› 6s0s

X-ray diffraction
2.4Å resolution

The crystal structure of kanamycin B dioxygenase (KanJ) from Streptomyces kanamyceticus in complex with nickel, ribostamycin B and 2-oxoglutarate

Released:
DOI: 10.2210/pdb6s0s/pdb
PDB entry 6s0s coloured by chain, front view.
PDB entry 6s0s coloured by chain, side view.
PDB entry 6s0s coloured by chain, top view.
Source organism: Streptomyces kanamyceticus
Primary publication:
A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates.
Mrugała B, Miłaczewska A, Porebski PJ, Niedzialkowska E, Guzik M, Minor W, Borowski T
FEBS J 288 1366-1386 (2021)
PMID: 32592631

Function and Biology Details

Reaction catalysed: 
Kanamycin B + 2-oxoglutarate + O(2) = 2'-dehydrokanamycin A + succinate + NH(3) + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179847 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Kanamycin B dioxygenase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 288 amino acids
Theoretical weight: 31.84 KDa
Source organism: Streptomyces kanamyceticus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6L732 (Residues: 1-285; Coverage: 100%)
Gene names: kacB, kanJ
Sequence domains: Phytanoyl-CoA dioxygenase (PhyH)

Ligands and Environments

4 bound ligands:
Ligand NI 6 x NI
Ligand AKG 6 x AKG
Ligand RIO 6 x RIO
Ligand CL 3 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 50.083Å b: 184.582Å c: 110.333Å
α: 90° β: 94.97° γ: 90°
R-values:
R R work R free
0.174 0.173 0.204
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 mention without citation

A study on the structure, mechanism, and biochemistry of kanamycin B dioxygenase (KanJ)-an enzyme with a broad range of substrates.
Mrugała et al. (2021)