Information on EC 1.5.5.2 - proline dehydrogenase

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The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota

EC NUMBER
COMMENTARY hide
1.5.5.2
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RECOMMENDED NAME
GeneOntology No.
proline dehydrogenase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-proline + a quinone = (S)-1-pyrroline-5-carboxylate + a quinol
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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-
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redox reaction
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-
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reduction
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
(5R)-carbapenem carboxylate biosynthesis
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L-citrulline biosynthesis
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L-Ndelta-acetylornithine biosynthesis
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L-proline degradation
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proline to cytochrome bo oxidase electron transfer
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proline metabolism
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Arginine and proline metabolism
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Metabolic pathways
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Biosynthesis of secondary metabolites
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Biosynthesis of antibiotics
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SYSTEMATIC NAME
IUBMB Comments
L-proline:quinone oxidoreductase
A flavoprotein (FAD). The electrons from L-proline are transferred to the FAD cofactor, and from there to a quinone acceptor [3]. In many organisms, ranging from bacteria to mammals, proline is oxidized to glutamate in a two-step process involving this enzyme and EC 1.2.1.88, L-glutamate gamma-semialdehyde dehydrogenase. Both activities are carried out by the same enzyme in enterobacteria.
CAS REGISTRY NUMBER
COMMENTARY hide
9050-70-8
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
PutA86-669
UniProt
Manually annotated by BRENDA team
mungbean
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-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
hydroxy-L-proline + acceptor + H2O
?
show the reaction diagram
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3%5 the rate of L-proline
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-
?
L-proline + 2,6-dichlorophenolindophenol + H2O
(S)-1-pyrroline-5-carboxylate + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
L-proline + 2,6-dichlorophenolindophenol + H2O
DELTA1-pyrroline-5-carboxylate + reduced 2,6-dichlorophenolindophenol
show the reaction diagram
L-proline + acceptor
(S)-1-pyrroline-5-carboxylate + reduced acceptor
show the reaction diagram
-
the bifunctional enzyme catalyzes the oxidation of proline in two steps. (S)-1-Pyrroline-5-carboxylate, the product of the first reaction is in spontaneous equilibrium with its tautomer L-glutamate gamma-semialdehyde: (1) L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor, (2) L-glutamate 5-semialdehyde + NAD+ + H2O = L-glutamate + NADH + H+
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-
?
L-proline + acceptor + H2O
(S)-1-pyrroline-5-carboxylate + reduced acceptor
show the reaction diagram
L-proline + FAD + H2O
(S)-1-pyrroline-5-carboxylate + FADH2
show the reaction diagram
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?
L-proline + ferricyanide + H2O
(S)-1-pyrroline-5-carboxylate + ferrocyanide
show the reaction diagram
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-
-
?
L-proline + oxidized dichlorophenolindophenol
1-pyrroline-5-carboxylate + reduced dichlorophenolindophenol
show the reaction diagram
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-
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?
L-thiazolidine-4-carboxylate + acceptor + H2O
N-formylcysteine + reduced acceptor
show the reaction diagram
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-
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?
trans-4-hydroxy-L-proline + oxidized dichlorophenolindophenol
?
show the reaction diagram
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?
additional information
?
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no substrate: D-proline, other L-amino acids, L-azetidine-2-carboxylate, succinate
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
L-proline + acceptor
(S)-1-pyrroline-5-carboxylate + reduced acceptor
show the reaction diagram
-
the bifunctional enzyme catalyzes the oxidation of proline in two steps. (S)-1-Pyrroline-5-carboxylate, the product of the first reaction is in spontaneous equilibrium with its tautomer L-glutamate gamma-semialdehyde: (1) L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor, (2) L-glutamate 5-semialdehyde + NAD+ + H2O = L-glutamate + NADH + H+
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-
?
L-proline + acceptor + H2O
(S)-1-pyrroline-5-carboxylate + reduced acceptor
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Iron
the alpha-subunit contains the [2Fe-2S] iron-sulfur flavoprotein. The gamma subunit is a typical [8Fe-8S] ferredoxin
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5-ethylpentyl-barbituric acid
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membrane-associated enzyme, not soluble enzyme
acetate
competitive
cyanide
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only membrane-associated enzyme, not soluble enzyme
D-lactate
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L-Azetidine-2-carboxylate
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competitive
L-lactate
L-tetrahydro-2-furoic acid
L-thiazolidine-4-carboxylate
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competitive
Lactate
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N-propargylglycine
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irreversibly inactivates PutA by covalently linking the flavin N(5) atom to the epsilon-amino of Lys329. Inactivation locks PutA into a conformation that may mimic the proline-reduced, membrane-associated form
pyruvate
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0034
2,6-dichlorophenolindophenol
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wild type enzyme, at 25C and pH 7.1 in 20 mM Tris-HCl
0.06 - 340
L-proline
190 - 750
trans-4-hydroxy-L-proline
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.5 - 100.6
L-proline
2 - 2.9
trans-4-hydroxy-L-proline
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
21.9 - 79.5
2,6-dichlorophenolindophenol
165
1.438 - 90.32
coenzyme Q1
1187
0.125
L-hydroxyproline
Pyrobaculum calidifontis
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in 200 mM Tris-HCl buffer (pH 8.0), at 50C
3080
0.00021 - 20.1
L-proline
243
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.1
D-lactate
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20
L-Azetidine-2-carboxylate
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1 - 1.4
L-lactate
0.084 - 7.9
L-tetrahydro-2-furoic acid
3.3
pyruvate
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.68
bifunctional dye-linked L-proline/NADH dehydrogenase complex
1.24
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25C, pH 7.5, proline oxidase activity of the bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
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L-proline + phenazine methosulfate
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
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assay at
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
76000
gel electrophoresis
120000
bifunctional dye-linked L-proline/NADH dehydrogenase complex, gel filtration
260000
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gel filtration
293000
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gel filtration, bifunctional enzyme: proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase, sucrose density centrifugation
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
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2 * 37000, SDS-PAGE
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2.15 A resolution structure of the PRODH inactivated by N-propargylglycine. The initial events involved in broadcasting the reduced flavin state to the distal membrane-binding domain include major reorganization of the flavin ribityl chain, severe butterfly bending of the isoalloxazine ring, and disruption of an electrostatic network involving the flavin N(5) atom, Arg431, and Asp370. The active site is incompletely assembled in the absence of the substrate, and the binding of proline draws together conserved residues in helix 8 and the beta1-alphal loop to complete the active site
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hanging drop method
mutant Y540S
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sitting-drop vaor diffusion method, structures of the PutA PRODH domain complexed with competitive inhibitors, acetate, L-lactate and L-tetrahydro-2-furoic acid
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 10
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50C, 10 min, stable
392570
4.5 - 9
stable
658668
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
50% loss of activity of wild-type PutA86-669 after 1 h, 50% loss of of L432P mutant form of PutA86-669 after 8 min
80
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120 min, 40% of activity remains
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
stabilized by 1 M NaCl, KCl
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
nickel affinity column chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene product PutA functions as proline dehydrogenase and as repressor of genes putP and putA
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wild-type PutA86-601 and site-directed mutants
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
isoform ProDH1 expression is dependent on salicylic acid (stimulation at 0.05-2.5 mM) and an increase in enzyme activity is detected in cells destined to die
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proline and NaCl induce gene expression
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salicylic acid has no effect on the isoform ProDH2 mRNA level, even at 2.5 mM
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sucrose represses ProDH2 expression
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D370A
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mutant form of PutA86-601. The ratio of turnover-number to Km-value is 2.8fold lower than the ratio of the wild-type PutA86-601
D370A/Y540F
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mutant form of PutA86-601. The ratio of turnover-number to Km-value is 15fold lower than the ratio of the wild-type PutA86-601
L432P
mutant form of PutA86-669, 5fold decrease in turnover-number and a severe loss in thermostability
W194F
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mutation in truncated enzyme containing residues 86-601, ratio of kcat to Km-value drops by 50%
W194F/W211F
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mutation in truncated enzyme containing residues 86-601, ratio of kcat to Km-value drops by 95%
W211F
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mutation in truncated enzyme containing residues 86-601, ratio of kcat to Km-value drops by 80%
Y540A
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a construct consisting of residue 86-630 of PutA is used
Y540F
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mutant form of PutA86-601. The ratio of turnover-number to Km-value is 5.8fold lower than the ratio of the wild-type PutA86-601
Y540S
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a construct consisting of residue 86-630 of PutA is used
Y203F
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the mutant shows severely reduced catalytic efficiency compared to the wild type enzyme
additional information
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