Modomics - A Database of RNA Modifications

ID Card:

Full name: tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6
Synonym: GCD10, TIF33
GI: 603585
Orf: YNL062C
COG: COG2519
UniProt: P41814
Structures: | 5EQJ | 5ERG |
Alpha Fold Predicted Structure: AF-P41814-F1
Complex: Trm6/Trm61


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:

MNALTTIDFNQHVIVRLPSKNYKIVELKPNTSVSLGKFGAFEVNDIIGYPFGLTFEIYYDGEEVSSDENRDSKPKNKIPIGKVRLLSQEIKDVNNDKDDGQSEPPLSIKEKSVSLELSSIDSSATNQNLVNMGSKAQELTVEEIEKMKQESLSSKEIIDKIIKSHKSFHNKTVYSQEKYVNRKKQKFAKYFTVEYLSSSNLLQFLIDKGDIQRVLDMSQESMGMLLNLANIQSEGNYLCMDETGGLLVYFLLERMFGGDNESKSKGKVIVIHENEHANLDLLKFANYSEKFIKEHVHTISLLDFFEPPTLQEIQSRFTPLPKEEARALKGGKKNSYYRKLRWYNTQWQILELTGEFLYDGLVMATTLHLPTLVPKLAEKIHGSRPIVCYGQFKETLLELAHTLYSDLRFLAPSILETRCRPYQSIRGKLHPLMTMKGGGGYLMWCHRVIPAPEPVSENATAADSSEKLAEHGAKKQKI

Comments:

Trm6 is the substrate-binding subunit of tRNA (adenine-N1-)-methyltransferase, which catalyzes the formation of N1-methyladenine at position 58 (m1A58) in initiator methionyl-tRNA ( Anderson et al. 1999, Anderson et al. 2000).





Alpha Fold Predicted Structure:






Clear Selection and Reset Camera

Protein sequence:

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

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-P41814-F1.pdb  
Alpha Fold Pdbx/mmCIF Files   AF-P41814-F1.cif  
DSSP Secondary Structures   P41814.dssp  





Publications:

Title Authors Journal Details PubMed Id DOI
The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae. Anderson J, Phan L, Hinnebusch AG Proc Natl Acad Sci U S A [details] 10779558 -
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 -