Description
Experimental Technique/Method:X-RAY DIFFRACTION
Resolution:2.3
Classification:HYDROLASE
Release Date:2013-04-03
Deposition Date:2013-03-05
Revision Date:2013-09-25#2014-02-19#2014-06-18#2014-07-23#2017-11-15
Molecular Weight:48742.02
Macromolecule Type:Protein
Residue Count:426
Atom Site Count:3044
DOI:10.2210/pdb4jid/pdb
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.
Resolution:2.3
Classification:HYDROLASE
Release Date:2013-04-03
Deposition Date:2013-03-05
Revision Date:2013-09-25#2014-02-19#2014-06-18#2014-07-23#2017-11-15
Molecular Weight:48742.02
Macromolecule Type:Protein
Residue Count:426
Atom Site Count:3044
DOI:10.2210/pdb4jid/pdb
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.
| Date made available | 2013 |
|---|---|
| Publisher | RCSB-PDB |