› 1x7d

X-ray diffraction
1.6Å resolution

Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms

Released:
DOI: 10.2210/pdb1x7d/pdb
PDB entry 1x7d coloured by chain, front view.
PDB entry 1x7d coloured by chain, side view.
PDB entry 1x7d coloured by chain, top view.
Source organism: Pseudomonas putida
Primary publication:
Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family.
Goodman JL, Wang S, Alam S, Ruzicka FJ, Frey PA, Wedekind JE
Biochemistry 43 13883-91 (2004)
PMID: 15518536

Function and Biology Details

Reaction catalysed: 
L-ornithine = L-proline + NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183466 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ornithine cyclodeaminase Chains: A, B
Molecule details ›
Chains: A, B
Length: 350 amino acids
Theoretical weight: 38.85 KDa
Source organism: Pseudomonas putida
Expression system: Escherichia coli
UniProt:
  • Canonical: Q88H32 (Residues: 1-350; Coverage: 100%)
Gene names: PP_3533, ocd
Sequence domains: Ornithine cyclodeaminase/mu-crystallin family
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 2 x NAD
4 bound ligands:
Ligand NA 2 x NA
Ligand ORN 2 x ORN
Ligand MPD 6 x MPD
Ligand MES 1 x MES
1 modified residue:
Ligand MSE 16 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P212121
Unit cell:
a: 69.88Å b: 78.62Å c: 119.94Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.17 0.19
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Role of Na+ and K+ in enzyme function.
Page et al. (2006)
4 more

5 mentions without citation

Mutation of L-2,3-diaminopropionic acid synthase genes blocks staphyloferrin B synthesis in Staphylococcus aureus.
Beasley et al. (2011)
4 more