› 2dbq

X-ray diffraction
1.7Å resolution

Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (I41)

Released:
DOI: 10.2210/pdb2dbq/pdb
PDB entry 2dbq coloured by chain, front view.
PDB entry 2dbq coloured by chain, side view.
PDB entry 2dbq coloured by chain, top view.
Source organism: Pyrococcus horikoshii
Primary publication:
Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
Yoshikawa S, Arai R, Kinoshita Y, Uchikubo-Kamo T, Wakamatsu T, Akasaka R, Masui R, Terada T, Kuramitsu S, Shirouzu M, Yokoyama S
Acta Crystallogr D Biol Crystallogr 63 357-65 (2007)
PMID: 17327673

Function and Biology Details

Reaction catalysed: 
Glycolate + NAD(+) = glyoxylate + NADH
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-129706 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glyoxylate reductase Chain: A
Molecule details ›
Chain: A
Length: 334 amino acids
Theoretical weight: 38.34 KDa
Source organism: Pyrococcus horikoshii
Expression system: Escherichia coli
UniProt:
  • Canonical: O58320 (Residues: 1-334; Coverage: 100%)
Gene names: PH0597, gyaR
Sequence domains:
Structure domains: NAD(P)-binding Rossmann-like Domain

Ligands and Environments


Cofactor: Ligand NAP 1 x NAP
2 bound ligands:
Ligand SO4 2 x SO4
Ligand GOL 5 x GOL
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: I41
Unit cell:
a: 114.252Å b: 114.252Å c: 119.598Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.131 0.131 0.143
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

Metabolism of pentose sugars in the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius.
Nunn et al. (2010)
5 more

5 mentions without citation

PyTMs: a useful PyMOL plugin for modeling common post-translational modifications.
Warnecke et al. (2014)
4 more