB-440
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
-
-
-
?
ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-([prokaryotic ubiquitin-like protein]-gamma-L-glutamyl)-[protein]-L-lysine
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-[[prokaryotic ubiquitin-like protein]-L-glutamate]-[[protein]-L-lysine]
pupylation targets the substrates for degradation by the proteasome
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ATP + [prokaryotic ubiquitin-like protein]-L-glutamate + [protein]-L-lysine
ADP + phosphate + N6-[[prokaryotic ubiquitin-like protein]-L-glutamate]-[[protein]-L-lysine]
pupylation targets the substrates for degradation by the proteasome
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additional information
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PafA can pupylate itself, extra-pupylation by PafA can also occur, mostly in the form of poly-pupylation. Unlike in the eukaryotic UPS where poly-ubiquitylation is seen, in vivo targets of the Pup-proteasome system are found almost exclusively to be monopupylated, except for PafA itself. Poly-pupylation occurs via pupylation of an already pupylated target, rather than by conjugation of pre-formed poly-Pup chains
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additional information
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Mycolicibacterium smegmatis ATCC 700084 / mc2155
PafA can pupylate itself, extra-pupylation by PafA can also occur, mostly in the form of poly-pupylation. Unlike in the eukaryotic UPS where poly-ubiquitylation is seen, in vivo targets of the Pup-proteasome system are found almost exclusively to be monopupylated, except for PafA itself. Poly-pupylation occurs via pupylation of an already pupylated target, rather than by conjugation of pre-formed poly-Pup chains
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Persistent Infection
Fluorescent Probes Reveal a Minimal Ligase Recognition Motif in the Prokaryotic Ubiquitin-like Protein from Mycobacterium tuberculosis.
Tuberculosis
Allosteric transitions direct protein tagging by PafA, the prokaryotic ubiquitin-like protein (Pup) ligase.
Tuberculosis
Identification of Serine 119 as an Effective Inhibitor Binding Site of M. tuberculosis Ubiquitin-like Protein Ligase PafA Using Purified Proteins and M. smegmatis.
Tuberculosis
Mycobacterium tuberculosis Proteasome Accessory Factor A (PafA) Can Transfer Prokaryotic Ubiquitin-Like Protein (Pup) between Substrates.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.22
[IdeR]-L-lysine
pH 7.5, 30°C, recombinant His-tagged enzyme
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0.084
[PanB]-L-lysine
pH 7.5, 30°C, recombinant His-tagged enzyme
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0.0014
[prokaryotic ubiquitin-like protein]-L-glutamate
25°C, pH 7.4
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additional information
additional information
Michaelis-Menten kinetic analysis of poly-pupylation, overview
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additional information
additional information
Michaelis-Menten kinetic analysis of poly-pupylation, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.014
[IdeR]-L-lysine
pH 7.5, 30°C, recombinant His-tagged enzyme
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0.0023
[prokaryotic ubiquitin-like protein]-L-glutamate
pH 8.0, 30°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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SwissProt
brenda
Micrococcus luteus ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230
i.e. Micrococcus lysodeikticus
UniProt
brenda
Renibacterium salmoninarum ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235
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UniProt
brenda
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SwissProt
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
evolution
PafA is a member of the glutamine synthetase (GS) family of proteins
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
evolution
the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview. Intrinsically disordered Pup is structurally unlike the stably folded ubiquitin
evolution
Bifidobacterium adolescentis ATCC 15703 / DSM 20083 / NCTC 11814 / E194a
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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evolution
Acidothermus cellulolyticus ATCC 43068 / 11B
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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evolution
Mycobacterium tuberculosis ATCC 25618 / H37Rv
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview. Intrinsically disordered Pup is structurally unlike the stably folded ubiquitin
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evolution
Mycobacterium tuberculosis ATCC 25618 / H37Rv
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PafA is a member of the glutamine synthetase (GS) family of proteins
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evolution
Renibacterium salmoninarum ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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evolution
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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evolution
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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evolution
Kocuria rhizophila ATCC 9341 / DSM 348 / NBRC 103217 / DC2201
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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evolution
Salinispora tropica ATCC BAA-916 / DSM 44818 / CNB-440
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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evolution
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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evolution
Mycolicibacterium smegmatis ATCC 700084 / mc2155
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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evolution
Rhodococcus erythropolis PR4 / NBRC 100887
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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evolution
Micrococcus luteus ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230
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the Pup-proteasome system (PPS) is functionally related to the eukaryotic Ub-proteasome system, but the number of the involved players is smaller, comparison of reaction mechanisms, overview
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malfunction
in a pafA knockout strain pupylated proteins are undetectable and proteasomal substrate proteins accumulate
malfunction
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in a pafA knockout strain pupylated proteins are undetectable and proteasomal substrate proteins accumulate
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metabolism
prokaryotic ubiquitin-like protein (Pup) is a post-translational modifier that attaches to more than 50 proteins in Mycobacteria. Proteasome accessory factor A (PafA) is responsible for Pup conjugation to substrates
metabolism
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proteasome-containing bacteria possess a tagging system that directs proteins to proteasomal degradation by conjugating them to a prokaryotic ubiquitin-like protein (Pup). A single ligating enzyme, PafA, is responsible for Pup conjugation to lysine side chains of protein substrates. As Pup is recognized by the regulatory subunit of the proteasome, Pup functions as a degradation tag. Ligating enzyme PafA and the proteasome can function as a modular machine for the tagging and degradation of cytoplasmic proteins
metabolism
pupylation is a bacterial post-translational modification of target proteins on lysine residues with prokaryotic ubiquitinlike protein (Pup). Pup-tagged substrates are recognized by a proteasome-interacting ATPase (Mpa) in Mycobacterium tuberculosis. Mpa unfolds pupylated substrates and threads them into the proteasome core particle for degradation
metabolism
pupylation is a posttranslational protein modification occurring in mycobacteria and other actinobacteria that is functionally analogous to ubiquitination
metabolism
posttranslational regulation of coordinated enzyme activities in the prokaryotic ubiquitin-like protein (Pup)-proteasome system (PPS), overview. Pup, a ubiquitin analogue, is conjugated to proteins through the activities of two enzymes, Dop (deamidase of Pup) and PafA (proteasome accessory factor A), the Pup ligase. The depupylase activity of Dop counteracts the actions of PafA. tight Pup binding and the limited degree of Dop interaction with high-molecular-weight pupylated proteins results in preferred Pup deamidation over protein depupylation by enzyme Dop. Dop is depleted in the absence of Pup in stationary-phase cells. Pup-PanB and Pup-IdeR act as tight-binding competitors versus Pup binding by Dop. Pup binding stabilizes Dop and prevents its depletion. PafA and Dop generate a high-molecular-weight pupylome
metabolism
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proteasome-containing bacteria possess a tagging system that directs proteins to proteasomal degradation by conjugating them to a prokaryotic ubiquitin-like protein (Pup). A single ligating enzyme, PafA, is responsible for Pup conjugation to lysine side chains of protein substrates. As Pup is recognized by the regulatory subunit of the proteasome, Pup functions as a degradation tag. Ligating enzyme PafA and the proteasome can function as a modular machine for the tagging and degradation of cytoplasmic proteins
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metabolism
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prokaryotic ubiquitin-like protein (Pup) is a post-translational modifier that attaches to more than 50 proteins in Mycobacteria. Proteasome accessory factor A (PafA) is responsible for Pup conjugation to substrates
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metabolism
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pupylation is a bacterial post-translational modification of target proteins on lysine residues with prokaryotic ubiquitinlike protein (Pup). Pup-tagged substrates are recognized by a proteasome-interacting ATPase (Mpa) in Mycobacterium tuberculosis. Mpa unfolds pupylated substrates and threads them into the proteasome core particle for degradation
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metabolism
Mycolicibacterium smegmatis ATCC 700084 / mc2155
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posttranslational regulation of coordinated enzyme activities in the prokaryotic ubiquitin-like protein (Pup)-proteasome system (PPS), overview. Pup, a ubiquitin analogue, is conjugated to proteins through the activities of two enzymes, Dop (deamidase of Pup) and PafA (proteasome accessory factor A), the Pup ligase. The depupylase activity of Dop counteracts the actions of PafA. tight Pup binding and the limited degree of Dop interaction with high-molecular-weight pupylated proteins results in preferred Pup deamidation over protein depupylation by enzyme Dop. Dop is depleted in the absence of Pup in stationary-phase cells. Pup-PanB and Pup-IdeR act as tight-binding competitors versus Pup binding by Dop. Pup binding stabilizes Dop and prevents its depletion. PafA and Dop generate a high-molecular-weight pupylome
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metabolism
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pupylation is a posttranslational protein modification occurring in mycobacteria and other actinobacteria that is functionally analogous to ubiquitination
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physiological function
in Mycobacterium tuberculosis Pup tagging is important for virulence
physiological function
pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond
physiological function
bacteria use an intrinsically disordered protein, Pup, to mark proteins for destruction. The protein degradation machinery of Mycobacterium tuberculosis includes a proteasome and a ubiquitin-like protein (Pup). Proteasome accessory factor A (PafA) attaches Pup to proteins to target them for degradation by the proteasome. PafA can move Pup from one proteasome substrate, inositol 1-phosphate synthetase (Ino1), to two different proteins, malonyl coenzyme A (CoA)-acyl carrier protein transacylase (FabD) and lonely guy (Log). This apparent transpupylation reaction requires a previously unrecognized depupylase activity in PafA, and, surprisingly, this depupylase activity is much more efficient than the activity of the dedicated depupylase Dop (deamidase of Pup). Thus, PafA can potentially use both newly synthesized Pup and recycled Pup to doom proteins for degradation. In contrast, enzyme Dop, in addition to deamidating PupGln to PupGlu, can remove Pup from proteins, which can rescue them from proteasomal degradation. PafA, unlike Dop, can-not deamidate PupGln to PupGlu, thus, PafA amidase activity appears to be limited to pupylated proteins
physiological function
enzyme PafA, the prokaryotic ubiquitin-like protein (Pup) ligase, catalyzes the Pup modification of bacterial proteins and targets the substrates for proteasomal degradation. Mycobacterium smegmatis PafA can be poly-pupylated. Self-pupylation of PafA is reversely regulated by Dop, a dual-functional enzyme, functioning as deaminase to convert PupQ to PupE and also as depupylase to remove Pup from the pupylated proteins. The self-pupylation of PafA is involved in the regulation of its stability
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. For Mycobacterium tuberculosis, pupylation and the recruitment of pupylated substrates to the proteasome support persistence inside host macrophages during pathogenesis. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
physiological function
prokaryotic ubiquitin-like protein, Pup, is conjugated to proteins by PafA, the only Pup ligase identified thus far, through the formation of an iso-peptide bond between the gamma-carboxylate of a glutamate side chain at the C terminus of Pup and the epsilon-amine of a lysine residue on the target protein. Pupylation is a cytoplasmic signal for proteasomal degradation. Pup ligase PafA conjugates the small protein Pup to lysine side chains of target proteins. Mono-Pup moieties are almost exclusively observed in vivo and are sufficient as degradation tags
physiological function
Pup, a ubiquitin analogue, is conjugated to proteins through the activities of two enzymes, Dop (deamidase of Pup) and PafA (proteasome accessory factor A), the Pup ligase. Dop also catalyzes depupylation. Pupylation is a reversible process, with pupylated proteins being rescued from degradation following depupylation by Dop (deamidase of Pup). PafA (proteasome accessory factor A) and Dop are homologous enzymes, both binding Pup through interaction with its extended C-terminal region
physiological function
pupylation, the bacterial equivalent of ubiquitylation, involves the conjugation of a prokaryotic ubiquitin-like protein (Pup) to protein targets. In contrast to the ubiquitin system, where many ubiquitin ligases exist, a single bacterial ligase, PafA, catalyzes the conjugation of Pup to a wide array of protein targets
physiological function
Bifidobacterium adolescentis ATCC 15703 / DSM 20083 / NCTC 11814 / E194a
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
Acidothermus cellulolyticus ATCC 43068 / 11B
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. For Mycobacterium tuberculosis, pupylation and the recruitment of pupylated substrates to the proteasome support persistence inside host macrophages during pathogenesis. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
bacteria use an intrinsically disordered protein, Pup, to mark proteins for destruction. The protein degradation machinery of Mycobacterium tuberculosis includes a proteasome and a ubiquitin-like protein (Pup). Proteasome accessory factor A (PafA) attaches Pup to proteins to target them for degradation by the proteasome. PafA can move Pup from one proteasome substrate, inositol 1-phosphate synthetase (Ino1), to two different proteins, malonyl coenzyme A (CoA)-acyl carrier protein transacylase (FabD) and lonely guy (Log). This apparent transpupylation reaction requires a previously unrecognized depupylase activity in PafA, and, surprisingly, this depupylase activity is much more efficient than the activity of the dedicated depupylase Dop (deamidase of Pup). Thus, PafA can potentially use both newly synthesized Pup and recycled Pup to doom proteins for degradation. In contrast, enzyme Dop, in addition to deamidating PupGln to PupGlu, can remove Pup from proteins, which can rescue them from proteasomal degradation. PafA, unlike Dop, can-not deamidate PupGln to PupGlu, thus, PafA amidase activity appears to be limited to pupylated proteins
-
physiological function
Renibacterium salmoninarum ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
pupylation, the bacterial equivalent of ubiquitylation, involves the conjugation of a prokaryotic ubiquitin-like protein (Pup) to protein targets. In contrast to the ubiquitin system, where many ubiquitin ligases exist, a single bacterial ligase, PafA, catalyzes the conjugation of Pup to a wide array of protein targets
-
physiological function
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
-
pupylation is a signal for proteasomal degradation in bacteria. The prokaryotic, ubiquitin-like protein (Pup) is conjugated through its C-terminal residue to lysine side chains of substrates via an isopeptide bond
-
physiological function
-
in Mycobacterium tuberculosis Pup tagging is important for virulence
-
physiological function
Kocuria rhizophila ATCC 9341 / DSM 348 / NBRC 103217 / DC2201
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
Salinispora tropica ATCC BAA-916 / DSM 44818 / CNB-440
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
prokaryotic ubiquitin-like protein, Pup, is conjugated to proteins by PafA, the only Pup ligase identified thus far, through the formation of an iso-peptide bond between the gamma-carboxylate of a glutamate side chain at the C terminus of Pup and the epsilon-amine of a lysine residue on the target protein. Pupylation is a cytoplasmic signal for proteasomal degradation. Pup ligase PafA conjugates the small protein Pup to lysine side chains of target proteins. Mono-Pup moieties are almost exclusively observed in vivo and are sufficient as degradation tags
-
physiological function
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
enzyme PafA, the prokaryotic ubiquitin-like protein (Pup) ligase, catalyzes the Pup modification of bacterial proteins and targets the substrates for proteasomal degradation. Mycobacterium smegmatis PafA can be poly-pupylated. Self-pupylation of PafA is reversely regulated by Dop, a dual-functional enzyme, functioning as deaminase to convert PupQ to PupE and also as depupylase to remove Pup from the pupylated proteins. The self-pupylation of PafA is involved in the regulation of its stability
-
physiological function
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
Pup, a ubiquitin analogue, is conjugated to proteins through the activities of two enzymes, Dop (deamidase of Pup) and PafA (proteasome accessory factor A), the Pup ligase. Dop also catalyzes depupylation. Pupylation is a reversible process, with pupylated proteins being rescued from degradation following depupylation by Dop (deamidase of Pup). PafA (proteasome accessory factor A) and Dop are homologous enzymes, both binding Pup through interaction with its extended C-terminal region
-
physiological function
Rhodococcus erythropolis PR4 / NBRC 100887
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
physiological function
Micrococcus luteus ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230
-
prokaryotic ubiquitin-like protein (Pup) is a small protein that can be covalently attached to lysine side chains of cellular proteins by Pup ligase PafA. Pupylation serves as a recruitment tool for proteasomal degradation. Pup serves as both recognition and threading element in proteasomal degradation of pupylated substrates. The degradation substrate covalently modified with Pup is recruited to the Mpa-proteasome complex by docking to the Mpa coiled-coil domain, which triggers Pup to undergo a disorder-to-order transition, forming an extended helix that associates into a shared three-stranded coil with the Mpa N-terminal coiled-coil domains. The disordered N-terminal region of Pup points into the Mpa central pore, where it is engaged by the ATPase-driven pore loops for unfolding and directional translocation into the proteasome core for degradation. Structure-function analysis, overview
-
Show AA Sequence and Transmembrane Helices (4101 entries)
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
?
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
x * 51000, recombinant His6-tagged enzyme, SDS-PAGE
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of the enzyme with ADP, protein (Pup) ligase PafA and the depupylase/deamidase Dop are are close structural homologues
the enzyme from Corynebacterium glutamicum is C-terminally fused with Pup or N-terminally truncated fragments of prokaryotic ubiquitin-like protein (Pup) from the same organism. Crystals are obtained only with the shortest fragment tested, PupE38-64. The crystal structure of Pup in complex with the enzyme, reveals that a long groove wrapping around the enzyme serves as a docking site for Pup. Upon binding, the C-terminal region of the intrinsically disordered Pup becomes ordered to form two helices connected by a linker, positioning the C-terminal glutamate in the active site of PafA
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A196S
site-directed mutagenesis, the mutant shows increased pupylation activity with substrate PanB compared to wild-type
D208A
site-directed mutagenesis, the mutant shows reduced pupylation activity with substrate PanB compared to wild-type
D64N
site-directed mutagenesis, a catalytically inactive mutant
E209A
site-directed mutagenesis, the mutant shows highly reduced pupylation activity with substrate PanB compared to wild-type
E70A
site-directed mutagenesis, a catalytically inactive mutant
N205A
site-directed mutagenesis, the mutant shows reduced pupylation activity with substrate PanB compared to wild-type
R199A
site-directed mutagenesis, the mutant shows highly reduced pupylation activity with substrate PanB compared to wild-type
R201A
site-directed mutagenesis, pupylation catalytically inactive mutant
R207A
T197A
site-directed mutagenesis, the mutant shows reduced pupylation activity with substrate PanB compared to wild-type
T198A
site-directed mutagenesis, the mutant shows highly reduced pupylation activity with substrate PanB compared to wild-type
V65S
site-directed mutagenesis, the mutant shows reduced pupylation activity with substrate PanB compared to wild-type
D208A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis, the mutant shows reduced pupylation activity with substrate PanB compared to wild-type
-
D64N
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis, a catalytically inactive mutant
-
R201A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis, pupylation catalytically inactive mutant
-
T197A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis, the mutant shows reduced pupylation activity with substrate PanB compared to wild-type
-
T198A
Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
-
site-directed mutagenesis, the mutant shows highly reduced pupylation activity with substrate PanB compared to wild-type
-
E9A
site-directed mutagenesis, the PafA mutant without ligase activity cannot be pupylated
K31R
site-directed mutagenesis, the mutation attenuates the poly-pupylation of PafA
K320R
site-directed mutagenesis, the self-pupylation of PafA K320R mutant is not totally eliminated, suggesting that PafA can be poorly modified by Pup on other lysine residue(s) besides K320 in the in vitro reaction system. Wild-type PafA is less stable than PafA K320R, which cannot be pupylated in vivo
K61R
site-directed mutagenesis, the mutation attenuates the poly-pupylation of PafA
K7R
site-directed mutagenesis, the mutation attenuates the poly-pupylation of PafA
E9A
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
site-directed mutagenesis, the PafA mutant without ligase activity cannot be pupylated
-
K320R
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
site-directed mutagenesis, the self-pupylation of PafA K320R mutant is not totally eliminated, suggesting that PafA can be poorly modified by Pup on other lysine residue(s) besides K320 in the in vitro reaction system. Wild-type PafA is less stable than PafA K320R, which cannot be pupylated in vivo
-
K61R
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
site-directed mutagenesis, the mutation attenuates the poly-pupylation of PafA
-
K7R
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
site-directed mutagenesis, the mutation attenuates the poly-pupylation of PafA
-
additional information
R207A
site-directed mutagenesis, the mutant shows highly reduced pupylation activity with substrate PanB compared to wild-type
R207A
site-directed mutagenesis, whereas extensive protein pupylation occurs with the wild-type enzyme, the R207A mutant catalyzes protein pupylation much more slowly. PafA residue R207 stabilizes the interaction of the enzyme with PanB, the R207A mutant amidates PupE and the wild-type variant
additional information
Mycobacterium smegmatis strains with the deletion of the 20S proteasome beta subunit or pafA gene are constructed by homologous recombination with p1NIL and pGOAL19 plasmids, respectively
additional information
Mycolicibacterium smegmatis ATCC 700084 / mc2155
-
Mycobacterium smegmatis strains with the deletion of the 20S proteasome beta subunit or pafA gene are constructed by homologous recombination with p1NIL and pGOAL19 plasmids, respectively
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged enzyme from Escherichia coli by nickel affinity chormatography
recombinant His6-tagged enzyme from Escherichia coli strain ER2566 by nickel affinity chormatography
recombinant N-terminal His6-tagged wild-type and mutant enzymes from Mycobacterium smegmatis or Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
recombinant His6-tagged enzyme from Escherichia coli strain ER2566 by nickel affinity chormatography
recombinant His6-tagged enzyme from Escherichia coli strain ER2566 by nickel affinity chormatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, recombinant expression of N-terminal His6-tagged enzyme in Mycobacterium smegmatis, and recombinant expression of N-terminal His6-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3), recombinant expression of HA- or Strep-tagged enzyme mutants in Mycobacterium smegmatis
recombinant expression of His6-tagged enzyme in Escherichia coli
recombinant expression of His6-tagged enzyme in Escherichia coli strain ER2566
reconstitution of the Mycobacterium tuberculosis pupylation pathway in Escherichia coli
the pafA gene is cloned with a C-terminal His6-tag, expression in Escherichia coli
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
gene pafA, genetic arrangement in the pupylation gene locus, comparisons, overview
recombinant expression of His6-tagged enzyme in Escherichia coli strain ER2566
recombinant expression of His6-tagged enzyme in Escherichia coli strain ER2566
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
drug development
the enzyme is a target for drug development in tuberculosis treatment
drug development
Mycobacterium tuberculosis ATCC 25618 / H37Rv
-
the enzyme is a target for drug development in tuberculosis treatment
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Forer, N.; Korman, M.; Elharar, Y.; Vishkautzan, M.; Gur, E.
Bacterial proteasome and PafA, the pup ligase, interact to form a modular protein tagging and degradation machine
Biochemistry
52
9029-9035
2013
Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618
brenda
Striebel, F.; Imkamp, F.; zcelik, D.; Weber-Ban, E.
Pupylation as a signal for proteasomal degradation in bacteria
Biochim. Biophys. Acta
1843
103-113
2014
Mycobacterium tuberculosis (P9WNU7), Mycobacterium tuberculosis ATCC 25618 (P9WNU7)
brenda
Cerda-Maira, F.A.; McAllister, F.; Bode, N.J.; Burns, K.E., Gygi, S.P.; Darwin, K.H.
Reconstitution of the Mycobacterium tuberculosis pupylation pathway in Escherichia coli
EMBO Rep.
12
863-870
2011
Mycobacterium tuberculosis (P9WNU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (P9WNU7)
brenda
Sutter, M.; Damberger, F.F.; Imkamp, F.; Allain, F.H.; Weber-Ban, E.
Prokaryotic ubiquitin-like protein (Pup) is coupled to substrates via the side chain of its C-terminal glutamate
J. Am. Chem. Soc.
132
5610-5612
2010
Mycobacterium tuberculosis (P9WNU7), Mycobacterium tuberculosis ATCC 25618 (P9WNU7)
brenda
Smirnov, D.; Dhall, A.; Sivanesam, K.; Sharar, R.J.; Chatterjee, C.
Fluorescent probes reveal a minimal ligase recognition motif in the prokaryotic ubiquitin-like protein from Mycobacterium tuberculosis
J. Am. Chem. Soc.
135
2887-2890
2013
Mycobacterium tuberculosis (P9WNU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (P9WNU7)
brenda
Barandun, J.; Delley, C.L.; Ban, N.; Weber-Ban, E.
Crystal structure of the complex between prokaryotic ubiquitin-like protein and its ligase PafA
J. Am. Chem. Soc.
135
:6794-6797
2013
Corynebacterium glutamicum (Q8NQE0), Corynebacterium glutamicum DSM 20300 (Q8NQE0)
brenda
Guth, E.; Thommen, M.; Weber-Ban, E.
Mycobacterial ubiquitin-like protein ligase PafA follows a two-step reaction pathway with a phosphorylated pup intermediate
J. Biol. Chem.
286
4412-4419
2011
Mycobacterium tuberculosis (P9WNU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (P9WNU7)
brenda
Delley, C.L.; Striebel, F.; Heydenreich, F.M.; zcelik, D.; Weber-Ban, E.
Activity of the mycobacterial proteasomal ATPase Mpa is reversibly regulated by pupylation
J. Biol. Chem.
287
7907-7914
2012
Mycobacterium tuberculosis (P9WNU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (P9WNU7)
brenda
Ofer, N.; Forer, N.; Korman, M.; Vishkautzan, M.; Khalaila, I.; Gur, E.
Allosteric transitions direct protein tagging by PafA, the prokaryotic ubiquitin-like protein (Pup) ligase
J. Biol. Chem.
288
11287-11293
2013
Mycobacterium tuberculosis (P9WNU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (P9WNU7)
brenda
zcelik, D.; Barandun, J.; Schmitz, N.; Sutter, M.; Guth, E.; Damberger, F.F.; Allain, F.H.; Ban, N.; Weber-Ban, E.
Structures of Pup ligase PafA and depupylase Dop from the prokaryotic ubiquitin-like modification pathway
Nat. Commun.
3
1014
2012
Corynebacterium glutamicum (Q8NQE1), Corynebacterium glutamicum DSM 20300 (Q8NQE1)
brenda
Striebel, F.; Imkamp, F.; Sutter, M.; Steiner, M.; Mamedov, A.; Weber-Ban, E.
Bacterial ubiquitin-like modifier Pup is deamidated and conjugated to substrates by distinct but homologous enzymes
Nat. Struct. Mol. Biol.
16
647-651
2009
Mycobacterium tuberculosis (P9WNU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 (P9WNU7)
brenda
Barandun, J.; Damberger, F.F.; Delley, C.L.; Laederach, J.; Allain, F.H.; Weber-Ban, E.
Prokaryotic ubiquitin-like protein remains intrinsically disordered when covalently attached to proteasomal target proteins
BMC Struct. Biol.
17
doi: 10.1186/s12900-017-0072-1
2017
Mycobacterium tuberculosis (P9WNU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 / H37Rv (P9WNU7)
brenda
Regev, O.; Roth, Z.; Korman, M.; Khalaila, I.; Gur, E.
A kinetic model for the prevalence of mono- over poly-pupylation
FEBS J.
282
4176-4186
2015
Mycolicibacterium smegmatis (A0QZ42), Mycolicibacterium smegmatis ATCC 700084 / mc2155 (A0QZ42)
brenda
Regev, O.; Korman, M.; Hecht, N.; Roth, Z.; Forer, N.; Zarivach, R.; Gur, E.
An extended loop of the Pup ligase, PafA, mediates interaction with protein targets
J. Mol. Biol.
428
4143-4153
2016
Corynebacterium glutamicum (Q8NQE1), Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 (Q8NQE1)
brenda
Delley, C.L.; Mueller, A.U.; Ziemski, M.; Weber-Ban, E.
Prokaryotic ubiquitin-like protein and its ligase/deligase enzymes
J. Mol. Biol.
429
3486-3499
2017
Acidothermus cellulolyticus (A0LU53), Mycolicibacterium smegmatis (A0QZ42), Bifidobacterium adolescentis (A1A0U7), Paenarthrobacter aurescens (A1R6Q9), Salinispora tropica (A4X747), Renibacterium salmoninarum (A9WSH9), Kocuria rhizophila (B2GIN9), Rhodococcus erythropolis (C0ZZU4), Micrococcus luteus (C5CBV0), Mycobacterium tuberculosis (P9WNU7), Thermobifida fusca (Q47NZ6), Corynebacterium glutamicum (Q8NQE1), Streptomyces coelicolor (Q9RJ61), Bifidobacterium adolescentis ATCC 15703 / DSM 20083 / NCTC 11814 / E194a (A1A0U7), Acidothermus cellulolyticus ATCC 43068 / 11B (A0LU53), Mycobacterium tuberculosis ATCC 25618 / H37Rv (P9WNU7), Renibacterium salmoninarum ATCC 33209 / DSM 20767 / JCM 11484 / NBRC 15589 / NCIMB 2235 (A9WSH9), Streptomyces coelicolor ATCC BAA-471 / A3(2) / M145 (Q9RJ61), Corynebacterium glutamicum ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025 (Q8NQE1), Kocuria rhizophila ATCC 9341 / DSM 348 / NBRC 103217 / DC2201 (B2GIN9), Salinispora tropica ATCC BAA-916 / DSM 44818 / CNB-440 (A4X747), Paenarthrobacter aurescens TC1 (A1R6Q9), Mycolicibacterium smegmatis ATCC 700084 / mc2155 (A0QZ42), Rhodococcus erythropolis PR4 / NBRC 100887 (C0ZZU4), Micrococcus luteus ATCC 4698 / DSM 20030 / JCM 1464 / NBRC 3333 / NCIMB 9278 / NCTC 2665 / VKM Ac-2230 (C5CBV0)
brenda
Zhang, S.; Burns-Huang, K.; Janssen, G.; Li, H.; Ovaa, H.; Hedstrom, L.; Darwin, K.
Mycobacterium tuberculosis proteasome accessory factor A (PafA) can transfer prokaryotic ubiquitin-like protein (Pup) between substrates
mBio
8
e00122-17
2017
Mycobacterium tuberculosis (P9WNU7), Mycobacterium tuberculosis, Mycobacterium tuberculosis ATCC 25618 / H37Rv (P9WNU7)
brenda
Chen, X.; Li, C.; Wang, L.; Liu, Y.; Li, C.; Zhang, J.
The mechanism of Mycobacterium smegmatis PafA self-pupylation
PLoS ONE
11
e0151021
2016
Mycolicibacterium smegmatis (A0QZ42), Mycolicibacterium smegmatis ATCC 700084 / mc2155 (A0QZ42)
brenda
Elharar, Y.; Roth, Z.; Hecht, N.; Rotkopf, R.; Khalaila, I.; Gur, E.
Posttranslational regulation of coordinated enzyme activities in the Pup-proteasome system
Proc. Natl. Acad. Sci. USA
113
E1605-E1614
2016
Mycolicibacterium smegmatis (A0QZ42), Mycolicibacterium smegmatis ATCC 700084 / mc2155 (A0QZ42)
brenda
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Release 2023.1 (January 2023)
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