1B74 | pdb_00001b74

GLUTAMATE RACEMASE FROM AQUIFEX PYROPHILUS

• PDB DOI: https://doi.org/10.2210/pdb1B74/pdb

• Classification: ISOMERASE
• Organism(s): Aquifex pyrophilus
• Mutation(s): No 


• Deposited: 1999-01-27 Released: 2000-01-28 
• Deposition Author(s): Hwang, K.Y., Cho, C.S., Kim, S.S., Yu, Y.G., Cho, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.286 (Depositor) 
• R-Value Work: 
  0.221 (Depositor) 

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

• PubMed: 10331867 
• DOI: https://doi.org/10.1038/8223
• Primary Citation Related Structures: 
  1B73, 1B74


• 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. 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.

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Organizational Affiliation: 
• Structural Biology Center, Korea Institute of Science and Technology, Seoul, South Korea.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 28.12 kDa 
• Atom Count: 2,066 
• Modeled Residue Count: 252 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE RACEMASE	A	254	Aquifex pyrophilus	Mutation(s): 0  EC: 5.1.1.3
UniProt
Find proteins for P56868 (Aquifex pyrophilus) Explore P56868  Go to UniProtKB:  P56868

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGN	B [auth A]	D-GLUTAMINE C5 H10 N2 O3 ZDXPYRJPNDTMRX-GSVOUGTGSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.286 (Depositor) 
• R-Value Work:  0.221 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.17	α = 90
b = 72.17	β = 90
c = 184.99	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-01-28 
Deposition Author(s): Hwang, K.Y., Cho, C.S., Kim, S.S., Yu, Y.G., Cho, Y.

Revision History  

• 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
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations