2JFN

Crystal structure of Escherichia coli glutamate racemase in complex with L- Glutamate and activator UDP-MurNAc-ala


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1038/nature05689
  • Primary Citation of Related Structures:  

  • 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 s ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE RACEMASE
A
285Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: murI (dga, glr, yijA)
EC: 5.1.1.3
Find proteins for P22634 (Escherichia coli (strain K12))
Go to UniProtKB:  P22634
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download SDF File 
Download CCD File 
A
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
UMA
Query on UMA

Download SDF File 
Download CCD File 
A
URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE
C23 H36 N4 O20 P2
NTMMCWJNQNKACG-KBKUWGQMSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.218 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 83.050α = 90.00
b = 112.820β = 90.00
c = 74.120γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
SOLVEphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-02-03 
  • Released Date: 2007-07-03 
  • Deposition Author(s): Lundqvist, T.

Revision History 

  • Version 1.0: 2007-07-03
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance