Crystal structure of scTrm10(84)-SAH complex

Experimental Data Snapshot

  • Resolution: 1.76 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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Crystal structure of tRNA m1G9 methyltransferase Trm10: insight into the catalytic mechanism and recognition of tRNA substrate.

Shao, Z.Yan, W.Peng, J.Zuo, X.Zou, Y.Li, F.Gong, D.Ma, R.Wu, J.Shi, Y.Zhang, Z.Teng, M.Li, X.Gong, Q.

(2014) Nucleic Acids Res 42: 509-525

  • DOI: https://doi.org/10.1093/nar/gkt869
  • Primary Citation of Related Structures:  
    4JWF, 4JWG, 4JWH, 4JWJ

  • PubMed Abstract: 

    Transfer RNA (tRNA) methylation is necessary for the proper biological function of tRNA. The N(1) methylation of guanine at Position 9 (m(1)G9) of tRNA, which is widely identified in eukaryotes and archaea, was found to be catalyzed by the Trm10 family of methyltransferases (MTases). Here, we report the first crystal structures of the tRNA MTase spTrm10 from Schizosaccharomyces pombe in the presence and absence of its methyl donor product S-adenosyl-homocysteine (SAH) and its ortholog scTrm10 from Saccharomyces cerevisiae in complex with SAH. Our crystal structures indicated that the MTase domain (the catalytic domain) of the Trm10 family displays a typical SpoU-TrmD (SPOUT) fold. Furthermore, small angle X-ray scattering analysis reveals that Trm10 behaves as a monomer in solution, whereas other members of the SPOUT superfamily all function as homodimers. We also performed tRNA MTase assays and isothermal titration calorimetry experiments to investigate the catalytic mechanism of Trm10 in vitro. In combination with mutational analysis and electrophoretic mobility shift assays, our results provide insights into the substrate tRNA recognition mechanism of Trm10 family MTases.

  • Organizational Affiliation

    Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China and X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60349, USA.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (guanine(9)-N1)-methyltransferase
A, B
202Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: O0926TRM10YOL093W
Find proteins for Q12400 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12400 
Go to UniProtKB:  Q12400
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12400
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SAH

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
C14 H20 N6 O5 S
Query on TRS

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
K [auth B]
C4 H12 N O3
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
F [auth A],
G [auth A],
I [auth B]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.76 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.583α = 90
b = 58.861β = 131.13
c = 99.767γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-16
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-11-08
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description