3LGA

Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-homocysteine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase.

Guelorget, A.Roovers, M.Guerineau, V.Barbey, C.Li, X.Golinelli-Pimpaneau, B.

(2010) Nucleic Acids Res 38: 6206-6218

  • DOI: https://doi.org/10.1093/nar/gkq381
  • Primary Citation of Related Structures:  
    3LGA, 3LHD, 3MB5

  • PubMed Abstract: 

    The S-adenosyl-L-methionine dependent methylation of adenine 58 in the T-loop of tRNAs is essential for cell growth in yeast or for adaptation to high temperatures in thermophilic organisms. In contrast to bacterial and eukaryotic tRNA m(1)A58 methyltransferases that are site-specific, the homologous archaeal enzyme from Pyrococcus abyssi catalyzes the formation of m(1)A also at the adjacent position 57, m(1)A57 being a precursor of 1-methylinosine. We report here the crystal structure of P. abyssi tRNA m(1)A57/58 methyltransferase ((Pab)TrmI), in complex with S-adenosyl-L-methionine or S-adenosyl-L-homocysteine in three different space groups. The fold of the monomer and the tetrameric architecture are similar to those of the bacterial enzymes. However, the inter-monomer contacts exhibit unique features. In particular, four disulfide bonds contribute to the hyperthermostability of the archaeal enzyme since their mutation lowers the melting temperature by 16.5°C. His78 in conserved motif X, which is present only in TrmIs from the Thermococcocales order, lies near the active site and displays two alternative conformations. Mutagenesis indicates His78 is important for catalytic efficiency of (Pab)TrmI. When A59 is absent in tRNA(Asp), only A57 is modified. Identification of the methylated positions in tRNAAsp by mass spectrometry confirms that (Pab)TrmI methylates the first adenine of an AA sequence.


  • Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 1 avenue de la Terrasse, 91198 Gif-sur-Yvette, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SAM-dependent methyltransferase
A, B, C, D
253Pyrococcus abyssi GE5Mutation(s): 0 
Gene Names: PAB0283
EC: 2.1.1.36 (PDB Primary Data), 2.1.1.219 (UniProt)
UniProt
Find proteins for Q9V1J7 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9V1J7 
Go to UniProtKB:  Q9V1J7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9V1J7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.216α = 90
b = 138.216β = 90
c = 121.119γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata 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: 2010-06-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Structure summary