Streptomyces AlbusGD‐Ala‐D‐Ala Carboxypeptidase

Abstract

The zinc D ‐Ala‐ D ‐Ala carboxypeptidase hydrolyzes the C‐terminal peptide bond of peptides of general structure R‐ D ‐Ala‐ D ‐Xaa. 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 hydrolyze the Streptomyces peptidoglycan. The sequence of the 213‐residue mature protein is related to the VanX, VanY, and VanXY proteins of vancomycin‐resistant enterococci. The molecule is an ellipsoid consisting of two globular domains in which the N‐terminal and the C‐terminal ends are pulled apart. The small N‐terminal domain, from residue Asp1 to Pro83, has an all‐α‐helices structure and exhibits a typical three‐helix bundle fold, characteristic of the peptidoglycan binding domain. The largest C‐terminal domain belongs to the α + β type secondary structure, and is related to the N‐terminal domain of the murine sonic hedgehog, a signaling protein involved in natal morphogenesis and formation of embryonic patterning centers, and to the VanX D ‐Ala‐ D ‐Ala dipeptidase of Enterococcus faecium , a protein involved in the vancomycin resistance systems in streptococci. The mixed five‐stranded β‐sheet forms the core of the C‐terminal domain and the lining of one side of the catalytic cavity. One zinc ion occupies a roughly central position in the active site and is coordinated by the His154 NE2, the Asp161 OD1, and the His197 ND1. Classical β‐lactam compounds, which readily inactivate active site serine DD ‐peptidases, are very sluggish inactivators of the zinc D ‐Ala‐ D ‐Ala carboxypeptidase. The best competitive inhibitors are thiol derivatives such as 2‐ and 3‐mercaptopropionate ( K i = 50 and 5 nM) that might behave as bidentate ligands of the Zn 2+ ion.

Tol-Pal System and Rgs Proteins Interact to Promote Unipolar Growth and Cell Division in Sinorhizobium meliloti

“…RgsC, present in all analyzed Rhizobiales families, contains a conserved M15 zincbinding metallopeptidase domain and shows structural similarities to a DD-carboxypeptidase from Gram-positive Streptomyces albus G (27). DD-Carboxypeptidases remove the terminal D-alanine residue from pentamuropeptide in PG, thus regulating the abundance of substrates for transpeptidation by the major bifunctional PG synthases (28).…”

Crystal Structure of the LasA Virulence Factor from Pseudomonas aeruginosa: Substrate Specificity and Mechanism of M23 Metallopeptidases

“…It is clear that the M23 family shares common structural features with bacteriophage DD-endopeptidases that hydrolyse peptidoglycan cross-links as part of viral entry to the bacterial cell. 36 A comparison of the active site of the S. aureus autolysin LytM with more distantly related D-Ala-DAla metallopeptidases, such as VanX 37 and S. albus G carboxypeptidase, 38 has led to the suggestion that M23 metallopeptidases are part of a larger metalloenzyme superfamily termed LAS enzymes, that act primarily as peptidoglycan hydrolases. 39 An increasing number of M23 metallopeptidases are undergoing experimental characterisation, [40][41][42][43] and crystal structures of some family members are now available, [44][45][46] but many aspects of these and related enzymes are poorly understood.…”

Structure to function prediction of hypothetical protein KPN_00953 (Ycbk) from Klebsiella pneumoniae MGH 78578 highlights possible role in cell wall metabolism

“…This resulted in the identification of one potential template, termed 1LBU with sequence identity of only 23%. 1LBU is a crystal structure of muramoyl-pentapeptide carboxypeptidase, a Zn 2+ D-Ala-D-Ala carboxypeptidase from Streptomyces albus [ 20 ] which contain the particular Peptidase_M15_3 superfamily domain. 1LBU was also ranked top by Phyre2 search within CombFunc server as having the highest structural similarity KPN_0053.…”