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EC Tree
The enzyme appears in viruses and cellular organisms
Reaction Schemes
cleavage of the bond: (Ac)2-L-lysyl-D-alanyl-/-D-alanine
Synonyms
dd-carboxypeptidase, pbp4a, d-alanyl-d-alanine carboxypeptidase, penicillin binding protein 4, dd-carboxypeptidase-transpeptidase, pbp4b, d-alanyl-d-alanine-cleaving carboxypeptidase, penicillin-binding protein 4a,
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D-alanyl-D-alanine carboxypeptidase
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D-Alanyl-D-alanine hydrolase
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D-Alanyl-D-alanine-cleaving carboxypeptidase
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DD-Carboxypeptidase-transpeptidase
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penicillin binding protein 4
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penicillin-binding protein 4a
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zinc D-Ala-D-Ala carboxypeptidase
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additional information
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the enzyme belongs to the serine protease family
DD-Carboxypeptidase
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cleavage of the bond: (Ac)2-L-lysyl-D-alanyl-/-D-alanine
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hydrolysis of peptide bond
hydrolysis of peptide bond
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hydrolysis of peptide bond
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Acetyl2-L-Lys-D-Ala-D-Ala + H2O
Acetyl2-L-Lys-D-Ala + D-Ala
Nalpha,Nepsilon-diacetyl-Lys-D-Ala-D-Ala + H2O
Nalpha,Nepsilon-diacetyl-Lys-D-Ala + D-Ala
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Nalpha-Acetyl-L-Lys-D-Ala-D-Ala + H2O
Nalpha-Acetyl-L-Lys-D-Ala + D-Ala
peptidoglycan + H2O
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hydrolyzes peptidoglycan interpeptide bonds between a D-alanine and another D-amino acid residue in alpha-position to a free carboxylate
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additional information
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Acetyl2-L-Lys-D-Ala-D-Ala + H2O
Acetyl2-L-Lys-D-Ala + D-Ala
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Acetyl2-L-Lys-D-Ala-D-Ala + H2O
Acetyl2-L-Lys-D-Ala + D-Ala
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Acetyl2-L-Lys-D-Ala-D-Ala + H2O
Acetyl2-L-Lys-D-Ala + D-Ala
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Nalpha-Acetyl-L-Lys-D-Ala-D-Ala + H2O
Nalpha-Acetyl-L-Lys-D-Ala + D-Ala
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Nalpha-Acetyl-L-Lys-D-Ala-D-Ala + H2O
Nalpha-Acetyl-L-Lys-D-Ala + D-Ala
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additional information
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DAP contributes to resistance against NO required for the intracellular growth of the bacterium
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additional information
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the DD-carboxypeptidase activity encoded by pbp4B is not essential for the cell growth of Escherichia coli
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additional information
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PBP4B shows penicillin-binding capacity and a low DD-carboxypeptidase activity
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additional information
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mechanism
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additional information
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weak beta-lactamase activity hydrolyzing penicillin into penicilloate
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additional information
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involved in bacterial cell wall metabolism
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additional information
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additional information
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DAP contributes to resistance against NO required for the intracellular growth of the bacterium
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additional information
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the DD-carboxypeptidase activity encoded by pbp4B is not essential for the cell growth of Escherichia coli
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additional information
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involved in bacterial cell wall metabolism
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Mg2+
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2-5 mM, optimal activity
Zinc
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a zinc enzyme
Zinc
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1 Zn2+ bound per enzyme molecule
Zinc
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Zn2+ cofactor is required for both DD-carboxypeptidase activity and binding of benzyl-penicillin
Zinc
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the Zn2+ ion is ligated by three histidine residues and located in a cleft in the C-terminal domain
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6-beta-iodopenicillinate
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causes permanent inactivation
L-3-mercaptoisobutyrate
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Infections
Staphylococcus aureus cell wall structure and dynamics during host-pathogen interaction.
Osteomyelitis
Identification of Penicillin Binding Protein 4 (PBP4) as a critical factor for Staphylococcus aureus bone invasion during osteomyelitis in mice.
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0.000001
3-Mercaptopropionate
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0.000001
L-3-mercaptoisobutyrate
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additional information
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8.03
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sequence calculation
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brenda
strain 544, ATCC 23448, a smooth virulent biovar 1 strain, gene dacF
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brenda
G
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brenda
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brenda
R39 and R61
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brenda
gene pbp4B
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brenda
the enzyme contains the mutation D261Y, relative to the SwissProt entry P24228; gene dacB
SwissProt
brenda
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brenda
additional information
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intracellular replication of Brucella abortus within murine macrophages and HeLa cells
brenda
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brenda
the enzyme contains a 5' leader sequence targeting it to the periplasm
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brenda
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brenda
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brenda
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brenda
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22080
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Streptomyces albus, calculation from amino acid sequence
38000
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Streptomyces sp. R61, gel filtration
50978
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x * 50978, sequence calculation
53300
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Streptomyces sp. R39, gel filtration
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?
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x * 50978, sequence calculation
monomer
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Streptomyces albus
additional information
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the enzyme consists of two globular domains, connected by a single link, the N-terminal domain has three alpha-helices, and the C-terminal domain has three alpha-helices and five beta-strands
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purified recombinant enzyme, wild-type or selenomethionine-labeled, 10-15 mg/ml protein, hanging drop vapour diffusion method, from 0.1 M MES, pH 6.5, and 3-10% PEG 20000, microseeding, 20°C, cryoprotection by 25% v/v glycerol, X-ray diffraction structure determination and analysis at 1.55-1.70 A resolution, modeling
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additional information
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the enzyme mutant K23 of Brucella abortus fails to replicate in mouse macrophages and HeLa cells, and shows less virulence than the wild type in mice, Under nitric oxide (NO) stress, the growth of the DAP mutant in vitro decreases, and it also has less capability to reduce NO than the wild type, intracellular replication of the DAP mutant is partially restored by pretreatment of macrophages with the NO synthase inhibitor 1-phenyl-imidazole and the level of expression of the NO reductase gene norB in the DAP mutant is lower than that in the wild type
additional information
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construction of gene pbp4B deletion mutants, the enzyme is not not essential for cell division, the strain lacking all known D-alanine carboxypeptidases is viable, overview
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recombinant enzyme from strain BL21(DE3) by anion exchange and hydrophobic interaction chromatography, followed by gel filtration
recombinant His-tagged enzyme from strain BL21(DE3) membranes by solubilization with 1% Triton X-100 and nickel affinity chromatography
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gene dacB, expression of the enzyme lacking the 5' leader peptide in strain BL21(DE3)
gene pbp4B, DNA and amino acid sequence determination and analysis, the pbp4B gene is located at the zipA-dapA region, subcloning in strain DH5alpha, expression of N-terminally His-tagged enzyme in strain BL21(DE3) membranes
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Joris, B.; van Beeumen, J.; Casagrande, F.; Gerday, C.; Frere, J.M.; Ghuysen, J.M.
The complete amino acid sequence of the Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase of streptomyces albus G
Eur. J. Biochem.
130
53-69
1983
Streptomyces albus
brenda
Dideberg, O.; Charlier, P.; Dive, G.; Joris, B.; Frere, J.M.; Ghuysen, J.M.
Structure of a Zn2+-containing D-alanyl-D-alanine-cleaving carboxypeptidase at 2.5 A resolution
Nature
299
469-470
1982
Streptomyces albus
brenda
Dideberg, O.; Joris, B.; Frere, J.M.; Ghuysen, J.M.; Weber, G.; Robaye, R.; Delbrouck, J.M.; Roelandts, I.
The exocellular DD-carboxypeptidase of Streptomyces albus G: a metallo (Zn2+) enzyme
FEBS Lett.
117
215-218
1980
Streptomyces albus
brenda
Frere, J.M.; Moreno, R.; Ghuysen, J.M.; Perkins, H.R.; Dierickx, L.; Delcambe, L.
Molecular weight, amino acid composition and physicochemical properties of the exocellular DD-carboxypeptidase-transpeptidase of Streptomyces R39
Biochem. J.
143
233-240
1974
Streptomyces sp.
brenda
Kikuchi, H.; Kim, S.; Watanabe, K.; Watarai, M.
Brucella abortus d-alanyl-d-alanine carboxypeptidase contributes to its intracellular replication and resistance against nitric oxide
FEMS Microbiol. Lett.
259
120-125
2006
Brucella abortus
brenda
Ghuysen, J.
Zinc D-Ala-D-Ala carboxypeptidase (Streptomyces)
Handbook of Proteolytic Enzymes (Barrett,A. J. ;Rawlings,N. D. ,Woessner)
1
857-858
2004
Streptomyces albus G
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brenda
Vega, D.; Ayala, J.A.
The DD-carboxypeptidase activity encoded by pbp4B is not essential for the cell growth of Escherichia coli
Arch. Microbiol.
185
23-27
2006
Escherichia coli
brenda
Kishida, H.; Unzai, S.; Roper, D.I.; Lloyd, A.; Park, S.Y.; Tame, J.R.
Crystal structure of penicillin binding protein 4 (dacB) from Escherichia coli, both in the native form and covalently linked to various antibiotics
Biochemistry
45
783-792
2006
Escherichia coli (P24228), Escherichia coli
brenda
Sauvage, E.; Duez, C.; Herman, R.; Kerff, F.; Petrella, S.; Anderson, J.W.; Adediran, S.A.; Pratt, R.F.; Frere, J.M.; Charlier, P.
Crystal structure of the Bacillus subtilis penicillin-binding protein 4a, and its complex with a peptidoglycan mimetic peptide
J. Mol. Biol.
371
528-539
2007
Bacillus subtilis
brenda
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