Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (guanine(6)-N2)-methyltransferase
Synonym: Trm14
GI: 46199459
Orf: TTC1157
COG: COG0116
UniProt: Q72IH5
Structures: | 3TMA |
Alpha Fold Predicted Structure: AF-Q72IH5-F1
Enzyme type: methyltransferase
Position of modification - modification: t:6 - m2G


PDB Structures:


3TMA

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

Methyltransferases (MTases) form a major class of tRNA-modifying enzymes needed for the proper functioning of tRNA. Recently, RNA MTases from the TrmN/Trm14 family that are present in Archaea, Bacteria and Eukaryota have been shown to specifically modify tRNA(Phe) at guanosine 6 in the tRNA acceptor stem. Here, we report the first X-ray crystal structures of the tRNA m(2)G6 (N(2)-methylguanosine) MTase (TTC)TrmN from Thermus thermophilus and its ortholog (Pf)Trm14 from Pyrococcus furiosus. Structures of (Pf)Trm14 were solved in complex with the methyl donor S-adenosyl-l-methionine (SAM or AdoMet), as well as the reaction product S-adenosyl-homocysteine (SAH or AdoHcy) and the inhibitor sinefungin. (TTC)TrmN and (Pf)Trm14 consist of an N-terminal THUMP domain fused to a catalytic Rossmann-fold MTase (RFM) domain. These results represent the first crystallographic structure analysis of proteins containing both THUMP and RFM domain, and hence provide further insight in the contribution of the THUMP domain in tRNA recognition and catalysis. Electrostatics and conservation calculations suggest a main tRNA binding surface in a groove between the THUMP domain and the MTase domain. This is further supported by a docking model of TrmN in complex with tRNA(Phe) of T. thermophilus and via site-directed mutagenesis.

Download RCSB-PDB Structures:

Pdb Files   3TMA.pdb  
Pdbx/mmCIF Files   3TMA.cif  


Protein sequence:

MWLEATTHPGLEDLLLEELSALYPGEGAEVDARKGRVRIPRAWVGEEALGLRLAHHLVLFRARLLLSREDPLGALERAALALPWPELEGAGSFRVEARREGEHPFTSPEVERRVGEALHRAYGVPVDLKRPAVRVRVDVRGEEAFLGVQLTERPLSRRFPKAALRGSLTPVLAQALLRLADARPGMRVLDPFTGSGTIALEAASTLGPTSPVYAGDLDEKRLGLAREAALASGLSWIRFLRADARHLPRFFPEVDRILANPPHGLRLGRKEGLFHLYWDFLRGALALLPPGGRVALLTLRPALLKRALPPGFALRHARVVEQGGVYPRVFVLEKL

Comments:

AdoMet is the methyl group donor.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m2G RNA tRNA 6 GAA GAA tRNAPheGAA acceptor-stem Prokaryotic Cytosol 22337946   

Alpha Fold Predicted Structure:






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Protein sequence:

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

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-Q72IH5-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-Q72IH5-F1.cif  
DSSP Secondary Structures   Q72IH5.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The open reading frame TTC1157 of Thermus thermophilus HB27 encodes the methyltransferase forming N(2)-methylguanosine at position 6 in tRNA. Roovers M, Oudjama Y, Fislage M, Bujnicki JM, Versees W, Droogmans L RNA [details] 22337946 -
Crystal structures of the tRNA:m2G6 methyltransferase Trm14/TrmN from two domains of life. Fislage M, Roovers M, Tuszynska I, Bujnicki JM, Droogmans L, Versees W... Nucleic Acids Res [details] 22362751 -