2JFW

Crystal structure of Enterococcus faecium glutamate racemase in complex with tartrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GLUTAMATE RACEMASE291Enterococcus faeciumMutation(s): 0 
EC: 5.1.1.3
UniProt
Find proteins for Q3XZW8 (Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO))
Explore Q3XZW8 
Go to UniProtKB:  Q3XZW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3XZW8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download Ideal Coordinates CCD File 
B [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.423α = 90
b = 85.423β = 90
c = 93.79γ = 120
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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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