› 1uwv

X-ray diffraction
1.95Å resolution

Crystal Structure of RumA, the iron-sulfur cluster containing E. coli 23S Ribosomal RNA 5-Methyluridine Methyltransferase

Released:
DOI: 10.2210/pdb1uwv/pdb
PDB entry 1uwv coloured by chain, front view.
PDB entry 1uwv coloured by chain, side view.
PDB entry 1uwv coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase.
Lee TT, Agarwalla S, Stroud RM
Structure 12 397-407 (2004)
PMID: 15016356

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + uracil(1939) in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil(1939) in 23S rRNA
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157205 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD Chain: A
Molecule details ›
Chain: A
Length: 433 amino acids
Theoretical weight: 48.68 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P55135 (Residues: 1-433; Coverage: 100%)
Gene names: JW2756, b2785, rlmD, rumA, ygcA
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand SF4 1 x SF4
Ligand NI 2 x NI
Ligand PO4 1 x PO4
Ligand CL 1 x CL
1 modified residue:
Ligand MSE 12 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21
Unit cell:
a: 35.938Å b: 99.448Å c: 58.519Å
α: 90° β: 100.57° γ: 90°
R-values:
R R work R free
0.186 0.186 0.227
Expression system: Escherichia coli BL21(DE3)

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Citations

5 review citations

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

9 mentions without citation

Mechanisms and inhibition of uracil methylating enzymes.
Mishanina et al. (2012)
8 more