Modomics - A Database of RNA Modifications

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

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.

Protein sequence:

MNSLFASTARGLEELLKTELENLGAVECQVVQGGVHFKGDTRLVYQSLMWSRLASRIMLPLGECKVYSDLDLYLGVQAINWTEMFNPGATFAVHFSGLND
TIRNSQYGAMKVKDAIVDAFTRKNLPRPNVDRDAPDIRVNVWLHKETASIALDLSGDGLHLRGYRDRAGIAPIKETLAAAIVMRSGWQPGTPLLDPMCGS
GTLLIEAAMLATDRAPGLHRGRWGFSGWAQHDEAIWQEVKAEAQTRARKGLAEYSSHFYGSDSDARVIQRARTNARLAGIGELITFEVKDVAQLTNPLPK
GPYGTVLSNPPYGERLDSEPALIALHSLLGRIMKNQFGGWNLSLFSASPDLLSCLQLRADKQYKAKNGPLDCVQKNYHVAESTPDSKPAMVAEDYTNRLR
KNLKKFEKWARQEGIECYRLYDADLPEYNVAVDRYADWVVVQEYAPPKTIDAHKARQRLFDIIAATISVLGIAPNKLVLKTRERQKGKNQYQKLGEKGEF
LEVTEYNAHLWVNLTDYLDTGLFLDHRIARRMLGQMSKGKDFLNLFSYTGSATVHAGLGGARSTTTVDMSRTYLEWAERNLRLNGLTGRAHRLIQADCLA
WLREANEQFDLIFIDPPTFSNSKRMEDAFDVQRDHLALMKDLKRLLRAGGTIMFSNNKRGFRMDLDGLAKLGLKAQEITQKTLSQDFARNRQIHNCWLIT
AA

Enzymatic activities:

Reaction	Substrate	Type	Position
G:m2G	rRNA (r)	LSU/23S/prokaryotic cytosol	2445
G:m7G	rRNA (r)	LSU/23S/prokaryotic cytosol	2069

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	-