› 3njr

X-ray diffraction
2.7Å resolution

Crystal structure of C-terminal domain of precorrin-6Y C5,15-methyltransferase from Rhodobacter capsulatus

Released:
DOI: 10.2210/pdb3njr/pdb
PDB entry 3njr coloured by chain, front view.
PDB entry 3njr coloured by chain, side view.
PDB entry 3njr coloured by chain, top view.
Source organism: Rhodobacter capsulatus SB 1003
Primary publication:
An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.
Deery E, Schroeder S, Lawrence AD, Taylor SL, Seyedarabi A, Waterman J, Wilson KS, Brown D, Geeves MA, Howard MJ, Pickersgill RW, Warren MJ
Nat Chem Biol 8 933-40 (2012)
PMID: 23042036

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + precorrin-6B = S-adenosyl-L-homocysteine + precorrin-7 + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
homo tetramer
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-112679 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tetrapyrrole methylase domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 204 amino acids
Theoretical weight: 22.02 KDa
Source organism: Rhodobacter capsulatus SB 1003
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: D5AV04 (Residues: 214-396; Coverage: 46%)
Gene names: RCAP_rcc02042, cobL
Structure domains: Vaccinia Virus protein VP39

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
2 bound ligands:
Ligand GOL 2 x GOL
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2
Unit cell:
a: 114.354Å b: 44.799Å c: 84.11Å
α: 90° β: 119.75° γ: 90°
R-values:
R R work R free
0.189 0.185 0.265
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

Microbial production of vitamin B12: a review and future perspectives.
Fang et al. (2017)
6 more

2 mentions without citation

An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis.
Deery et al. (2012)
1 more