Zinc D-Ala-D-Ala carboxypeptidase

 

The zinc D-Ala-D-Ala carboxypeptidase belongs to the peptidase M15 family and hydrolyses the C-terminal peptide bond of the peptides of general structure R-DAla-D-Xaa, it is secreted by Streptomyces albus G. The lytic activity of the enzyme and its extracellular location suggest that it might be used by Streptomyces for fighting competitors in its ecological niche, since the enzyme does not hydrolyse the Streptomyces peptidoglycan.

 

Reference Protein and Structure

Sequence
P00733 UniProt (3.4.17.14) IPR009045 (Sequence Homologues) (PDB Homologues)
Biological species
Streptomyces albus G (Bacteria) Uniprot
PDB
1lbu - HYDROLASE METALLO (ZN) DD-PEPTIDASE (1.8 Å) PDBe PDBsum 1lbu
Catalytic CATH Domains
3.30.1380.10 CATHdb (see all for 1lbu)
Cofactors
Zinc(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:3.4.17.14)

water
CHEBI:15377ChEBI
+
L-alanyl-L-alanine
CHEBI:72816ChEBI
→
L-alanine
CHEBI:16977ChEBI
+
L-alanine
CHEBI:16977ChEBI
Alternative enzyme names: D-alanyl-D-alanine hydrolase, D-alanyl-D-alanine-cleaving carboxypeptidase, DD-carboxypeptidase, DD-carboxypeptidase-transpeptidase, G enzyme, Zn(2+) G peptidase,

Enzyme Mechanism

Introduction

The reaction proceeds as follows: The carbonyl oxygen of substrate peptide bond is bound to zinc ion, which polarises it. The catalytic water bound to the zinc is slightly shifted to His237 via a hydrogen-bond. His237 acts as a general base, to activate the catalytic water along with the zinc ion. The activated water makes a nucleophilic attack on the carbonyl carbon of the substrate, leading to the formation of tetrahedral oxyanion intermediate. The negative charge on the intermediate is stabilized by the side chains of His234 and Tyr231 together with the zinc ion. A proton from a water molecule is transferred to the amide bond nitrogen via Asp236 to protonate the leaving group on break down of the tetrahedral intermediate.

Catalytic Residues Roles

UniProt PDB* (1lbu)
Asp203, His196, His239 Asp161A, His154A, His197A Form Zinc binding site
Asp236 Asp194A Aids His195 activity via a hydrogen-bond. Also abstracts a proton from a water molecule to protonate the leaving amine group. proton shuttle (general acid/base), electrostatic stabiliser
His237 His195A Acts as a general base to deprotonate the zinc-bound water molecule to create a nucleophile. Part of His-Asp dyad. proton shuttle (general acid/base)
Tyr231, His234 Tyr189A, His192A Forms an oxyanion hole, to stabilise the build up of negative charge via hydrogen bonding. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Charlier P et al. (2011), Encyclopedia of Inorganic and Bioinorganic Chemistry, 3-164. Streptomyces Albus GD-Ala-D-Ala Carboxypeptidase. DOI:10.1002/9781119951438.eibc0498.

Step 1.

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Catalytic Residues Roles

Residue Roles
His195A proton shuttle (general acid/base)
Asp194A electrostatic stabiliser, proton shuttle (general acid/base)
His192A electrostatic stabiliser
Tyr189A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Anna Waters, Craig Porter, Gemma L. Holliday, Charity Hornby