2JFZ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.205 

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:  2JFN, 2JFO, 2JFU, 2JFV, 2JFW, 2JFX, 2JFP, 2JFQ, 2JFY

  • 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, B
255Helicobacter pylori (strain J99 / ATCC 700824)Gene Names: murI (glr)
EC: 5.1.1.3
Find proteins for Q9ZLT0 (Helicobacter pylori (strain J99 / ATCC 700824))
Go to UniProtKB:  Q9ZLT0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGL
Query on DGL

Download SDF File 
Download CCD File 
A, B
D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N
 Ligand Interaction
003
Query on 003

Download SDF File 
Download CCD File 
A, B
5-METHYL-7-(2-METHYLPROPYL)-2-(NAPHTHALEN-1-YLMETHYL)-3-PYRIDIN-4-YL-2H-PYRAZOLO[3,4-D]PYRIMIDINE-4,6(5H,7H)-DIONE
C26 H25 N5 O2
NNZDBCPMOOEFTE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
003IC50: 1400 nM (93) BINDINGDB
003Kd: 2900 - 3900 nM (93) BINDINGDB
003Ki: 5800 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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 = 61.410α = 90.00
b = 76.310β = 90.00
c = 108.920γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-02-06 
  • 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