Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA large subunit methyltransferase I
Synonym: yccW, JW5898
GI: 13432272
Orf: b0967
COG: COG1092
UniProt: P75876
Structures: | 3C0K |
Enzyme type: methyltransferase
Position of modification - modification: l:1962(1962) - m5C


PDB Structures:


3C0K

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

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.

Download RCSB-PDB Structures:

Pdb Files   3C0K.pdb  
Pdbx/mmCIF Files   3C0K.cif  


Protein sequence:

MSVRLVLAKGREKSLLRRHPWVFSGAVARMEGKASLGETIDIVDHQGKWLARGAYSPASQIRARVWTFDPSESIDIAFFSRRLQQAQKWRDWLAQKDGLDSYRLIAGESDGLPGITIDRFGNFLVLQLLSAGAEYQRAALISALQTLYPECSIYDRSDVAVRKKEGMELTQGPVTGELPPALLPIEEHGMKLLVDIQHGHKTGYYLDQRDSRLATRRYVENKRVLNCFSYTGGFAVSALMGGCSQVVSVDTSQEALDIARQNVELNKLDLSKAEFVRDDVFKLLRTYRDRGEKFDVIVMDPPKFVENKSQLMGACRGYKDINMLAIQLLNEGGILLTFSCSGLMTSDLFQKIIADAAIDAGRDVQFIEQFRQAADHPVIATYPEGLYLKGFACRVM

Comments:

RlmI specifically methylates the C5-residue of conserved cytosine 1962 (m5C), located in position just precedding hairpin 71 of domain IV in 23S rRNA. In vitro, it works on naked 23S rRNA isolated from the yccW knockout strain, and not in assembled 50S subunits or ribosomes. The methyl donor group is AdoMet. 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. On evolutionary point of view, RlmI is similar to known m5U (5-methyluridine) RNA methyltransferases.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
C:m5C RNA rRNA 1962 LSU-23S Prokaryotic Cytosol 18786544   



Publications:

Title Authors Journal Details PubMed Id DOI
YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962. Purta E, O'Connor M, Bujnicki JM, Douthwaite S J Mol Biol [details] 18786544 -
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 [details] 18789337 -
5-methylcytosine in RNA: detection, enzymatic formation and biological functions. Motorin Y, Lyko F, Helm M Nucleic Acids Res [details] 20007150 -