Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (guanine-N(1)-)-methyltransferase
GI: 731672
Orf: YHR070W
COG: COG2520
UniProt: P38793
Alpha Fold Predicted Structure: AF-P38793-F1
Enzyme type: methyltransferase
Position of modification - modification: t:37 - yW
t:37 - m1I
t:37 - m1G



Protein sequence:

MKIALPVFQKFNRLISSCKMSGVFPYNPPVNRQMRELDRSFFITKIPMCAVKFPEPKNISVFSKNFKNCILRVPRIPHVVKLNSSKPKDELTSVQNKKLKTADGNNTPVTKGVLLHESIHSVEDAYGKLPEDALAFLKENSAEIVPHEYVLDYDFWKAEEILRAVLPEQFLEEVPTGFTITGHIAHLNLRTEFKPFDSLIGQVILDKNNKIECVVDKVSSIATQFRTFPMKVIAGKSDSLVVEQKESNCTFKFDFSKVYWNSRLHTEHERLVKQYFQPGQVVCDVFAGVGPFAVPAGKKDVIVLANDLNPESYKYLKENIALNKVAKTVKSFNMDGADFIRQSPQLLQQWIQDEEGGKITIPLPLKKRHRSQQHNDQQPPQPRTKELIIPSHISHYVMNLPDSAISFLGNFRGIFAAHTKGATDTIQMPWVHVHCFEKYPPGDQVTEDELHARVHARIIAALKVTADDLPLNAVSLHLVRKVAPTKPMYCASFQLPANV

Comments:

S-Adenosyl methionine (SAM or AdoMet) consists of an adenosyl cation attached to the sulfur methionine. It is synthesized from ATP and methionine by S-Adenosylmethionine synthetase enzyme through the reaction of ATP with L-methionine and water forming as catalytical product S-adenosyl-L-methionine. SAM is a common cosubstrate involved in several reactions, among which methyl group transfers. Trm5 is a site-specific enzyme methylating the N1 position of guanosine-37 in various cytoplasmic and mitochondrial tRNAs using SAM as a cosubstrate ( Lee et al. 2007). Methylation is not dependent on the nature of the nucleoside 5' of the target nucleoside. This is the first step in the biosynthesis of wybutosine (yW), a modified base adjacent to the anticodon of tRNAs and required for accurate decoding ( Björk et al. 2001). It also methylates I at position 37.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
G:m1G RNA tRNA 37 UAG UAG tRNALeuUAG anticodon-loop Nucleus
G:m1G RNA tRNA 37 CAA CAA tRNALeuCAA anticodon-loop Nucleus
G:m1G RNA tRNA 37 UAA UAA tRNALeuUAA anticodon-loop Nucleus
G:m1G RNA tRNA 37 UGG UGG tRNAProUGG anticodon-loop Nucleus
G:m1G RNA tRNA 37 GUG GUG tRNAHisGUG anticodon-loop Nucleus
G:m1G RNA tRNA 37 GUC GUC tRNAAspGUC anticodon-loop Nucleus
G:m1G RNA tRNA 37 GAA GAA tRNAPheGAA anticodon-loop Nucleus
G:m1G RNA tRNA 37 GAG GAG tRNALeuGAG anticodon-loop Nucleus

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P38793-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P38793-F1.cif  
DSSP Secondary Structures   P38793.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. Noma A, Kirino Y, Ikeuchi Y, Suzuki T EMBO J [details] 16642040 -
A primordial tRNA modification required for the evolution of life? Bjork GR, Jacobsson K, Nilsson K, Johansson MJ, Bystrom AS, Persson OP EMBO J [details] 11226173 -
Control of catalytic cycle by a pair of analogous tRNA modification enzymes. Christian T, Lahoud G, Liu C, Hou YM J Mol Biol [details] 20452364 -
Mechanism of N-methylation by the tRNA m1G37 methyltransferase Trm5. Christian T, Lahoud G, Liu C, Hoffmann K, Perona JJ, Hou YM RNA [details] 20980671 -
Yeast mitochondrial initiator tRNA is methylated at guanosine 37 by the Trm5-encoded tRNA (guanine-N1-)-methyltransferase. Lee C, Kramer G, Graham DE, Appling DR J Biol Chem [details] 17652090 -

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