Modomics - A Database of RNA Modifications

ID Card:

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

PDB Structures:


Structure Description:


Abstract of the PDB Structure's related Publication:

The radical S-adenosyl-L-methionine (SAM) enzymes RlmN and Cfr methylate 23S ribosomal RNA, modifying the C2 or C8 position of adenosine 2503. The methyl groups are installed by a two-step sequence involving initial methylation of a conserved Cys residue (RlmN Cys(355)) by SAM. Methyl transfer to the substrate requires reductive cleavage of a second equivalent of SAM. Crystal structures of RlmN and RlmN with SAM show that a single molecule of SAM coordinates the [4Fe-4S] cluster. Residue Cys(355) is S-methylated and located proximal to the SAM methyl group, suggesting the SAM that is involved in the initial methyl transfer binds at the same site. Thus, RlmN accomplishes its complex reaction with structural economy, harnessing the two most important reactivities of SAM within a single site.

Download RCSB-PDB Structures:

Pdb Files   3RF9.pdb   3RFA.pdb  
Pdbx/mmCIF Files   3RF9.cif   3RFA.cif  

Protein sequence:



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.

Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:m2A RNA rRNA 2503 LSU-23S Prokaryotic Cytosol 22891362   
A:m2A RNA tRNA 37 many - isoaceptors anticodon Prokaryotic Cytosol 22891362   


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