Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (guanine-N(1)-)-methyltransferase
Synonym: O0926
GI: 74645051
Orf: YOL093W
COG: COG2419
UniProt: Q12400
Structures: | 4JWJ |
Enzyme type: methyltransferase
Position of modification - modification: t:9 - m1G

PDB Structures:


Structure Description:


Abstract of the PDB Structure's related Publication:

Transfer RNA (tRNA) methylation is necessary for the proper biological function of tRNA. The N(1) methylation of guanine at Position 9 (m(1)G9) of tRNA, which is widely identified in eukaryotes and archaea, was found to be catalyzed by the Trm10 family of methyltransferases (MTases). Here, we report the first crystal structures of the tRNA MTase spTrm10 from Schizosaccharomyces pombe in the presence and absence of its methyl donor product S-adenosyl-homocysteine (SAH) and its ortholog scTrm10 from Saccharomyces cerevisiae in complex with SAH. Our crystal structures indicated that the MTase domain (the catalytic domain) of the Trm10 family displays a typical SpoU-TrmD (SPOUT) fold. Furthermore, small angle X-ray scattering analysis reveals that Trm10 behaves as a monomer in solution, whereas other members of the SPOUT superfamily all function as homodimers. We also performed tRNA MTase assays and isothermal titration calorimetry experiments to investigate the catalytic mechanism of Trm10 in vitro. In combination with mutational analysis and electrophoretic mobility shift assays, our results provide insights into the substrate tRNA recognition mechanism of Trm10 family MTases.

Download RCSB-PDB Structures:

Pdb Files   4JWJ.pdb  
Pdbx/mmCIF Files   4JWJ.cif  

Protein sequence:



Monomeric cytoplasmic enzyme. AdoMet is the methyl group donor. Bears no detectable resemblance to the yeast m1G37 methyltransferase, Trm5, or its orthologs. Homologs are found widely only in eukaryotes and archaea, with multiple homologs in several metazoans (at least three in humans). Not essential, yet it plays a role in translation termination efficiency. The substrate specificity of this enzyme is broader than expected from modification status of tRNA obtained from wild type S. cerevisiae (additional substrates were found via in vitro experiments and studies with overexpressed enzyme). Sequence or structure determinants of specificity are unknown.

Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m1G RNA tRNA 9 IGC IGC tRNAAlaIGC ~ Cytoplasm
G:m1G RNA tRNA 9 UCU UCU tRNAArgUCU ~ Cytoplasm
G:m1G RNA tRNA 9 ICG ICG tRNAArgICG ~ Cytoplasm
G:m1G RNA tRNA 9 GCC GCC tRNAGlyGCC ~ Cytoplasm
G:m1G RNA tRNA 9 IAU IAU tRNAIleIAU ~ Cytoplasm
G:m1G RNA tRNA 9 UGG UGG tRNAProUGG ~ Prokaryotic Cytosol
G:m1G RNA tRNA 9 CCA CCA tRNATrpCCA ~ Cytoplasm
G:m1G RNA tRNA 9 IAC IAC tRNAValIAC ~ Cytoplasm
G:m1G RNA tRNA 9 CUU CUU tRNALysCUU ~ Cytoplasm
G:m1G RNA tRNA 9 CAU CAU tRNAIniCAU ~ Cytoplasm
G:m1G RNA tRNA 9 UAC UAC tRNAValUAC ~ Cytoplasm 23793893   
G:m1G RNA tRNA 9 GCA GCA tRNACysGCA ~ Cytoplasm 23793893   
G:m1G RNA tRNA 9 AGU AGU tRNAThrAGU ~ Cytoplasm 23793893   
G:m1G RNA tRNA 9 CCC CCC tRNAGlyCCC ~ Cytoplasm 23793893   
G:m1G RNA tRNA 9 CGU CGU tRNAThrCGU ~ Cytoplasm 23793893   
G:m1G RNA tRNA 9 CUU CUU tRNALysCUU ~ Cytoplasm 23793893   


Title Authors Journal Details PubMed Id DOI
Identification of the yeast gene encoding the tRNA m1G methyltransferase responsible for modification at position 9. Jackman JE, Montange RK, Malik HS, Phizicky EM RNA [details] 12702816 -
Variants in SUP45 and TRM10 underlie natural variation in translation termination efficiency in Saccharomyces cerevisiae. Torabi N, Kruglyak L PLoS Genet [details] 21829385 -
Unexpected expansion of tRNA substrate recognition by the yeast m1G9 methyltransferase Trm10. Swinehart WE, Henderson JC, Jackman JE... RNA [details] 23793893 -
Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate Shao Z, Yan W, Peng J, Zuo X, Zou Y, Li F, Gong D, Ma R, Wu J, Shi Y, Zhang Z, Teng M, Li X, Gong Q Nucleic Acids Res. [details] 24081582 10.1093/nar/gkt869