› 3wev

X-ray diffraction
1.98Å resolution

Crystal structure of the Schiff base intermediate of L-Lys epsilon-oxidase from Marinomonas mediterranea with L-Lys

Released:
DOI: 10.2210/pdb3wev/pdb
PDB entry 3wev coloured by chain, front view.
PDB entry 3wev coloured by chain, side view.
PDB entry 3wev coloured by chain, top view.
Source organism: Marinomonas mediterranea MMB-1
Primary publication:
X-ray crystallographic evidence for the presence of the cysteine tryptophylquinone cofactor in L-lysine ε-oxidase from Marinomonas mediterranea.
Okazaki S, Nakano S, Matsui D, Akaji S, Inagaki K, Asano Y
J Biochem 154 233-6 (2013)
PMID: 23908359

Function and Biology Details

Reaction catalysed: 
L-lysine + O(2) + H(2)O = (S)-2-amino-6-oxohexanoate + H(2)O(2) + NH(3)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-123377 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
L-lysine 6-oxidase Chains: A, B
Molecule details ›
Chains: A, B
Length: 726 amino acids
Theoretical weight: 80.98 KDa
Source organism: Marinomonas mediterranea MMB-1
Expression system: Marinomonas mediterranea MMB-1
UniProt:
  • Canonical: F2JXJ3 (Residues: 1-726; Coverage: 100%)
Gene names: Marme_2662, lodA
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand LYS 2 x LYS
Ligand SO4 5 x SO4
Ligand EDO 12 x EDO
Ligand DIO 1 x DIO
1 modified residue:
Ligand TRQ 2 x TRQ

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: C2
Unit cell:
a: 194.992Å b: 126.164Å c: 70.865Å
α: 90° β: 99.03° γ: 90°
R-values:
R R work R free
0.152 0.15 0.189
Expression system: Marinomonas mediterranea MMB-1

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Citations

4 review citations

Protein-Derived Cofactors Revisited: Empowering Amino Acid Residues with New Functions.
Davidson VL. (2018)
3 more

2 mentions without citation

Roles of active site residues in LodA, a cysteine tryptophylquinone dependent ε-lysine oxidase.
Sehanobish et al. (2015)
1 more