Modomics - A Database of RNA Modifications

ID Card:

Full name: Ribosomal RNA large subunit methyltransferase KL
Synonym: YcbY
GI: 2501582
Orf: b0948, JW0931
COG: COG0116
UniProt: P75864
Structures: | 3V8V | 3V97 |
Enzyme type: methyltransferase
Position of modification - modification: l:2069(2069) - m7G
l:2445(2445) - m2G


PDB Structures:


3V8V

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The 23S rRNA nucleotide m(2)G2445 is highly conserved in bacteria, and in Escherichia coli this modification is added by the enzyme YcbY. With lengths of around 700 amino acids, YcbY orthologs are the largest rRNA methyltransferases identified in Gram-negative bacteria, and they appear to be fusions from two separate proteins found in Gram-positives. The crystal structures described here show that both the N- and C-terminal halves of E. coli YcbY have a methyltransferase active site and their folding patterns respectively resemble the Streptococcus mutans proteins Smu472 and Smu776. Mass spectrometric analyses of 23S rRNAs showed that the N-terminal region of YcbY and Smu472 are functionally equivalent and add the m(2)G2445 modification, while the C-terminal region of YcbY is responsible for the m(7)G2069 methylation on the opposite side of the same helix (H74). Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs. The E.coli YcbY enzyme is the first example of a methyltransferase catalyzing two mechanistically different types of RNA modification, and has been renamed as the Ribosomal large subunit methyltransferase, RlmKL. Our structural and functional data provide insights into how this bifunctional enzyme evolved.

Download RCSB-PDB Structures:

Pdb Files   3V8V.pdb   3V97.pdb  
Pdbx/mmCIF Files   3V8V.cif   3V97.cif  


Protein sequence:

MNSLFASTARGLEELLKTELENLGAVECQVVQGGVHFKGDTRLVYQSLMWSRLASRIMLPLGECKVYSDLDLYLGVQAINWTEMFNPGATFAVHFSGLNDTIRNSQYGAMKVKDAIVDAFTRKNLPRPNVDRDAPDIRVNVWLHKETASIALDLSGDGLHLRGYRDRAGIAPIKETLAAAIVMRSGWQPGTPLLDPMCGSGTLLIEAAMLATDRAPGLHRGRWGFSGWAQHDEAIWQEVKAEAQTRARKGLAEYSSHFYGSDSDARVIQRARTNARLAGIGELITFEVKDVAQLTNPLPKGPYGTVLSNPPYGERLDSEPALIALHSLLGRIMKNQFGGWNLSLFSASPDLLSCLQLRADKQYKAKNGPLDCVQKNYHVAESTPDSKPAMVAEDYTNRLRKNLKKFEKWARQEGIECYRLYDADLPEYNVAVDRYADWVVVQEYAPPKTIDAHKARQRLFDIIAATISVLGIAPNKLVLKTRERQKGKNQYQKLGEKGEFLEVTEYNAHLWVNLTDYLDTGLFLDHRIARRMLGQMSKGKDFLNLFSYTGSATVHAGLGGARSTTTVDMSRTYLEWAERNLRLNGLTGRAHRLIQADCLAWLREANEQFDLIFIDPPTFSNSKRMEDAFDVQRDHLALMKDLKRLLRAGGTIMFSNNKRGFRMDLDGLAKLGLKAQEITQKTLSQDFARNRQIHNCWLITAA

Comments:

RlmKL is a bifunctional protein (700 amino acids) that catalyzes the in vitro formation of two different methylated residues (m7G and m2G) within the same helix 74 in domain IV (Peptidyl Transferase Center) of 23S rRNA purified from the ycbY knock-out strain (positions 2069 and 2445 respectively). Assembled 50 S subunits are not a substrate for the RlmKL. It contains two Rossmann-fold methyltransferase domains. The N-terminal domain (RlmL domain) is a member of COG0116 and consists of a MTase domain and a RNA-binding THUMP domain. The C-terminal domain (RlmK domain) is a MTase and member of COG1092. AdoMet is the methyl group donor. RlmKL was shown to have an activity to unwind 23S rRNA helix 74 during substrate recognition and methylation. The proposed mechanism for the methylation of two target sites: first the 2069 m7G is introduced by RlmK domain, then the 2445 m2G by RlmL domain. The presence of RlmK domain facilitates methylation in position 2445 but the reactions are independent. P-loop of helix 80 is critical for substrate recognition. Phylogenetic analysis suggests that bifunctional RlmKL is only present in Gammaproteobacteria, and that the separated RlmK and RlmL are found in the genus Neisseria.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m2G RNA rRNA 2445 LSU-23S Prokaryotic Cytosol 17010378   
G:m7G RNA rRNA 2069 LSU-23S Prokaryotic Cytosol 22210896   



Publications:

Title Authors Journal Details PubMed Id DOI
Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA. Lesnyak DV, Sergiev PV, Bogdanov AA, Dontsova OA J Mol Biol [details] 17010378 -
Ribosomal RNA guanine-(N2)-methyltransferases and their targets. Sergiev PV, Bogdanov AA, Dontsova OA Nucleic Acids Res [details] 17389639 -
Base methylations in the double-stranded RNA by a fused methyltransferase bearing unwinding activity. Kimura S, Ikeuchi Y, Kitahara K, Sakaguchi Y, Suzuki T, Suzuki T Nucleic Acids Res [details] 22210896 -
Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA. Wang KT, Desmolaize B, Nan J, Zhang XW, Li LF, Douthwaite S, Su XD Nucleic Acids Res [details] 22362734 -