› 2z9x

X-ray diffraction
1.94Å resolution

Crystal structure of pyridoxamine-pyruvate aminotransferase complexed with pyridoxyl-L-alanine

Released:
DOI: 10.2210/pdb2z9x/pdb
PDB entry 2z9x coloured by chain, front view.
PDB entry 2z9x coloured by chain, side view.
PDB entry 2z9x coloured by chain, top view.
Source organism: Mesorhizobium loti
Primary publication:
Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099.
Yoshikane Y, Yokochi N, Yamasaki M, Mizutani K, Ohnishi K, Mikami B, Hayashi H, Yagi T
J Biol Chem 283 1120-7 (2008)
PMID: 17989071

Function and Biology Details

Reaction catalysed: 
Pyridoxamine + pyruvate = pyridoxal + L-alanine
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-189126 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyridoxamine--pyruvate transaminase Chains: A, B
Molecule details ›
Chains: A, B
Length: 392 amino acids
Theoretical weight: 41.5 KDa
Source organism: Mesorhizobium loti
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q988B8 (Residues: 2-393; Coverage: 100%)
Gene names: mlr6806, ppaT
Sequence domains: Aminotransferase class-V
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand SO4 8 x SO4
Ligand CL 2 x CL
Ligand ALA 2 x ALA
Ligand PXL 2 x PXL
Ligand GOL 10 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: P43212
Unit cell:
a: 68.72Å b: 68.72Å c: 311.942Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.147 0.145 0.184
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

Evolutionary origin and functional diversification of aminotransferases.
Koper et al. (2022)
1 more

1 mention without citation

Crystal Structure Of Photorespiratory Alanine:Glyoxylate Aminotransferase 1 (AGT1) From Arabidopsis thaliana.
Liepman et al. (2019)