› 4wxh

X-ray diffraction
1.9Å resolution

Carminomycin-4-O-methyltransferase (DnrK) variant (298Ser insert) in complex with S-adenosyl-L-homocysteine (SAH) and aclacinomycin T

Released:
DOI: 10.2210/pdb4wxh/pdb
PDB entry 4wxh coloured by chain, front view.
PDB entry 4wxh coloured by chain, side view.
PDB entry 4wxh coloured by chain, top view.
Source organism: Streptomyces peucetius
Primary publication:
Divergent evolution of an atypical S-adenosyl-l-methionine-dependent monooxygenase involved in anthracycline biosynthesis.
Grocholski T, Dinis P, Niiranen L, Niemi J, Metsä-Ketelä M
Proc Natl Acad Sci U S A 112 9866-71 (2015)
PMID: 26216966

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + carminomycin = S-adenosyl-L-homocysteine + daunorubicin
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170362 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Carminomycin 4-O-methyltransferase DnrK Chains: A, B
Molecule details ›
Chains: A, B
Length: 367 amino acids
Theoretical weight: 40.2 KDa
Source organism: Streptomyces peucetius
Expression system: Escherichia coli
UniProt:
  • Canonical: Q06528 (Residues: 2-297, 298-356; Coverage: 100%)
Gene name: dnrK
Sequence domains: O-methyltransferase domain
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand SAH 2 x SAH
Ligand 3VL 2 x 3VL
Ligand DTU 1 x DTU
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P21
Unit cell:
a: 60.803Å b: 100.995Å c: 62.398Å
α: 90° β: 102.47° γ: 90°
R-values:
R R work R free
0.195 0.193 0.234
Expression system: Escherichia coli

Quick links

Citations

3 review citations

New insights into bacterial type II polyketide biosynthesis.
Zhang et al. (2017)
2 more

4 mentions without citation

Diversity of the reaction mechanisms of SAM-dependent enzymes.
Sun et al. (2021)
3 more