› 1r0m

X-ray diffraction
1.3Å resolution

Structure of Deinococcus radiodurans N-acylamino acid racemase at 1.3 : insights into a flexible binding pocket and evolution of enzymatic activity

Released:
DOI: 10.2210/pdb1r0m/pdb
PDB entry 1r0m coloured by chain, front view.
PDB entry 1r0m coloured by chain, side view.
PDB entry 1r0m coloured by chain, top view.
Source organism: Deinococcus radiodurans
Primary publication:
Structural basis for catalytic racemization and substrate specificity of an N-acylamino acid racemase homologue from Deinococcus radiodurans.
Wang WC, Chiu WC, Hsu SK, Wu CL, Chen CY, Liu JS, Hsu WH
J Mol Biol 342 155-69 (2004)
PMID: 15313614

Function and Biology Details

Reaction catalysed: 
(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H(2)O
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193349 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
N-succinylamino acid racemase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 375 amino acids
Theoretical weight: 41.06 KDa
Source organism: Deinococcus radiodurans
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9RYA6 (Residues: 1-375; Coverage: 100%)
Gene name: DR_0044
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL12B2
Spacegroup: P4
Unit cell:
a: 116.367Å b: 116.367Å c: 120.467Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.155 0.154 0.173
Expression system: Escherichia coli

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Citations

9 citation in other articles

Structure-stability-activity relationship in covalently cross-linked N-carbamoyl D-amino acid amidohydrolase and N-acylamino acid racemase.
Chiu et al. (2006)
8 more

2 mentions without citation

Unusual arginine formations in protein function and assembly: rings, strings, and stacks.
Neves et al. (2012)
1 more