5C0O

m1A58 tRNA methyltransferase mutant - Y78A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.235 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The m1A58 modification in eubacterial tRNA: An overview of tRNA recognition and mechanism of catalysis by TrmI.

Degut, C.Ponchon, L.Folly-Klan, M.Barraud, P.Tisne, C.

(2016) Biophys Chem 210: 27-34

  • DOI: https://doi.org/10.1016/j.bpc.2015.06.012
  • Primary Citation of Related Structures:  
    5C0O, 5C1I

  • PubMed Abstract: 

    The enzymes of the TrmI family catalyze the formation of the m(1)A58 modification in tRNA. We previously solved the crystal structure of the Thermus thermophilus enzyme and conducted a biophysical study to characterize the interaction between TrmI and tRNA. TrmI enzymes are active as a tetramer and up to two tRNAs can bind to TrmI simultaneously. In this paper, we present the structures of two TrmI mutants (D170A and Y78A). These residues are conserved in the active site of TrmIs and their mutations result in a dramatic alteration of TrmI activity. Both structures of TrmI mutants revealed the flexibility of the N-terminal domain that is probably important to bind tRNA. The structure of TrmI Y78A catalytic domain is unmodified regarding the binding of the SAM co-factor and the conformation of residues potentially interacting with the substrate adenine. This structure reinforces the previously proposed role of Y78, i.e. stabilize the conformation of the A58 ribose needed to hold the adenosine in the active site. The structure of the D170A mutant shows a flexible active site with one loop occupying in part the place of the co-factor and the second loop moving at the entrance to the active site. This structure and recent data confirms the central role of D170 residue binding the amino moiety of SAM and the exocyclic amino group of adenine. Possible mechanisms for methyl transfer are then discussed.


  • Organizational Affiliation

    Laboratoire de Cristallographie et RMN biologiques, CNRS, Université Paris Descartes, Paris Sorbonne Cité, 4 avenue de l'Observatoire, 75006, Paris.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA (adenine(58)-N(1))-methyltransferase TrmIA [auth E],
B [auth F],
C [auth G],
D [auth H]
255Thermus thermophilus HB27Mutation(s): 1 
Gene Names: trmITT_C0244
EC: 2.1.1.220
UniProt
Find proteins for Q8GBB2 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q8GBB2 
Go to UniProtKB:  Q8GBB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GBB2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.235 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.54α = 90
b = 79.86β = 90
c = 184γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2016-03-02
    Changes: Database references
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description