2VDU

Structure of trm8-trm82, THE YEAST TRNA m7G methylation complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the Yeast tRNA M7G Methylation Complex.

Leulliot, N.Chaillet, M.Durand, D.Ulryck, N.Blondeau, K.Van Tilbeurgh, H.

(2008) Structure 16: 52

  • DOI: https://doi.org/10.1016/j.str.2007.10.025
  • Primary Citation of Related Structures:  
    2VDU, 2VDV

  • PubMed Abstract: 

    Loss of N7-methylguanosine (m7G) modification is involved in the recently discovered rapid tRNA degradation pathway. In yeast, this modification is catalyzed by the heterodimeric complex composed of a catalytic subunit Trm8 and a noncatalytic subunit Trm82. We have solved the crystal structure of Trm8 alone and in complex with Trm82. Trm8 undergoes subtle conformational changes upon Trm82 binding which explains the requirement of Trm82 for activity. Cocrystallization with the S-adenosyl-methionine methyl donor defines the putative catalytic site and a guanine binding pocket. Small-angle X-ray scattering in solution of the Trm8-Trm82 heterodimer in complex with tRNA(Phe) has enabled us to propose a low-resolution structure of the ternary complex which defines the tRNA binding mode of Trm8-Trm82 and the structural elements contributing to specificity.


  • Organizational Affiliation

    Institut de Biochimie et de Biophysique Moléculaire et Cellulaire, UMR8619, Bât 430, Université de Paris-Sud, IFR115, Orsay Cedex, France. nicolas.leulliot@u-psud.fr


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRNA (GUANINE-N(7)-)-METHYLTRANSFERASE-ASSOCIATED WD REPEAT PROTEIN TRM82A [auth B],
B [auth D]
450Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q03774 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03774 
Go to UniProtKB:  Q03774
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03774
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TRNA (GUANINE-N(7)-)-METHYLTRANSFERASEC [auth E],
D [auth F]
254Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.1.1.33
UniProt
Find proteins for Q12009 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12009 
Go to UniProtKB:  Q12009
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12009
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.376α = 90
b = 107.676β = 91.53
c = 127.749γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance