Crystal Structure of Pyrococcus abyssi Trm5a

  • Classification: TRANSFERASE
  • Organism(s): Pyrococcus abyssi GE5
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-01-13 Released: 2016-10-12 
  • Deposition Author(s): Xie, W., Wang, C., Jia, Q.
  • Funding Organization(s): Guangdong Innovative Research Team, Science and Technology Program of Guangzhou, Fundamental Research Funds for the Central Universities

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Crystal structures of the bifunctional tRNA methyltransferase Trm5a

Wang, C.Jia, Q.Chen, R.Wei, Y.Li, J.Ma, J.Xie, W.

(2016) Sci Rep 6: 33553-33553

  • DOI: https://doi.org/10.1038/srep33553
  • Primary Citation of Related Structures:  
    5HJI, 5HJJ, 5HJK, 5HJM

  • PubMed Abstract: 

    tRNA methyltransferase Trm5 catalyses the transfer of a methyl group from S-adenosyl-L-methionine to G37 in eukaryotes and archaea. The N1-methylated guanosine is the product of the initial step of the wyosine hypermodification, which is essential for the maintenance of the reading frame during translation. As a unique member of this enzyme family, Trm5a from Pyrococcus abyssi (PaTrm5a) catalyses not only the methylation of N1, but also the further methylation of C7 on 4-demethylwyosine at position 37 to produce isowyosine, but the mechanism for the double methylation is poorly understood. Here we report four crystal structures of PaTrm5a ranging from 1.7- to 2.3-Å, in the apo form or in complex with various SAM analogues. These structures reveal that Asp243 specifically recognises the base moiety of SAM at the active site. Interestingly, the protein in our structures all displays an extended conformation, quite different from the well-folded conformation of Trm5b from Methanocaldococcus jannaschii reported previously, despite their similar overall architectures. To rule out the possibilities of crystallisation artefacts, we conducted the fluorescence resonance energy transfer (FRET) experiments. The FRET data suggested that PaTrm5a adopts a naturally extended conformation in solution, and therefore the open conformation is a genuine state of PaTrm5a.

  • Organizational Affiliation

    State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510275, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (guanine(37)-N1)-methyltransferase Trm5a352Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: trm5aPYRAB01130PAB2272
Find proteins for Q9V2G1 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V2G1 
Go to UniProtKB:  Q9V2G1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V2G1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.832α = 90
b = 54.324β = 90
c = 129.015γ = 90
Software Package:
Software NamePurpose
CrysalisProdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Guangdong Innovative Research TeamChina2011Y038
Science and Technology Program of GuangzhouChina201504010025
Fundamental Research Funds for the Central UniversitiesChina15lgjc02

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description