› 3c0k

X-ray diffraction
2Å resolution

Crystal Structure of a ribosomal RNA methyltranferase

Released:
DOI: 10.2210/pdb3c0k/pdb
PDB entry 3c0k coloured by chain, front view.
PDB entry 3c0k coloured by chain, side view.
PDB entry 3c0k coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes.
Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, Douthwaite S, Bujnicki JM, Sivaraman J
J Mol Biol 383 652-66 (2008)
PMID: 18789337

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + cytosine(1962) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(1962) in 23S rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160016 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ribosomal RNA large subunit methyltransferase I Chains: A, B
Molecule details ›
Chains: A, B
Length: 396 amino acids
Theoretical weight: 44.88 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P75876 (Residues: 1-396; Coverage: 100%)
Gene names: JW5898, b0967, rlmI, yccW
Sequence domains:
Structure domains:

Ligands and Environments

No bound ligands
1 modified residue:
Ligand MSE 20 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12C
Spacegroup: P21
Unit cell:
a: 64.312Å b: 80.875Å c: 66.155Å
α: 90° β: 98.91° γ: 90°
R-values:
R R work R free
0.194 0.194 0.242
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Mapping and significance of the mRNA methylome.
Sibbritt et al. (2013)
3 more

2 mentions without citation

5-methylcytosine in RNA: detection, enzymatic formation and biological functions.
Motorin et al. (2010)
1 more