Modomics - A Database of RNA Modifications

Full name: tRNA (adenosine(37)-C2)-methyltransferase / Ribosomal RNA large subunit methyltransferase N
Synonym: TrmG, YfgB
GI: 549552
Orf: b2517
COG: COG0820
UniProt: P36979
Structures: | 3RF9 | 3RFA |
Enzyme type: methyltransferase
Position of modification - modification: l:2503(2503) - m2A
t:37 - m2A


Dual-specificity enzyme that catalyzes methylation of both rRNA and tRNA. Two acronyms have been assigned to one protein in this case and they denote the activitiy on rRNA (RlmN) or on tRNA (TrmG). RlmN carries out the AdoMet-dependent methylation of an amidine carbon of an adenine target (formation of m2A) at position 2503 of the Peptidyl Transferase Center of 23S rRNA (in single stranded region between hairpins 89 and 90 of Domain V). TrmG is responsible for the m(2)A synthesis at purine 37 in a tRNA. The enzyme can utilize protein-free 23S rRNA as a substrate, but not the fully assembled large ribosomal subunit. The key recognition elements in the 23S rRNA are helices 90-92 and the adjacent single stranded RNA that encompasses A2503.RlmN belongs to Radical SAM superfamily and contains the characteristic cysteine-rich CX(3)CX(2)C motif. It is evolutionarily related to the enzyme Cfr of the Gram-positive Staphylococcus aureus catalyzing a similar reaction (formation of m8A) on the same target in rRNA A2503.

Protein sequence:


Enzymatic activities:

Reaction Substrate Type Position
A:m2A rRNA (r) LSU/23S/prokaryotic cytosol 2503
A:m2A tRNA (t) many 37


Title Authors Journal Details PubMed Id DOI
The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. Toh SM, Xiong L, Bae T, Mankin AS RNA [details] 18025251 -
Structural basis for methyl transfer by a radical SAM enzyme. Boal AK, Grove TL, McLaughlin MI, Yennawar NH, Booker SJ, Rosenzweig AC Science [details] 21527678 -
RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA Yan F, LaMarre JM, Röhrich R, Wiesner J, Jomaa H, Mankin AS, Fujimori DG J Am Chem Soc [details] 20184321 -
RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift. Yan F, Fujimori DG Proc Natl Acad Sci U S A [details] 21368151 -
Radical-mediated enzymatic methylation: a tale of two SAMS. Zhang Q, van der Donk WA, Liu W Acc Chem Res [details] 22097883 -
Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation. Grove TL, Radle MI, Krebs C, Booker SJ J Am Chem Soc [details] 21916495 -
The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. Benitez-Paez A, Villarroya M, Armengod ME... RNA [details] 22891362 -
Covalent Intermediate in the Catalytic Mechanism of the Radical S-Adenosyl-l-methionine Methyl Synthase RlmN Trapped by Mutagenesis. McCusker KP, Medzihradszky KF, Shiver AL, Nichols RJ, Yan F, Maltby DA, Gross CA, Galonic Fujimori D... J Am Chem Soc [details] 23088750 -
Emerging themes in radical SAM chemistry. Shisler KA, Broderick JB... Curr Opin Struct Biol [details] 23141873 -
Biochemical and Computational Analysis of the Substrate Specificities of Cfr and RlmN Methyltransferases Ntokou E, Hansen LH, Kongsted J, Vester B PLoS One [details] 26700482 10.1371/journal.pone.0145655



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