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 

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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, 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTAMATE RACEMASEA, B255Helicobacter pyloriMutation(s): 0 
EC: 5.1.1.3
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
003
Query on 003
Download Ideal Coordinates CCD File 
C [auth A],
E [auth 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
DGL
Query on DGL
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		D-GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-GSVOUGTGSA-N		 Ligand Interaction
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

  • 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 = 61.41α = 90
b = 76.31β = 90
c = 108.92γ = 90
Software Package:
Software NamePurpose
CNXrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2007-02-06 
  • Released Date: 2007-07-03 
    • Deposition Author(s): Lundqvist, T.

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