› 7vnt

X-ray diffraction
1.92Å resolution

Structure of aminotransferase-substrate complex

Released:
DOI: 10.2210/pdb7vnt/pdb
PDB entry 7vnt coloured by chain, front view.
PDB entry 7vnt coloured by chain, side view.
PDB entry 7vnt coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
Crystal structure of a novel type of ornithine δ-aminotransferase from the hyperthermophilic archaeon Pyrococcus horikoshii.
Kawakami R, Ohshida T, Hayashi J, Yoneda K, Furumoto T, Ohshima T, Sakuraba H
Int J Biol Macromol 208 731-740 (2022)
PMID: 35337912

Function and Biology Details

Reaction catalysed: 
L-ornithine + a 2-oxo acid = L-glutamate 5-semialdehyde + an L-amino acid
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-129303 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ornithine aminotransferase Chains: A, B
Molecule details ›
Chains: A, B
Length: 454 amino acids
Theoretical weight: 50.68 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: O50131 (Residues: 1-454; Coverage: 100%)
Gene name: PH1423
Sequence domains: Aminotransferase class-III

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
3 bound ligands:
Ligand ORN 1 x ORN
Ligand GOL 1 x GOL
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P6522
Unit cell:
a: 113.747Å b: 113.747Å c: 289.562Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.183 0.181 0.215
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 citations in other articles

Biochemical and genetic examination of two aminotransferases from the hyperthermophilic archaeon Thermococcus kodakarensis.
Su et al. (2023)