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X-ray diffraction
1.85Å resolution

Crystal structure of N-methyltransferase NodS from Bradyrhizobium japonicum WM9 in complex with S-adenosyl-l-homocysteine (SAH)

Released:
DOI: 10.2210/pdb3ofk/pdb
PDB entry 3ofk coloured by chain, front view.
PDB entry 3ofk coloured by chain, side view.
PDB entry 3ofk coloured by chain, top view.
Source organism: Bradyrhizobium sp. WM9
Primary publication:
Crystal structures of NodS N-methyltransferase from Bradyrhizobium japonicum in ligand-free form and as SAH complex.
Cakici O, Sikorski M, Stepkowski T, Bujacz G, Jaskolski M
J Mol Biol 404 874-89 (2010)
PMID: 20970431

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189597 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nodulation protein S Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 216 amino acids
Theoretical weight: 24.15 KDa
Source organism: Bradyrhizobium sp. WM9
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9AQ22 (Residues: 1-209; Coverage: 100%)
Gene name: nodS
Sequence domains: Nodulation protein S (NodS)
Structure domains: Vaccinia Virus protein VP39

Ligands and Environments

1 bound ligand:
Ligand SAH 4 x SAH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P21212
Unit cell:
a: 81.01Å b: 143.3Å c: 75.85Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.19 0.19 0.238
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Architectures, mechanisms and molecular evolution of natural product methyltransferases.
Liscombe et al. (2012)
7 other articles

4 mentions without citation

Biological Catalysis and Information Storage Have Relied on N-Glycosyl Derivatives of β-D-Ribofuranose since the Origins of Life.
Wozniak et al. (2023)
3 more