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3.4.16.4: serine-type D-Ala-D-Ala carboxypeptidase

This is an abbreviated version!
For detailed information about serine-type D-Ala-D-Ala carboxypeptidase, go to the full flat file.

Word Map on EC 3.4.16.4

Reaction

Preferential cleavage: (Ac)2-L-Lys-D-Ala-/-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine =

Synonyms

carboxypeptidase I, CPase, D,D-carboxypeptidase, D,D-carboxypeptidase R39, D,D-dipeptidase, D-Ala-D-Ala carboxypeptidase, D-Ala-D-Ala peptidase, D-Ala-D-Ala(D,D) carboxypeptidase, D-alanine carboxypeptidase, D-alanine carboxypeptidase I, D-alanine-carboxypeptidase, D-alanyl carboxypeptidase, D-alanyl-D-alanine carboxypeptidase, D-alanyl-D-alanine carboxypeptidase/transpeptidase, D-Alanyl-D-alanine hydrolase, D-alanyl-D-alanine peptidase, D-alanyl-D-alanine transpeptidase, D-alanyl-D-alanine-carboxypeptidase, D-alanyl-D-alanine-cleaving peptidase, D-alanyl-D-alanine-cleaving-peptidase, D-alanyl-D-alanine-transpeptidase, D-amino acid amidase, DAA, Dac, dacA, DacA-1, DacB, DacC, DacD, DAP, Dbv7, DD-Carboxypeptidase, DD-CPase, DD-CPase1, DD-peptidase, DD-transpeptidase, DD-transpeptidase/penicillin-binding protein, LMM-PBP, low molecular mass penicillin binding protein, PBP, PBP 2, PBP 3, PBP 4, PBP 5, PBP 6, PBP-5*, PBP-6B, PBP1a, PBP1b, PBP2x, PBP3, PBP4, PBP4a, PBP5, PBP6, PBP6a, PBP6b, penicillin binding protein 4, penicillin binding protein 5, penicillin binding proteins, penicillin-binding protein, penicillin-binding protein 1B, penicillin-binding protein 4a, penicillin-binding protein 5, penicillin-binding protein 5a, R39 PBP, SCO4439, serine type D-alanyl-D-alanine carboxypeptidase/transpeptidase, serine-type D-Ala-D-Ala carboxypeptidase, serine-type-D-Ala-D-Ala carboxypeptidase, transpeptidase, VanX, VanXY, VanY, VanY(D) DD-carboxypeptidase, VanYD, VanYn, VC_0947, VP2468, zinc D-Ala-D-Ala carboxypeptidase

ECTree

     3 Hydrolases
         3.4 Acting on peptide bonds (peptidases)
             3.4.16 Serine-type carboxypeptidases
                3.4.16.4 serine-type D-Ala-D-Ala carboxypeptidase

Crystallization

Crystallization on EC 3.4.16.4 - serine-type D-Ala-D-Ala carboxypeptidase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
by hanging drop vapor diffusion, at 1.8 A and 2.4 A resolution, R39 structure is composed of one penicillin binding domain and two unknown domains, the R39 active site does not undergo a great structural deformation upon beta-lactam binding
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in complex with inhibitor (2R)-2-amino-7-oxo-7-[(4,4,4-trifluoro-3-oxobutan-2-yl)amino]heptanoic acid. The inhibitor is covalently bonded to the active serine Ser49, the carbonyl carbon is now tetrahedral, and the ketone oxygen occupies the oxyanion hole, defined by the backbone NH groups of Ser49 and Thr413. The D-methyl group is directed into a hydrophobic pocket comprised residues Gly148, Leu 349 and Met414. Branching from the tetrahedral carbon bonded to Ser49Ogamma, the CF3 group occupies the likely position of a leaving group in the tetrahedral intermediate of a peptidase substrate
the structure of the R39 DD-peptidase bound to cephalosporin is refined to 2.4 A and the structure with a further peptidoglycan-mimetic ligand is refined to 2.25 A
the crystal structure of the protein alone is solved at a resolution of 2.1 A, and in complex with D-alpha-aminopymelyl-eta-D-alanyl-D-alanine at a resolution of 2.8 A
the crystal structures of native D-amino acid amidase and of the D-phenylalanine/D-amino acid amidase complex are determined at 2.1 and at 2.4 A resolution, respectively
crystal structures of VanXY mutant D59S and VanXY wild-type in apo and transition state analog-bound forms and of the mutant in complex with the D-Ala-D-Ala substrate and D-Ala product. Structural and biochemical analysis identifies the molecular determinants of VanXY dual specificity acting on dipeptide D-Ala-D-Ala or pentapeptide UDP-MurNac-L-Ala-D-Glu-L-Lys-D-Ala-D-Ala, respectively. VanXY residues 110-115 form a mobile cap over the catalytic site, whose flexibility is involved in the switch between di- and pentapeptide hydrolysis. VanY pentapeptidases lack this element, which promotes binding of the penta- rather than that of the dipeptide
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crystal structure at 1.6 A resolution of PBP5 in complex with a substrate-like peptide boronic acid, suggesting a hydrogen-bonding network, involving Lys-213, Ser-110, and a bridging water molecule, to polarize the hydrolytic water molecule
three dimensional structure of the G105D mutant enzyme at 2.3 A resolution
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vapor diffusion hanging drop technique. Three-dimensional structure of a soluble form of wild-type enzyme at 1.85 A resolution and structure of the G105D mutant form at 1.9 A resolution
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the structure in complex with cephalosporin is refined to 1.6 A and with penicillin to 2.0 A
purified Pbp1b in complex with N-benzoyl-D-Ala or pseudo-substrate N-benzoyl-D-alanylmercaptoacetic acid thioester, hanging drop vapor diffusion method, mixing of 0.001 ml of 6-10 mg/ml protein and 5 mM N-benzoyl-D-alanylmercaptoacetic acid thioester, with 0.001 ml of well solution containing 50 mM HEPES, pH 7.0, 0.8 M (NH4)2SO4, 2.8 M NaCl at 15°C, X-ray difraction structure determination and analysis at 2.5 A resolution, molecular replacement
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by hanging drop vapor diffusion, to 2.8 A resolution, PBP3 folds into an NH2-terminal,D,D-carboxypeptidase-like domain and a COOH-terminal, elongated beta-rich region
Streptomyces pneumoniae
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1.2 A resolution X-ray structure of cephalosporin bound to the active site of the bifunctional serine type D-alanyl-D-alanine carboxypeptidase/transpeptidase
characterization of the noncovalent interactions based on cocrystallized structures of benzylpenicillin and perfect penicillin covalently bound to DD-peptidase by computational methods. Benzylpenicillin’s phenyl group forms an extended pi?pi network with Phe120 and Trp233 that contributes significantly to its efficacy in DD-peptidase. This aromatic stabilization is conserved in beta-lactamases. Interactions between the protein and the peptidomimetic tail region, particularly carboxylate 2 and the terminal N4H3+ unit, form unique hydrogen bonding and strong electrostatic interactions. Between Asp217 and the N4H3+ there is a water mediated salt bridge
hanging drop vapor diffusion method. Mutant enzymes S96A, K38H, C98A and C98N are produced in culture medium of Streptomyces lividans
hanging drop vapor diffusion, crystal structure of the phosphonal enzyme. The 1.1 A resolution structure of the enzyme in complex with phenyl glycyl-L-alpha-aminopimelyl-epsilon-(D-2-aminoethyl)phosphonate shows that the inhibitor is phosphorylated by the catalytic Ser62
X-ray structure, the energetically most stable configuration has a neutral Lys213 residue, the K15 active site is characterized by a dense hydrogen-bonding network that interconnects the catalytically relevant residues and some solvent molecules, the hydroxyl group of the nucleophilic serine (Ser35) is located in the oxy-anion-hole formed by the backbone NH groups of Ser35 and Ser216
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by hanging drop vapor diffusion, to 1.1 A resolution
by hanging-drop, vapor-diffusion method, to 1.5 A resolution, X-ray structure of non-covalent and covalent complexes of beta-lactams with DD-peptidase
molecular dynamics simulations of noncovalent interactions in binding and specificity of benzylpenicillin and beta-lactam peptidomimetic perfect penicillin. Benzylpenicillin's phenyl group forms an extended pi-pi network with Phe120 and Trp233 that contributes significantly to its efficacy in DD-peptidase. Interactions between the protein and the peptidomimetic tail region, particularly carboxylate 2 and the terminal N4H3+ unit, form unique hydrogen bonding and strong electrostatic interactions, particularly the water-mediated salt bridge between Asp217 and the N4H3+