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X-ray diffraction
2.3Å resolution

Structural Basis for Catalytic Racemization and Substrate Specificity of an N-Acylamino Acid Racemase Homologue from Deinococcus radiodurans

Released:
DOI: 10.2210/pdb1xpy/pdb
PDB entry 1xpy coloured by chain, front view.
PDB entry 1xpy coloured by chain, side view.
PDB entry 1xpy 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

2 bound ligands:
Ligand MG 4 x MG
Ligand NLQ 2 x NLQ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL12B2
Spacegroup: P4
Unit cell:
a: 116.159Å b: 116.159Å c: 120.426Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.171 0.227
Expression system: Escherichia coli

Quick links

Citations

9 citation in other articles

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

1 mention without citation

Comparison of Alicyclobacillus acidocaldarius o-Succinylbenzoate Synthase to Its Promiscuous N-Succinylamino Acid Racemase/ o-Succinylbenzoate Synthase Relatives.
Odokonyero et al. (2018)