Information on EC 3.4.17.13 - Muramoyltetrapeptide carboxypeptidase

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

EC NUMBER
COMMENTARY hide
3.4.17.13
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RECOMMENDED NAME
GeneOntology No.
Muramoyltetrapeptide carboxypeptidase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
hydrolysis of the bond: N-acetyl-D-glucosaminyl-N-acetylmuramoyl-L-Ala-D-glutamyl-6-carboxy-L-lysyl-/-D-alanine
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of peptide bond
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
anhydromuropeptides recycling
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-
muropeptide degradation
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peptidoglycan maturation (meso-diaminopimelate containing)
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-
CAS REGISTRY NUMBER
COMMENTARY hide
60063-80-1
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
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Manually annotated by BRENDA team
K12
-
-
Manually annotated by BRENDA team
MC6RP1
-
-
Manually annotated by BRENDA team
strain MG1655, gene ldcA
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-
Manually annotated by BRENDA team
W3110
-
-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
P18
-
-
Manually annotated by BRENDA team
P18
-
-
Manually annotated by BRENDA team
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SwissProt
Manually annotated by BRENDA team
strain ATCC 29062 and other strains, e.g. strain SS1 and SS2, overview
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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
GlcNAc-MurNAc tetrapeptide + H2O
?
show the reaction diagram
substrate prepared from purified murein by lysozyme, cleaves specifically between meso-diaminopimelic acid and D-alanine
-
-
?
L-Ala-D-Gln-L-Lys-D-Ala + H2O
L-Ala-D-Gln-L-Lys + D-Ala
show the reaction diagram
L-Ala-D-Glu-(L)-meso-diaminopimelic-acid-(omegaNH2)-(L)-D-Ala + H2O
L-Ala-D-Glu-(L)-meso-diaminopimelic-acid-(omegaNH2) + (L)-D-Ala
show the reaction diagram
L-Ala-gamma-D-Glu-L-Lys-D-Ala + H2O
?
show the reaction diagram
L-Ala-gamma-D-Glu-meso-diaminopimelyl-D-Ala + H2O
L-Ala-gamma-D-Glu-meso-diaminopimelyl + D-Ala
show the reaction diagram
Modified muropeptides + H2O
?
show the reaction diagram
muropeptides + H2O
?
show the reaction diagram
N-Acetylglucosamine-N-acetylmuramyl-Ala-D-Glu-Dap-D-Ala + H2O
N-Acetylglucosamine-N-acetylmuramyl-Ala-D-Glu-Dap + D-Ala
show the reaction diagram
N-acetylmuramoyl-Ala-D-Glu-Dap-D-Ala + H2O
N-acetylmuramoyl-Ala-D-Glu-Dap + D-Ala
show the reaction diagram
N-acetylmuramoyl-L-Ala-D-Glu-L-Lys-D-Ala + H2O
N-acetylmuramoyl-L-Ala-D-Glu-L-Lys + D-Ala
show the reaction diagram
N-acetylmuramyl-L-Ala-D-Glu-meso-diaminopimelyl-D-Ala + H2O
N-acetylmuramyl-L-Ala-D-Glu-meso-diaminopimelate + D-Ala
show the reaction diagram
peptidoglycan + H2O
?
show the reaction diagram
the enzyme is involved in peptidoglycan recycling
-
-
?
UDP-N-acetylmuramyl-Ala-D-Glu-Dap-D-Ala + H2O
UDP-N-acetylmuramyl-Ala-D-Glu-Dap + D-Ala
show the reaction diagram
UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-meso-diaminopimelyl-D-Ala + H2O
UDP-N-acetylmuramyl-L-Ala-D-Glu-meso-diaminopimelate + D-Ala
show the reaction diagram
additional information
?
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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-Ala-gamma-D-Glu-meso-diaminopimelyl-D-Ala + H2O
L-Ala-gamma-D-Glu-meso-diaminopimelyl + D-Ala
show the reaction diagram
-
-
-
-
?
peptidoglycan + H2O
?
show the reaction diagram
Q9HTZ1
the enzyme is involved in peptidoglycan recycling
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-
?
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ca2+
-
can replace Mg2+ in stimulation
Mg2+
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stimulates, optimal concentration: 10 mM, inhibition above
Mn2+
-
can replace Mg2+ in stimulation
Zn2+
isoform LcdB is active in the presence of Zn2+ ions and inactive in the presence of EDTA
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(3Z)-3-[(3-ethoxypropyl)imino]-N,N-diethyl-3H-1,2,4-dithiazol-5-amine
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i.e. DTZ, a dithiazoline inhibitor, specificity, overview, the compound has slight antibacterial activity against strain MG1655
Azthreonam
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-
Ca2+
-
10 mM
D-Amino acids
EDTA
isoform LcdB is inactive in the presence of EDTA
iodoacetamide
-
-
Mn2+
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10 mM
nocardicin A
penicillin G
Thienamycin
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.25
L-Ala-D-Glu-(L)-meso-diaminopimelic-acid-(omegaNH2)
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(L)-D-Ala
0.17
L-Ala-gamma-D-Glu-meso-diaminopimelyl-D-Ala
pH 8.0, 37C
0.8
N-acetylmuramoyl-L-Ala-D-Glu-L-Lys-D-Ala
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-
0.108 - 0.4
UDP-N-acetylmuramyl-Ala-D-Glu-Dap-D-Ala
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
160
L-Ala-gamma-D-Glu-meso-diaminopimelyl-D-Ala
Novosphingobium aromaticivorans
Q2G8F3
pH 8.0, 37C
additional information
additional information
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
24.5
substrate UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-meso-diaminopimelyl-D-Ala, pH 8.0, 37C
30
substrate N-acetylmuramyl-L-Ala-D-Glu-meso-diaminopimelyl-D-Ala, pH 8.0, 37C
230
substrate L-Ala-gamma-D-Glu-meso-diaminopimelyl-D-Ala, pH 8.0, 37C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5 - 8.2
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.8 - 9.5
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5.8: about 40% of activity maximum, 9.5: about 30% of activity maximum
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
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assay at
30 - 60
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incorporation of diaminopimelate into cell walls
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10 - 60
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10C: 27% of activity maximum, 60C: 99% of activity maximum
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
-
bacteriocyte
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
11800
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E. coli, gel filtration
12000
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1 * 12000, SDS-PAGE
34600
2 * 34600, about, sequence calculation
39000
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E. coli, gel filtration
51000
recombinant enzyme, high salt condition gel filtration
60000
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1 * 60000, Bacillus megaterium, gel filtration
additional information
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the encoded protein, DacB, is a 249-residue protein with a putative signal sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
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x *37800, calculated
dimer
2 * 34600, about, sequence calculation
monomer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
to 1.89 A resolution, abd modeling of interaction with substrate
purified recombinant wild-type enzyme and mutants S115A and H285A, sitting drop vapour diffusion method, 0.004 ml of 6 mg/ml protein containing solution is mixed with an equal volume of reservoir solution containing 20 mM CaCl2 dihydrate, 0.1 M sodium acetate trihydrate, pH 4.6, and 30% v/v 2-methyl-2,4-pentanediol, room temperature, 6 mg/ml selenomethionine-labeled enzyme from 50 mM citric acid, pH 4.5, 21C, X-ray diffraction structure determination and analysis at 1.5-2.4 A resolution
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-85C, protein concentration: 0.5 mg/ml, stable for 4 months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme from Escherichia coli
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, functional expression in Escherichia coli
expression in Escherichia coli
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gene ldcA, cloning from genomic DNA of strain MG1655, DNA and amino acid sequence determination and analysis
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using the pGEM-T easy vector system
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
higher transcript levels in the bacteriocyte than in the whole body oder in the embryo or midgut
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E217A
site-directed mutagenesis, nearly inactive mutant, lack of activity might possibly be due to a folding defect, no crystallization of the mutant enzyme
H285A
site-directed mutagenesis, nearly inactive mutant, lack of activity is not due to a folding defect
S115A
site-directed mutagenesis, nearly inactive mutant, lack of activity is not due to a folding defect
additional information
Show AA Sequence (1215 entries)
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