PDBsum entry: 2bh2

Transferase

PDB id: 2bh2

Contents

Protein chains

418 a.a. *

DNA/RNA

Ligands

SAH ×2

SF4 ×2

Waters ×340

* Residue conservation analysis

PDB id:

2bh2

Name:

Transferase

Title:

Crystal structure of e. Coli 5-methyluridine methyltransferase ruma in complex with ribosomal RNA substrate and s-adenosylhomocysteine.

Structure:

23s rrna (uracil-5-)-methyltransferase ruma. Chain: a, b. Synonym: 23s rrna(m-5-u1939)-methyltransferase, 23s rrna uracil-5-methyltransferase ruma. Engineered: yes. Other_details: iron-sulfur cluster linked by cys81, cys87, cys90, and cys162. 23s ribosomal RNA 1932-1968. Chain: c, d.

Source:

Escherichia coli. Organism_taxid: 562. Strain: k12. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Strain: k12

Biol. unit:

Dimer (from PDB file)

Resolution:

2.15Å R-factor: 0.177 R-free: 0.229

Authors:

T.T.Lee,S.Agarwalla,R.M.Stroud

Key ref:

T.T.Lee et al. (2005). A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell, 120, 599-611. PubMed id: 15766524 DOI: 10.1016/j.cell.2004.12.037

Date:

06-Jan-05 Release date: 30-Mar-05

Protein chains

P55135  (RUMA_ECOLI) -  23S rRNA (uracil-5-)-methyltransferase RumA

Seq: 433 a.a.

Struc: 418 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.190 - 23S rRNA (uracil(1939)-C(5))-methyltransferase.
• Reaction: S-adenosyl-L-methionine + uracil₁₉₃₉ in 23S rRNA = S-adenosyl-L- homocysteine + 5-methyluracil₁₉₃₉ in 23S rRNA

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: methylation (4 terms)
• Biochemical function: transferase activity (7 terms)

Added reference

DOI no: 10.1016/j.cell.2004.12.037

Cell 120:599-611 (2005)

PubMed id: 15766524

A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.

T.T.Lee, S.Agarwalla, R.M.Stroud.

ABSTRACT

A single base (U1939) within E. coli 23S ribosomal RNA is methylated by its dedicated enzyme, RumA. The structure of RumA/RNA/S-adenosylhomocysteine uncovers the mechanism for achieving unique selectivity. The single-stranded substrate is "refolded" on the enzyme into a compact conformation with six key intra-RNA interactions. The RNA substrate contributes directly to catalysis. In addition to the target base, a second base is "flipped out" from the core loop to stack against the adenine of the cofactor S-adenosylhomocysteine. Nucleotides in permuted sequence order are stacked into the site vacated by the everted target U1939 and compensate for the energetic penalty of base eversion. The 3' hairpin segment of the RNA binds distal to the active site and provides binding energy that contributes to enhanced catalytic efficiency. Active collaboration of RNA in catalysis leads us to conclude that RumA and its substrate RNA may reflect features from the earliest RNA-protein era.

Selected figure(s)

Figure 1.
Figure 1. The Proposed Catalytic Mechanism of RNA m^5U MTases

Figure 3.
Figure 3. Structural Comparison of the RumA Substrate in the Cocrystal Structure and that in Ribosome

The above figures are reprinted by permission from Cell Press: Cell (2005, 120, 599-611) copyright 2005.

Figures were selected by the author.