1B74

GLUTAMATE RACEMASE FROM AQUIFEX PYROPHILUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 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 Biol 6: 422-426

  • DOI: 10.1038/8223
  • Primary Citation of Related Structures:  
    1B74, 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUTAMATE RACEMASEA254Aquifex pyrophilusMutation(s): 0 
Gene Names: murI
EC: 5.1.1.3
UniProt
Find proteins for P56868 (Aquifex pyrophilus)
Explore P56868 
Go to UniProtKB:  P56868
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGN
Query on DGN

Download Ideal Coordinates CCD File 
B [auth A]D-GLUTAMINE
C5 H10 N2 O3
ZDXPYRJPNDTMRX-GSVOUGTGSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DGN PDBBind:  1B74 Ki: 5.00e+7 (nM) from 1 assay(s)
Binding MOAD:  1B74 Ki: 5.00e+7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.221 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.17α = 90
b = 72.17β = 90
c = 184.99γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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