Pyrococcus abyssi methyltransferase PaTrm5a bound by SAH and cognate tRNA

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 

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Structural insight into the methyltransfer mechanism of the bifunctional Trm5.

Wang, C.Jia, Q.Zeng, J.Chen, R.Xie, W.

(2017) Sci Adv 3: e1700195-e1700195

  • DOI: https://doi.org/10.1126/sciadv.1700195
  • Primary Citation of Related Structures:  
    5WT1, 5WT3

  • PubMed Abstract: 

    The wyosine derivatives present at position 37 in transfer RNAs (tRNAs) are critical for reading frame maintenance. The methyltransferase Trm5a from Pyrococcus abyssi (PaTrm5a) plays a key role in this hypermodification process in generating m 1 G37 and imG2, two products of the wyosine biosynthetic pathway, through two methyl transfers to distinct substrates, but the mechanism is currently unknown. We report two cocrystal structures of PaTrm5a in complex with tRNA Phe and reveal the structural basis for substrate recognition, which was supported by in vitro activity assays. The crystal structures showed that the D1 domain of the enzyme undergoes large conformational changes upon the binding of tRNA. The deletion of this domain greatly reduces the affinity and activity of PaTrm5a toward its RNA substrate, indicating that the enzyme recognizes the overall shape of tRNA. Using the small-angle x-ray scattering technique and crystallographic analysis, we discovered that PaTrm5a adopts distinct open conformations before and after the binding of tRNA. Last, through structure comparison with its ortholog Methanococcus jannaschii Trm5b (MjTrm5b), we propose a reaction mechanism for the double methylation capability of this unique enzyme.

  • Organizational Affiliation

    Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, 135 West Xingang Rd., 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 Trm5aA,
C [auth B]
333Pyrococcus 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
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (76-MER)B [auth C],
D [auth F]
76Pyrococcus abyssi GE5
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.249 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.096α = 90
b = 57.017β = 101.53
c = 115.807γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description