|Protein name||D-alanyl-D-alanine carboxypeptidase||serine-type D-Ala-D-Ala carboxypeptidaseDD-peptidaseD-alanyl-D-alanine-carboxypeptidaseD-alanyl-D-alanine-cleaving-peptidaseD-alanyl-D-alanine-cleaving peptidaseDD-transpeptidaseD-alanine carboxypeptidaseDD-carboxypeptidaseD-alanyl carboxypeptidase|
|Synonyms||DD-carboxypeptidaseDD-peptidaseEC 220.127.116.11Penicillin-binding proteinPBP|
|Activity||Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|- D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.|
|Subcellular location||Secreted (Potential).|
|Compound table: links to PDB-related databases & PoSSuM|
|Type||peptide/protein||H2O||amino acids,amide group,carboxyl group,lipid,peptide/protein||amino acids||peptide/protein||amino acids,amide group,carboxyl group,peptide/protein,lipid,peptide/protein|
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|References for Catalytic Mechanism|
|References||Sections||No. of steps in catalysis|
|Comments||X-ray crystallography (2.0 Angstroms)|
|Journal||J Biol Chem|
|Authors||Fonze E, Vermeire M, Nguyen-Disteche M, Brasseur R, Charlier P|
|Title||The crystal structure of a penicilloyl-serine transferase of intermediate penicillin sensitivity. The DD-transpeptidase of streptomyces K15.|
|Authors||Rhazi N, Charlier P, Dehareng D, Engher D, Vermeire M, Frere JM, Nguyen-Disteche M, Fonze E|
|Title||Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis.|
|Theis enzyme belongs either to peptidase family-S11.|
The enzyme can act as a bifunctional enzyme, catalyzing both hydrolysis and acyl group transfer reaction.
The hydrolysis involves two steps, acylation and deacylation. The acylation proceeds as follows:
(1) Despite no clear evidence, Lys38 has been implicated to act as a general base, which can activate the catalytic Ser35, according to the paper .
(2) The catalytic Ser35 acts as a nucleophile, which makes an attack on the carbonyl carbon atom to form an acyl-enzyme, accoriding to the literature , .
(3) An oxyanion hole, formed by mainchain amide groups of Ser35 and Ser216, stabilize the polarized carbonyl group of the substrate and tetrahedral intermediate during the transition state (see ).
(4) Lys38 acts as a general acid to protonate the leaving nitrogen, through the hydroxyl group of Ser96. (Ser96 acts as a proton shuttle.)
As for the deacylation, it has not been elucidated which residue can activate the hydrolytic water, which would attack the acyl-enzyme intermediate (see ). Probably, either Lys38 or Ser96 might play the role in activating the water (see ).