Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61
Synonym: GCD14
GI: 6322336
Orf: YJL125C
COG: COG2519
UniProt: P46959
Structures: | 5EQJ | 5ERG |
Alpha Fold Predicted Structure: AF-P46959-F1
Complex: Trm6/Trm61
Enzyme type: methyltransferase
Position of modification - modification: t:58 - m1A


PDB Structures:


5EQJ

Structure Description:

Title:
Classification:
Technique:

Abstract of the PDB Structure's related Publication:

The N(1) methylation of adenine at position 58 (m(1)A58) of tRNA is an important post-transcriptional modification, which is vital for maintaining the stability of the initiator methionine tRNAi(Met). In eukaryotes, this modification is performed by the TRM6-TRM61 holoenzyme. To understand the molecular mechanism that underlies the cooperation of TRM6 and TRM61 in the methyl transfer reaction, we determined the crystal structure of TRM6-TRM61 holoenzyme from Saccharomyces cerevisiae in the presence and absence of its methyl donor S-Adenosyl-L-methionine (SAM). In the structures, two TRM6-TRM61 heterodimers assemble as a heterotetramer. Both TRM6 and TRM61 subunits comprise an N-terminal β-barrel domain linked to a C-terminal Rossmann-fold domain. TRM61 functions as the catalytic subunit, containing a methyl donor (SAM) binding pocket. TRM6 diverges from TRM61, lacking the conserved motifs used for binding SAM. However, TRM6 cooperates with TRM61 forming an L-shaped tRNA binding regions. Collectively, our results provide a structural basis for better understanding the m(1)A58 modification of tRNA occurred in Saccharomyces cerevisiae

Download RCSB-PDB Structures:

Pdb Files   5EQJ.pdb   5ERG.pdb  
Pdbx/mmCIF Files   5EQJ.cif   5ERG.cif  


Protein sequence:

MSTNCFSGYKDLIKEGDLTLIWVSRDNIKPVRMHSEEVFNTRYGSFPHKDIIGKPYGSQIAIRTKGSNKFAFVHVLQPTPELWTLSLPHRTQIVYTPDSSYIMQRLNCSPHSRVIEAGTGSGSFSHAFARSVGHLFSFEFHHIRYEQALEEFKEHGLIDDNVTITHRDVCQGGFLIKKGDTTSYEFGNNETAASLNANVVFLDLPAPWDAIPHLDSVISVDEKVGLCCFSPCIEQVDKTLDVLEKYGWTDVEMVEIQGRQYESRRQMVRSLNDALERLRDIKRHKLQGVERRKRMFNNTIDSNDEKVGKRNEDGVPLTEKAKFNPFGKGSRIKEGDSNYKWKEVTKMEAEIKSHTSYLTFAFKVVNRSRDDEKVNEILRSTEK

Comments:

AdoMet is the methyl group donor. Heterotetramer composed of mutually related subunits: 2 copies of Trm6p and two copies of Trm61p. Trm61p is a catalytic subunit, Trm6p is a tRNA-binding subunit. Trm6/Trm61 are structuraly related.




Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
A:m1A RNA tRNA 58 ICG ICG tRNAArgICG TΨC-loop Nucleus
A:m1A RNA tRNA 58 GUU GUU tRNAAsnGUU TΨC-loop Nucleus
A:m1A RNA tRNA 58 GCA GCA tRNACysGCA TΨC-loop Nucleus
A:m1A RNA tRNA 58 IAU IAU tRNAIleIUA TΨC-loop Nucleus
A:m1A RNA tRNA 58 UAU UAU tRNAIleUAU TΨC-loop Nucleus
A:m1A RNA tRNA 58 UAG UAG tRNALeuUAG TΨC-loop Nucleus
A:m1A RNA tRNA 58 UAA UAA tRNALeuUAA TΨC-loop Nucleus
A:m1A RNA tRNA 58 CUU CUU tRNALysCUU TΨC-loop Nucleus
A:m1A RNA tRNA 58 SUU SUU tRNALysSUU TΨC-loop Nucleus
A:m1A RNA tRNA 58 CAU CAU tRNAMetCAU TΨC-loop Cytoplasm
A:m1A tRNA (t) Phe/GAA/prokaryotic cytosol 58
A:m1A tRNA (t) Pro/UGG/prokaryotic cytosol 58
A:m1A tRNA (t) Thr/IGU/prokaryotic cytosol 58
A:m1A tRNA (t) Trp/CCA/prokaryotic cytosol 58
A:m1A tRNA (t) Tyr/GUA/prokaryotic cytosol 58
A:m1A tRNA (t) Val/UAC/prokaryotic cytosol 58
A:m1A tRNA (t) Val/CAC/prokaryotic cytosol 58
A:m1A tRNA (t) Val/IAC/prokaryotic cytosol 58

Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P46959-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P46959-F1.cif  
DSSP Secondary Structures   P46959.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. Anderson J, Phan L, Cuesta R, Carlson BA, Pak M, Asano K, Bjork GR, Tamame M, Hinnebusch AG Genes Dev [details] 9851972 -
Conserved amino acids in each subunit of the heteroligomeric tRNA m1A58 Mtase from Saccharomyces cerevisiae contribute to tRNA binding. Ozanick SG, Bujnicki JM, Sem DS, Anderson JT Nucleic Acids Res [details] 17932071 -