5EQJ

Crystal structure of the two-subunit tRNA m1A58 methyltransferase from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


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Literature

Crystal structure of the two-subunit tRNA m(1)A58 methyltransferase TRM6-TRM61 from Saccharomyces cerevisiae.

Wang, M.Zhu, Y.Wang, C.Fan, X.Jiang, X.Ebrahimi, M.Qiao, Z.Niu, L.Teng, M.Li, X.

(2016) Sci Rep 6: 32562-32562

  • DOI: 10.1038/srep32562
  • Primary Citation of Related Structures:  
    5EQJ, 5ERG

  • PubMed Abstract: 
  • 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 ...

    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.


    Organizational Affiliation

    Key Laboratory of Structural Biology, Hefei Science Center of CAS, Chinese Academy of Science, Hefei, Anhui, 230026, People's Republic of China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6A488Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GCD10TIF33TRM6YNL062CN2422
UniProt
Find proteins for P41814 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41814 
Go to UniProtKB:  P41814
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41814
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRM61B383Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GCD14TRM61YJL125CJ0710
EC: 2.1.1.220
UniProt
Find proteins for P46959 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46959 
Go to UniProtKB:  P46959
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46959
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.645α = 90
b = 138.645β = 90
c = 102.727γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SCALAdata scaling
AutoSolphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release