4OX3

Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition

Summary for 4OX3

• Entry DOI: 10.2210/pdb4ox3/pdb
• Related: 4OX5 4OXD
• Descriptor: Putative carboxypeptidase YodJ, ZINC ION, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: las family, ld-carboxypeptidase, cell wall modifying enzyme, hydrolase
• Biological source: Bacillus subtilis
• Total number of polymer chains: 1
• Total formula weight: 25423.70

Authors

Hoyland, C.N.,Aldridge, C.,Cleverley, R.M.,Sidiq, K.,Duchene, M.C.,Daniel, R.A.,Vollmer, W.,Lewis, R.J. (deposition date: 2014-02-04, release date: 2014-06-11, Last modification date: 2023-12-27)

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 Å)