PDBsum entry: 3c0k

Transferase

PDB id: 3c0k

Contents

Protein chains

395 a.a. *

Waters ×458

* Residue conservation analysis

PDB id:

3c0k

Name:

Transferase

Title:

Crystal structure of a ribosomal RNA methyltranferase

Structure:

Upf0064 protein yccw. Chain: a, b. Engineered: yes

Source:

Escherichia coli k12. Organism_taxid: 83333. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.194 R-free: 0.242

Authors:

S.Subramanian,S.Jayaraman,J.Bujnicki

Key ref:

S.Sunita et al. (2008). Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. J Mol Biol, 383, 652-666. PubMed id: 18789337 DOI: 10.1016/j.jmb.2008.08.062

Date:

21-Jan-08 Release date: 04-Nov-08

Protein chains

P75876  (RLMI_ECOLI) -  Ribosomal RNA large subunit methyltransferase I

Seq: 396 a.a.

Struc: 395 a.a.

Enzyme reactions

• Enzyme class: E.C.2.1.1.191 - 23S rRNA (cytosine(1962)-C(5))-methyltransferase.
• Reaction: S-adenosyl-L-methionine + cytosine₁₉₆₂ in 23S rRNA = S-adenosyl-L- homocysteine + 5-methylcytosine₁₉₆₂ in 23S rRNA

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: biofilm formation (5 terms)
• Biochemical function: transferase activity (5 terms)

Added reference

DOI no: 10.1016/j.jmb.2008.08.062

J Mol Biol 383:652-666 (2008)

PubMed id: 18789337

Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes.

S.Sunita, K.L.Tkaczuk, E.Purta, J.M.Kasprzak, S.Douthwaite, J.M.Bujnicki, J.Sivaraman.

ABSTRACT

Methylation is the most common RNA modification in the three domains of life. Transfer of the methyl group from S-adenosyl-l-methionine (AdoMet) to specific atoms of RNA nucleotides is catalyzed by methyltransferase (MTase) enzymes. The rRNA MTase RlmI (rRNA large subunit methyltransferase gene I; previously known as YccW) specifically modifies Escherichia coli 23S rRNA at nucleotide C1962 to form 5-methylcytosine. Here, we report the crystal structure of RlmI refined at 2 A to a final R-factor of 0.194 (R(free)=0.242). The RlmI molecule comprises three domains: the N-terminal PUA domain; the central domain, which resembles a domain previously found in RNA:5-methyluridine MTases; and the C-terminal catalytic domain, which contains the AdoMet-binding site. The central and C-terminal domains are linked by a beta-hairpin structure that has previously been observed in several MTases acting on nucleic acids or proteins. Based on bioinformatics analyses, we propose a model for the RlmI-AdoMet-RNA complex. Comparative structural analyses of RlmI and its homologs provide insight into the potential function of several structures that have been solved by structural genomics groups and furthermore indicate that the evolutionary paths of RNA and DNA 5-methyluridine and 5-methylcytosine MTases have been closely intertwined.

Selected figure(s)

Figure 8.
Fig. 8. Docking model of RlmI with AdoMet and the RNA substrate. The protein backbone is shown as a gray C^α trace. The RNA is shown in yellow, with the target C1962 residue shown in orange. AdoMet is shown in magenta. Conserved residues predicted to be important for RNA binding, AdoMet binding, and catalysis are shown in blue, green, and red, respectively.

Figure 10.
Fig. 10. Electron density maps. (a) Stereo view of the experimental electron density map (RESOLVE density-modified map). The map is contoured at a level of 1.0σ. (b) Simulated annealing F[o] − F[c] omit map in the active-site region of RlmI. Ser339 and all atoms within 2.5 Å were omitted prior to refinement. The cysteine in the active site is labeled. The map is contoured at a level of 3.0σ. These figures were prepared using PyMol [http://www.pymol.org].

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 383, 652-666) copyright 2008.

Figures were selected by an automated process.