1B74

GLUTAMATE RACEMASE FROM AQUIFEX PYROPHILUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and mechanism of glutamate racemase from Aquifex pyrophilus.

Hwang, K.Y.Cho, C.S.Kim, S.S.Sung, H.C.Yu, Y.G.Cho, Y.

(1999) Nat.Struct.Mol.Biol. 6: 422-426

  • DOI: 10.1038/8223
  • Primary Citation of Related Structures:  1B73

  • PubMed Abstract: 
  • Glutamate racemase (MurI) is responsible for the synthesis of D-glutamate, an essential building block of the peptidoglycan layer in bacterial cell walls. The crystal structure of glutamate racemase from Aquifex pyrophilus, determined at 2.3 A resolu ...

    Glutamate racemase (MurI) is responsible for the synthesis of D-glutamate, an essential building block of the peptidoglycan layer in bacterial cell walls. The crystal structure of glutamate racemase from Aquifex pyrophilus, determined at 2.3 A resolution, reveals that the enzyme forms a dimer and each monomer consists of two alpha/beta fold domains, a unique structure that has not been observed in other racemases or members of an enolase superfamily. A substrate analog, D-glutamine, binds to the deep pocket formed by conserved residues from two monomers. The structural and mutational analyses allow us to propose a mechanism of metal cofactor-independent glutamate racemase in which two cysteine residues are involved in catalysis.


    Organizational Affiliation

    Structural Biology Center, Korea Institute of Science and Technology, Seoul, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTAMATE RACEMASE
A
254Aquifex pyrophilusGene Names: murI
EC: 5.1.1.3
Find proteins for P56868 (Aquifex pyrophilus)
Go to UniProtKB:  P56868
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGN
Query on DGN

Download SDF File 
Download CCD File 
A
D-GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-GSVOUGTGSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DGNKi: 50000000 nM BINDINGMOAD
DGNKi: 50000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.221 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 72.170α = 90.00
b = 72.170β = 90.00
c = 184.990γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-28
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance