4OXD

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.273 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

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.

(2014) Structure 22: 949-960

  • DOI: 10.1016/j.str.2014.04.015
  • Primary Citation of Related Structures:  

  • 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. ...

    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.


    Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LdcB LD-carboxypeptidase
A, B, C, D, E
187Streptococcus pneumoniae (strain ATCC BAA-255 / R6)Mutation(s): 0 
Find proteins for Q8DQQ1 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Go to UniProtKB:  Q8DQQ1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MUB-ALA-ZGL-LYS-DSG
H
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
LYS
Query on LYS

Download SDF File 
Download CCD File 
B
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
MUB
Query on MUB
H
NON-POLYMERC11 H19 N O8

--

ZGL
Query on ZGL
H
D-peptide linkingC5 H10 N2 O3

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DSG
Query on DSG
H
D-PEPTIDE LINKINGC4 H8 N2 O3

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.273 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 345.954α = 90.00
b = 42.549β = 93.07
c = 79.318γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BBSRCUnited Kingdom--

Revision History 

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-07-16
    Type: Database references
  • Version 1.2: 2014-10-01
    Type: Database references
  • Version 1.3: 2015-01-07
    Type: Database references