› 5wyf

X-ray diffraction
2.12Å resolution

Structure of amino acid racemase, 2.12 A

Released:
DOI: 10.2210/pdb5wyf/pdb
PDB entry 5wyf coloured by chain, front view.
PDB entry 5wyf coloured by chain, side view.
PDB entry 5wyf coloured by chain, top view.
Source organism: Lentilactobacillus buchneri
Primary publication:
Crystal structure of the novel amino-acid racemase isoleucine 2-epimerase from Lactobacillus buchneri.
Hayashi J, Mutaguchi Y, Minemura Y, Nakagawa N, Yoneda K, Ohmori T, Ohshima T, Sakuraba H
Acta Crystallogr D Struct Biol 73 428-437 (2017)
PMID: 28471367

Function and Biology Details

Reaction catalysed: 
L-isoleucine = D-allo-isoleucine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-125924 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Isoleucine 2-epimerase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 462 amino acids
Theoretical weight: 50.71 KDa
Source organism: Lentilactobacillus buchneri
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: M1GRN3 (Residues: 1-450; Coverage: 100%)
Sequence domains: Aminotransferase class-III
Structure domains: Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Ligands and Environments

2 bound ligands:
Ligand ILP 4 x ILP
Ligand CD 36 x CD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P21
Unit cell:
a: 59.514Å b: 85.277Å c: 186.566Å
α: 90° β: 96.93° γ: 90°
R-values:
R R work R free
0.178 0.176 0.221
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Human Serine Racemase: Key Residues/Active Site Motifs and Their Relation to Enzyme Function.
Graham et al. (2019)
2 other articles