› 2bh2

X-ray diffraction
2.15Å resolution

Crystal Structure of E. coli 5-methyluridine methyltransferase RumA in complex with ribosomal RNA substrate and S-adenosylhomocysteine.

Released:
DOI: 10.2210/pdb2bh2/pdb
PDB entry 2bh2 coloured by chain, front view.
PDB entry 2bh2 coloured by chain, side view.
PDB entry 2bh2 coloured by chain, top view.
Source organism: Escherichia coli
Primary publication:
A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.
Lee TT, Agarwalla S, Stroud RM
Cell 120 599-611 (2005)
PMID: 15766524

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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157206 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD Chains: A, B
Molecule details ›
Chains: A, B
Length: 433 amino acids
Theoretical weight: 48.11 KDa
Source organism: Escherichia coli
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:
23S RIBOSOMAL RNA 1932-1968 Chains: C, D
Molecule details ›
Chains: C, D
Length: 37 nucleotides
Theoretical weight: 11.88 KDa
Source organism: Escherichia coli
Expression system: Not provided

Ligands and Environments


Cofactor: Ligand SAH 2 x SAH
1 bound ligand:
Ligand SF4 2 x SF4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: C2
Unit cell:
a: 190.061Å b: 63.542Å c: 112.019Å
α: 90° β: 125.15° γ: 90°
R-values:
R R work R free
0.177 0.174 0.229
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

6 review citations

Structure, dynamics, and function of RNA modification enzymes.
Ishitani et al. (2008)
5 more

20 mentions without citation

The Blueprint of a Minimal Cell: MiniBacillus.
Reuß et al. (2016)
19 more