› 1y56

X-ray diffraction
2.86Å resolution

Crystal structure of L-proline dehydrogenase from P.horikoshii

Released:
DOI: 10.2210/pdb1y56/pdb
PDB entry 1y56 coloured by chain, front view.
PDB entry 1y56 coloured by chain, side view.
PDB entry 1y56 coloured by chain, top view.
Source organism: Pyrococcus horikoshii OT3
Primary publication:
Crystal structure of a novel FAD-, FMN-, and ATP-containing L-proline dehydrogenase complex from Pyrococcus horikoshii.
Tsuge H, Kawakami R, Sakuraba H, Ago H, Miyano M, Aki K, Katunuma N, Ohshima T
J Biol Chem 280 31045-9 (2005)
PMID: 16027125

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero octamer
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-129806 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
hypothetical protein PH1363 Chain: A
Molecule details ›
Chain: A
Length: 493 amino acids
Theoretical weight: 55.64 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O59088 (Residues: 1-493; Coverage: 100%)
Gene name: PH1363
Sequence domains:
Structure domains:
FAD dependent oxidoreductase domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 382 amino acids
Theoretical weight: 42.74 KDa
Source organism: Pyrococcus horikoshii OT3
Expression system: Escherichia coli
UniProt:
  • Canonical: O59089 (Residues: 1-382; Coverage: 100%)
Gene names: PH1364, proDH-B1
Sequence domains: FAD dependent oxidoreductase
Structure domains:

Ligands and Environments


Cofactor: Ligand FAD 1 x FAD
6 bound ligands:
Ligand FE 1 x FE
Ligand SO4 1 x SO4
Ligand FMN 1 x FMN
Ligand ATP 1 x ATP
Ligand CXS 1 x CXS
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P6422
Unit cell:
a: 172.219Å b: 172.219Å c: 175.398Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.184 0.182 0.226
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Structural biology of proline catabolism.
Tanner JJ. (2008)
2 more

12 mentions without citation

The natural history of ubiquitin and ubiquitin-related domains.
Burroughs et al. (2012)
11 more