4MPH

Crystal structure of BaLdcB / VanY-like L,D-carboxypeptidase Zinc(II)-bound

Summary for 4MPH

• Entry DOI: 10.2210/pdb4mph/pdb
• Related: 4JID
• Descriptor: D-alanyl-D-alanine carboxypeptidase family protein, ZINC ION, CHLORIDE ION, ... (5 entities in total)
• Functional Keywords: structural genomics, niaid, national institute of allergy and infectious diseases, center for structural genomics of infectious diseases, csgid, hedgehog/dd-peptidase fold, vany-like family, merops family m15b, zinc-dependent metallopeptidase, peptidoglycan metallopeptidase, baldcb, l, d-carboxypeptidase, tetrapeptidase, substrate l-ala-d-iso-gln-l-lys-d-ala, hydrolase
• Biological source: Bacillus anthracis (anthrax,anthrax bacterium)
• Total number of polymer chains: 2
• Total formula weight: 44493.35

Authors

Stogios, P.J.,Wawrzak, Z.,Onopriyenko, O.,Skarina, T.,Shatsman, S.,Peterson, S.N.,Savchenko, A.,Anderson, W.F.,Center for Structural Genomics of Infectious Diseases (CSGID) (deposition date: 2013-09-12, release date: 2013-09-25, Last modification date: 2024-02-28)

Primary citation

Hoyland, C.N.,Aldridge, C.,Cleverley, R.M.,Duchene, M.C.,Minasov, G.,Onopriyenko, O.,Sidiq, K.,Stogios, P.J.,Anderson, W.F.,Daniel, R.A.,Savchenko, A.,Vollmer, W.,Lewis, R.J.
Structure of the LdcB LD-Carboxypeptidase Reveals the Molecular Basis of Peptidoglycan Recognition.
Structure, 22:949-960, 2014

PubMed Abstract: Peptidoglycan surrounds the bacterial cytoplasmic membrane to protect the cell against osmolysis. The biosynthesis of peptidoglycan, made of glycan strands crosslinked by short peptides, is the target of antibiotics like β-lactams and glycopeptides. Nascent peptidoglycan contains pentapeptides that are trimmed by carboxypeptidases to tetra- and tripeptides. The well-characterized DD-carboxypeptidases hydrolyze the terminal D-alanine from the stem pentapeptide to produce a tetrapeptide. However, few LD-carboxypeptidases that produce tripeptides have been identified, and nothing is known about substrate specificity in these enzymes. We report biochemical properties and crystal structures of the LD-carboxypeptidases LdcB from Streptococcus pneumoniae, Bacillus anthracis, and Bacillus subtilis. The enzymes are active against bacterial cell wall tetrapeptides and adopt a zinc-carboxypeptidase fold characteristic of the LAS superfamily. We have also solved the structure of S. pneumoniae LdcB with a product mimic, elucidating the residues essential for peptidoglycan recognition and the conformational changes that occur on ligand binding.

PubMed: 24909784
DOI: 10.1016/j.str.2014.04.015

Experimental method

X-RAY DIFFRACTION (2.0301 Å)