› 5yu3

X-ray diffraction
1.79Å resolution

Structural basis for recognition of L-lysine, L-ornithine, and L-2,4-diamino butyric acid by lysine cyclodeaminase

Released:
DOI: 10.2210/pdb5yu3/pdb
PDB entry 5yu3 coloured by chain, front view.
PDB entry 5yu3 coloured by chain, side view.
PDB entry 5yu3 coloured by chain, top view.
Source organism: Streptomyces pristinaespiralis
Primary publication:
Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase.
Min K, Yoon HJ, Matsuura A, Kim YH, Lee HH
OpenAccess logo Mol Cells 41 331-341 (2018)
PMID: 29629557

Function and Biology Details

Reaction catalysed: 
L-ornithine = L-proline + NH(3)
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-113035 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Lysine cyclodeaminase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 344 amino acids
Theoretical weight: 36.59 KDa
Source organism: Streptomyces pristinaespiralis
Expression system: Escherichia coli
UniProt:
  • Canonical: D9UBW0 (Residues: 1-344; Coverage: 97%)
Gene names: SPRI_0308, SPRI_7045, pipA
Sequence domains: Ornithine cyclodeaminase/mu-crystallin family

Ligands and Environments


Cofactor: Ligand NAD 4 x NAD
2 bound ligands:
Ligand NA 4 x NA
Ligand PRO 4 x PRO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: C2
Unit cell:
a: 271.529Å b: 64.783Å c: 106.858Å
α: 90° β: 104.2° γ: 90°
R-values:
R R work R free
0.167 0.166 0.193
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Interconnected Set of Enzymes Provide Lysine Biosynthetic Intermediates and Ornithine Derivatives as Key Precursors for the Biosynthesis of Bioactive Secondary Metabolites.
Liras et al. (2023)
2 other articles

1 mention without citation

Structural Basis for Recognition of L-lysine, L-ornithine, and L-2,4-diamino Butyric Acid by Lysine Cyclodeaminase.
Min et al. (2018)