› 7cl5

X-ray diffraction
2.5Å resolution

The crystal structure of KanJ in complex with kanamycin B and N-oxalylglycine

Released:
DOI: 10.2210/pdb7cl5/pdb
Model geometry
Fit model/data
PDB entry 7cl5 coloured by chain, front view.
PDB entry 7cl5 coloured by chain, side view.
PDB entry 7cl5 coloured by chain, top view.
Source organism: Streptomyces kanamyceticus
Primary publication:
Stepwise Post-glycosylation Modification of Sugar Moieties in Kanamycin Biosynthesis.
Kudo F, Kitayama Y, Miyanaga A, Numakura M, Eguchi T
Chembiochem 22 1668-1675 (2021)
PMID: 33403742

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:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-179848 (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: 301 amino acids
Theoretical weight: 33.6 KDa
Source organism: Streptomyces kanamyceticus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6L732 (Residues: 1-285; Coverage: 100%)
Gene names: kacB, kanJ
Sequence domains: Phytanoyl-CoA dioxygenase (PhyH)

Ligands and Environments

3 bound ligands:
Ligand NI 6 x NI
Ligand OGA 6 x OGA
Ligand 9CS 6 x 9CS
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 50.083Å b: 184.259Å c: 109.771Å
α: 90° β: 97.68° γ: 90°
R-values:
R R work R free
0.198 0.197 0.214
Expression system: Escherichia coli

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Citations

1 citations in other articles

Facile and selective N-alkylation of gentamicin antibiotics via chemoenzymatic synthesis.
Stojanovski et al. (2022)