Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (cytosine(38)-C(5))-methyltransferase
Synonym: GSU0227
GI: 39995337
UniProt: Q74GL9
Alpha Fold Predicted Structure: AF-Q74GL9-F1
Enzyme type: methyltransferase
Position of modification - modification: t:38 - m5C



Protein sequence:

MRAVELFCGIGGFAAAVEGTGVRVVAAMDQDEAALATYRLNFPGHGARKVDLERVSAWELTAGGVDLWWLSPPCQPYCERGVRRDLADPRARSLVHILNLAARMSDEALPRHLALENVAGFVGSEAHGRLTEVLSSRGYRLQERLLCPTELGIPSRRPRYYLAASRESLAPAEVLSPLPRQPLAEYLDLLPANGQPAELLLSPAIVERFGAGFRILDPADPDAYTTCFTSGYGRSLTASGAYLRCSDGVRRFSPEEIARLLHFPPSFRFPEEVPLRKRWQLVGNSLSVAAVREVLRALPLPAEEG

Comments:

In contrast to Dnmt2 methyltransferases from eukaryotes which methylate C38 of tRNAAsp, this enzyme methylates C38 in tRNAGlu. This swapped tRNA specificity is dependent on the differences in the sequence of the variable-loop in the substrate tRNAs (Shanmugam et al. 2011 ). Shanmugam and coauthors compared the secondary structures of tRNAAsp and tRNAGlu from several species and noticed that Gs-tRNAAsp has a longer variable loop with extra guanine. Furthermore, the variable loops of all preferred Dnmt2 substrates (namely tRNAAsp from all species but Geobacter and Gs-tRNAGlu) have at least one A at position 45 or 46 of the variable loop, while all the inactive counterparts contain a GG dinucleotide. Based on this, the authors speculated that the variable loop may be a specificity determinant of GsDnmt2. To test this hypothesis, the variable loop of murine tRNAAsp was swapped with that of murine tRNAGlu by an exchange of two nucleotides (AGAC to CGGC) which introduced the GG dinucleotide sequence into tRNAAsp. The mutant tRNAAsp was synthesized by in vitro transcription. Equal amounts of the wild-type and mutant tRNAs were used in methylation reactions with GsDnmt2. Strikingly, the alteration of these two bases in the variable loop of murine tRNAAsp led to a strong decrease in the methylation rate. This result supports the hypothesis of the involvement of the variable loop in the enzyme-substrate recognition of GsDnmt2 (Shanmugam et al. 2011 ).




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
C:m5C RNA tRNA 38 UUC UUC tRNAGluUUC Anticodon Prokaryotic cytoplasm 24711368   

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

M R A V E L F C G I G G F A A A V E G T G V R V V A A M D Q D E A A L A T Y R L N F P G H G A R K V D L E R V S A W E L T A G G V D L W W L S P P C Q P Y C E R G V R R D L A D P R A R S L V H I L N L A A R M S D E A L P R H L A L E N V A G F V G S E A H G R L T E V L S S R G Y R L Q E R L L C P T E L G I P S R R P R Y Y L A A S R E S L A P A E V L S P L P R Q P L A E Y L D L L P A N G Q P A E L L L S P A I V E R F G A G F R I L D P A D P D A Y T T C F T S G Y G R S L T A S G A Y L R C S D G V R R F S P E E I A R L L H F P P S F R F P E E V P L R K R W Q L V G N S L S V A A V R E V L R A L P L P A E E G

Secondary Structure Alphabet

  • G: 3-turn helix (310helix)
  • H: α-helix
  • I: 𝝅-helix (5 - turn helix)
  • T: Hydrogen Bonded Turn
  • B: β-sheet
  • S: Bend
  • C: Coil (residues not present in any of the above conformations)
  • N: Not assigned

Download PDB Structures & DSSP Secondary Structures:

Alpha Fold Pdb Files   AF-Q74GL9-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q74GL9-F1.cif  
DSSP Secondary Structures   Q74GL9.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The Dnmt2 RNA methyltransferase homolog of Geobacter sulfurreducens specifically methylates tRNA-Glu. Shanmugam R, Aklujkar M, Schafer M, Reinhardt R, Nickel O, Reuter G, Lovley DR, Ehrenhofer-Murray A, Nellen W, Ankri S, Helm M, Jurkowski TP, Jeltsch A... Nucleic Acids Res [details] 24711368 -

Links:

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