Information on EC 3.4.17.8 - muramoylpentapeptide carboxypeptidase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY hide
3.4.17.8
-
RECOMMENDED NAME
GeneOntology No.
muramoylpentapeptide carboxypeptidase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
cleavage of the bond UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-6-carboxy-L-lysyl-D-alanyl-/-D-alanine
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of peptide bond
-
-
exopeptidase, C-terminus, amino acid
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CAS REGISTRY NUMBER
COMMENTARY hide
9077-67-2
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
KM
-
-
Manually annotated by BRENDA team
KM
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
strain BM4174, bifunctional enzyme with activities of EC 3.4.17.8 and 3.4.13.22
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-
Manually annotated by BRENDA team
strain BM4174, bifunctional enzyme with activities of EC 3.4.17.8 and 3.4.13.22
-
-
Manually annotated by BRENDA team
wild-type strain ATCC 9790, gene pbp5
-
-
Manually annotated by BRENDA team
strain MG1655
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
strain ATCC 29062 and other strains, e.g. strain SS1 and SS2, overview
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-[(ammonioacetyl)amino]-3-[[3-([2-[(1-carboxylatoethyl)amino]-1-methyl-2-oxoethyl]amino)-3-oxopropyl]sulfanyl]propanoate + H2O
?
show the reaction diagram
-
-
-
-
?
2-[(ammonioacetyl)amino]-3-[[3-([2-[(1-carboxylatoethyl)sulfanyl]-1-methyl-2-oxoethyl]amino)-3-oxopropyl]sulfanyl]propanoate + H2O
?
show the reaction diagram
-
-
-
-
?
2-[(ammonioacetyl)amino]-7-([2-[(1-carboxylatoethyl)amino]-1-methyl-2-oxoethyl]amino)-7-oxoheptanoate + H2O
?
show the reaction diagram
-
-
-
-
?
2-[[N-(phenylacetyl)alanyl]sulfanyl]propanoic acid + H2O
?
show the reaction diagram
-
-
-
-
?
3-[[N-(phenylacetyl)alanyl]oxy]benzoic acid + H2O
?
show the reaction diagram
-
-
-
-
?
3-[[N-(phenylacetyl)glycyl]oxy]benzoic acid + H2O
?
show the reaction diagram
-
-
-
-
?
acetyl-Gly-D-Ala-D-Ala + H2O
acetyl-Gly-D-Ala + D-Ala
show the reaction diagram
-
-
-
-
?
acetyl-L-Ala-D-Ala-D-Ala + H2O
acetyl-L-Ala-D-Ala + D-Ala
show the reaction diagram
-
-
-
-
?
diacetyl-L-diaminobutyryl-D-Ala-D-Ala + H2O
diacetyl-L-diaminobutyryl-D-Ala + D-Ala
show the reaction diagram
-
-
-
-
?
diacetyl-L-Lys-D-Ala-D-Ala + H2O
diacetyl-L-Lys-D-Ala + D-Ala
show the reaction diagram
-
-
-
-
?
L-Ala-D-gamma-Glu-L-Lys-D-Ala-D-Ala + H2O
L-Ala-D-gamma-Glu-L-Lys-D-Ala + D-Ala
show the reaction diagram
-
D,D-carboxypeptidase activity of penicillin-binding proteins
-
-
?
methyl N-acetylmuramate-L-Ala-gamma-D-Glu-meso-diaminopimelate-D-Ala-D-Ala + H2O
methyl N-acetylmuramate-L-Ala-gamma-D-Glu-meso-diaminopimelate-D-Ala + D-Ala
show the reaction diagram
muramoylpentapeptide + H2O
muramoyltetrapeptide + D-Ala
show the reaction diagram
-
-
-
-
?
N,N'-diacetyl-L-lysyl-D-alanyl-D-alanine + H2O
N,N'-diacetyl-L-lysyl-D-alanine + D-alanine
show the reaction diagram
-
-
-
-
?
Nalpha, Nepsilon-diacetyl L-Lys-D-Ala-Gly + H2O
Nalpha,Nepsilon-diacetyl-L-Lys-D-Ala + Gly
show the reaction diagram
Nalpha,Nepsilon-diacetyl-L-Lys-D-Ala-D-Ala + H2O
Nalpha,Nepsilon-diacetyl-L-Lys-D-Ala + D-Ala
show the reaction diagram
penicillin + H2O
a carboxylate + 6-aminopenicillanate
show the reaction diagram
-
very slow hydrolysis
-
?
UDP-MurNAc-pentapeptide + H2O
UDP-MurNAc-tetrapeptide + D-Ala
show the reaction diagram
UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine + H2O
?
show the reaction diagram
UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-L-lysyl-D-alanyl-D-alanine + H2O
UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-L-lysyl-D-alanine + D-alanine
show the reaction diagram
UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-L-mesodiaminopimelyl-D-Ala-D-Ala + H2O
UDP-N-acetylmuramyl-L-Ala-gamma-D-Glu-L-mesodiaminopimelyl-D-Ala + D-Ala
show the reaction diagram
additional information
?
-
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
UDP-MurNAc-pentapeptide + H2O
UDP-MurNAc-tetrapeptide + D-Ala
show the reaction diagram
-
i.e. UDP-acetylmuramic acid-L-Ala-D-iGlu-L-Lys-D-Ala-D-Ala
-
-
?
UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine + H2O
?
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
-
activation
additional information
-
no metalloenzyme
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(5R,6R)-6-[(7-ammonio-7-carboxylatoheptanoyl)amino]-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylate
-
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5,5'-dithiobis(2-nitrobenzoate)
-
-
6-beta(D-alpha-aminopimelyl)-aminopenicillanic acid
-
-
6-beta(N-acetyl-L-alanyl-gamma-D-glutamyl-L-alanyl)-aminopenicillanic acid
-
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7-beta(D-alpha-aminopimelyl)-aminocephalosporanic acid
-
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Acetyl-D-Ala-D-Glu
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acetyl-Gly-D-Ala-D-Glu
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acetyl-Gly3-D-Ala-D-Asp
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alpha,epsilon-disuccinyl-L-Lys-D-Ala-D-Glu
-
-
-
ampicillin
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inhibits the D,D-carboxypeptidase activity of penicillin-binding proteins
benzylpenicillin
-
-
carbenicillin
-
-
Cephalothin
-
-
D-Ala-D-Glu
-
-
D-Ala-D-Ser
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30% inhibition
D-alpha-phenylpropionate
-
-
D-hexahydromandelate
-
-
D-lactate
-
-
D-mandelate
-
-
D-phenyllactate
-
-
diacetyl-L-Lys-D-Ala-L-Ala
-
-
diacetyl-L-Lys-l-Ala-D-Ala
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-
glycolyl-L-Phe
-
-
iodoacetic acid
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-
Methicillin
-
-
p-chloromercuribenzene sulfonic acid
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p-Iodo-7-beta-phenyl-acetylaminocephalosporamic acid
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penicillin G
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Ristocetin
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succinyl-D-Ala-D-cycloserine
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-
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UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-L-lysyl-D-alanyl-D-serine
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30% inhibition
Vancomycin
-
-
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
no activation by D-lactate or D-phenyllactate
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.1
acetyl-Gly-D-Ala-D-Ala
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-
3.3
acetyl-L-Ala-D-Ala-D-Ala
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-
0.6
diacetyl-L-diaminobutyryl-D-Ala-D-Ala
-
-
6.1
methyl N-acetylmuramate-L-Ala-gamma-D-Glu-meso-diaminopimelate-D-Ala-D-Ala
pH not specified in the publication, temperature not specified in the publication
0.33 - 8.7
Nalpha,Nepsilon-Diacetyl-L-Lys-D-Ala-D-Ala
0.4
UDP-N-acetylmuramoyl-L-Ala-gamma-D-Glu-L-mesodiaminopimelyl-D-Ala-D-Ala
1.5 - 18.8
UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-L-lysyl-D-alanyl-D-alanine
additional information
additional information
-
kinetics of wild-type and mutant enzymes
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.31
methyl N-acetylmuramate-L-Ala-gamma-D-Glu-meso-diaminopimelate-D-Ala-D-Ala
Pseudomonas aeruginosa
G3XD74
pH not specified in the publication, temperature not specified in the publication
0.59
Nalpha,Nepsilon-Diacetyl-L-Lys-D-Ala-D-Ala
Pseudomonas aeruginosa
G3XD74
pH not specified in the publication, temperature not specified in the publication
6.2 - 23
UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-L-lysyl-D-alanyl-D-alanine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.055
methyl N-acetylmuramate-L-Ala-gamma-D-Glu-meso-diaminopimelate-D-Ala-D-Ala
Pseudomonas aeruginosa
G3XD74
pH not specified in the publication, temperature not specified in the publication
199241
0.065
Nalpha,Nepsilon-Diacetyl-L-Lys-D-Ala-D-Ala
Pseudomonas aeruginosa
G3XD74
pH not specified in the publication, temperature not specified in the publication
3220
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
15.5
D-alpha-phenylpropionate
-
pH 7.5, 25C
7
D-hexahydromandelate
-
pH 7.5, 25C
11.6
D-mandelate
-
pH 7.5, 25C
17.8
D-phenyllactate
-
pH 7.5, 25C
19.3
glycolyl-L-Phe
-
pH 7.5, 25C
additional information
additional information
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0076
-
mutant D344S
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
-
assay at
8.5
-
assay at
9.5 - 10.5
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
pH profile, wild-type and mutant enzymes
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
-
assay at
30
-
assay at
37
-
assay at
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
17000
-
small-angle X-ray scattering
22080
-
amino acid sequence
50000
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gel filtration in presence of guanidine-HCl
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure of recombinant protein, with deletion off the C-terminal anchor, at a 2.05 A resolution. Strucuture contains a shortened loop spanning residues 74 to 78 near the active site and two active-site residues, Ser101 and Lys203. An active-site flexibility may explain its carbapenemase activity
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, membrane preparation, pH 7.8 or 5.0, 1 year
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant enzymes from strain BL21(DE3) by ion exchange chromatography, gel filtration, and ultrafiltration
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
gene pbp5, complementation of a PBP5-deficient Enterococcus hirae strain SL1 and a PBP3-deficient Enterococcus hirae strain SL2
-
gene pbp5, expression of wild-type and mutant enzymes in Escherichia coli, complementation of the pbp5-deficient mutant strain SL1 and of the pbp3-deficient strain SL2 by wild-type and mutant enzymes, recombinant strains, overview
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gene pbp5, expression of wild-type and mutant enzymes in strain BL21(DE3)
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D344S
-
the mutant shows highly reduced activity compared to the wild-type
D59A
-
73% decrease in ratio kcat/KM for D-Ala-D-Ala substrate, EC3.4.13.B1 activity
D59S
-
strong increase in ratio kcat/KM for EC 3.4.17.8 activity, 50% increase in ratio kcat/KM for D-Ala-D-Ala substrate, EC3.4.13.B1 activity
D59A
-
73% decrease in ratio kcat/KM for D-Ala-D-Ala substrate, EC3.4.13.B1 activity
-
D59S
-
strong increase in ratio kcat/KM for EC 3.4.17.8 activity, 50% increase in ratio kcat/KM for D-Ala-D-Ala substrate, EC3.4.13.B1 activity
-
K172N/R173N
-
site-directed mutagenesis, M1 mutant, the mutant enzyme shows altered complementation of the pbp3-deficient mutant strain SL2 compared to the wild-type enzyme, the mutant enzyme shows complementation of the pbp5-deficient mutant strain SL1, overview
K199Q
-
site-directed mutagenesis, M5 mutant, the mutant enzyme shows complementation of the pbp5-deficient mutant strain SL1
K199Q/K203Q
-
site-directed mutagenesis, M2 mutant, the mutant enzyme shows altered complementation of the pbp3-deficient mutant strain SL2 compared to the wild-type enzyme, the mutant enzyme shows complementation of the pbp5-deficient mutant strain SL1, overview
K203Q
-
site-directed mutagenesis, M3 mutant, the mutant enzyme shows altered complementation of the pbp3-deficient mutant strain SL2 compared to the wild-type enzyme, the mutant enzyme shows complementation of the pbp5-deficient mutant strain SL1, overview
R173N
-
site-directed mutagenesis, M4 mutant, the mutant enzyme shows complementation of the pbp5-deficient mutant strain SL1
S422A
-
site-directed mutagenesis, M6 mutant, inactive mutant
C115S
-
site-directed mutagenesis, truncated mutant of PBP5, pH-dependency, kinetics, and activity compared to the wild-type enzyme
K213C/C115S
-
site-directed mutagenesis, truncated double mutant of PBP5, pH-dependency, kinetics, and activity compared to the wild-type enzyme
K47C/C115S
-
site-directed mutagenesis, truncated double mutant of PBP5, pH-dependency, kinetics, and activity compared to the wild-type enzyme
additional information