› 3rfa

X-ray diffraction
2.05Å resolution

X-ray structure of RlmN from Escherichia coli in complex with S-adenosylmethionine

Released:
DOI: 10.2210/pdb3rfa/pdb
PDB entry 3rfa coloured by chain, front view.
PDB entry 3rfa coloured by chain, side view.
PDB entry 3rfa coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Structural basis for methyl transfer by a radical SAM enzyme.
Boal AK, Grove TL, McLaughlin MI, Yennawar NH, Booker SJ, Rosenzweig AC
Science 332 1089-92 (2011)
PMID: 21527678

Function and Biology Details

Reaction catalysed: 
2 S-adenosyl-L-methionine + adenine(2503) in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine(2503) in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-153276 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Dual-specificity RNA methyltransferase RlmN Chains: A, B
Molecule details ›
Chains: A, B
Length: 404 amino acids
Theoretical weight: 45.33 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P36979 (Residues: 1-384; Coverage: 100%)
Gene names: JW2501, b2517, rlmN, yfgB
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand SAM 2 x SAM
1 bound ligand:
Ligand SF4 2 x SF4
1 modified residue:
Ligand SMC 2 x SMC

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P212121
Unit cell:
a: 55.18Å b: 55.621Å c: 252.179Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.202 0.242
Expression system: Escherichia coli

Quick links

Citations

28 review citations

Resistance to linezolid caused by modifications at its binding site on the ribosome.
Long et al. (2012)
27 more

17 mentions without citation

Radical S-adenosylmethionine enzymes.
Broderick et al. (2014)
16 more