Crystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate and an inhibitor

Experimental Data Snapshot

  • Resolution: 1.86 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Exploitation of Structural and Regulatory Diversity in Glutamate Racemases

Lundqvist, T.Fisher, S.L.Kern, G.Folmer, R.H.A.Xue, Y.Newton, D.T.Keating, T.A.Alm, R.A.De Jonge, B.L.M.

(2007) Nature 447: 817

  • DOI: https://doi.org/10.1038/nature05689
  • Primary Citation of Related Structures:  
    2JFN, 2JFO, 2JFP, 2JFQ, 2JFU, 2JFV, 2JFW, 2JFX, 2JFY, 2JFZ

  • PubMed Abstract: 

    Glutamate racemase is an enzyme essential to the bacterial cell wall biosynthesis pathway, and has therefore been considered as a target for antibacterial drug discovery. We characterized the glutamate racemases of several pathogenic bacteria using structural and biochemical approaches. Here we describe three distinct mechanisms of regulation for the family of glutamate racemases: allosteric activation by metabolic precursors, kinetic regulation through substrate inhibition, and D-glutamate recycling using a d-amino acid transaminase. In a search for selective inhibitors, we identified a series of uncompetitive inhibitors specifically targeting Helicobacter pylori glutamate racemase that bind to a cryptic allosteric site, and used these inhibitors to probe the mechanistic and dynamic features of the enzyme. These structural, kinetic and mutational studies provide insight into the physiological regulation of these essential enzymes and provide a basis for designing narrow-spectrum antimicrobial agents.

  • Organizational Affiliation

    AstraZeneca Global Structural Chemistry, AstraZeneca R&D Mölndal, SE-431 83, Mölndal, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
255Helicobacter pyloriMutation(s): 0 
Find proteins for Q9ZLT0 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore Q9ZLT0 
Go to UniProtKB:  Q9ZLT0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZLT0
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DGL BindingDB:  2JFZ Ki: 5800 (nM) from 1 assay(s)
003 Binding MOAD:  2JFZ Ki: 5800 (nM) from 1 assay(s)
BindingDB:  2JFZ Kd: min: 2900, max: 3900 (nM) from 2 assay(s)
IC50: 1400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.86 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.41α = 90
b = 76.31β = 90
c = 108.92γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description