PDBsum entry 4oxd

Hydrolase

PDB id: 4oxd

Contents

Protein chains

185 a.a.

167 a.a.

171 a.a.

Ligands

ALA-ZGL-LYS-DSG

LYS

MUB

Metals

_MG

_CL ×2

_ZN ×18

Waters ×111

PDB id:

4oxd

Name:

Hydrolase

Title:

Structure of the ldcb ld-carboxypeptidase reveals the molecular basis of peptidoglycan recognition

Structure:

Ldcb ld-carboxypeptidase. Chain: a, b, c, d, e. Fragment: unp residues 56-238. Engineered: yes. Mub-ala-zgl-lys-dsg. Chain: h

Source:

Streptococcus pneumoniae r6. Organism_taxid: 171101. Strain: r6. Gene: spr0554. Expressed in: escherichia coli. Expression_system_taxid: 562. Lactobacillus acidophilus. Organism_taxid: 1579

Resolution:

2.80Å R-factor: 0.276 R-free: 0.334

Authors:

C.N.Hoyland,C.Aldridge,R.M.Cleverley,K.Sidiq,M.C.Duchene,R.A.Daniel, W.Vollmer,R.J.Lewis

Key ref:

C.N.Hoyland et al. (2014). Structure of the LdcB LD-carboxypeptidase reveals the molecular basis of peptidoglycan recognition. Structure, 22, 949-960. PubMed id: 24909784 DOI: 10.1016/j.str.2014.04.015

Date:

05-Feb-14 Release date: 21-May-14

Protein chains

Q8DQQ1  (Q8DQQ1_STRR6) -  Peptidase M15B domain-containing protein from Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

Seq: 238 a.a.

Struc: 185 a.a.*

Protein chains

Q8DQQ1  (Q8DQQ1_STRR6) -  Peptidase M15B domain-containing protein from Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

Seq: 238 a.a.

Struc: 167 a.a.

Protein chain

Q8DQQ1  (Q8DQQ1_STRR6) -  Peptidase M15B domain-containing protein from Streptococcus pneumoniae (strain ATCC BAA-255 / R6)

Seq: 238 a.a.

Struc: 171 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DOI no: 10.1016/j.str.2014.04.015

Structure 22:949-960 (2014)

PubMed id: 24909784

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

C.N.Hoyland, C.Aldridge, R.M.Cleverley, M.C.Duchêne, G.Minasov, O.Onopriyenko, K.Sidiq, P.J.Stogios, W.F.Anderson, R.A.Daniel, A.Savchenko, W.Vollmer, R.J.Lewis.

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.