structural and mutational analysis of tRNA-intron splicing endonuclease from Thermoplasma acidophilum DSM1728

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

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Structural and Mutational Analysis of tRNA Intron-Splicing Endonuclease from Thermoplasma acidophilum DSM 1728: Catalytic Mechanism of tRNA Intron-Splicing Endonucleases

Kim, Y.K.Mizutani, K.Rhee, K.H.Nam, K.H.Lee, W.H.Lee, E.H.Kim, E.E.Park, S.Y.Hwang, K.Y.

(2007) J Bacteriol 189: 8339-8346

  • DOI: https://doi.org/10.1128/JB.00713-07
  • Primary Citation of Related Structures:  
    2OHC, 2OHE

  • PubMed Abstract: 

    In archaea, RNA endonucleases that act specifically on RNA with bulge-helix-bulge motifs play the main role in the recognition and excision of introns, while the eukaryal enzymes use a measuring mechanism to determine the positions of the universally positioned splice sites relative to the conserved domain of pre-tRNA. Two crystallographic structures of tRNA intron-splicing endonuclease from Thermoplasma acidophilum DSM 1728 (EndA(Ta)) have been solved to 2.5-A and 2.7-A resolution by molecular replacement, using the 2.7-A resolution data as the initial model and the single-wavelength anomalous-dispersion phasing method using selenomethionine as anomalous signals, respectively. The models show that EndA(Ta) is a homodimer and that it has overall folding similar to that of other archaeal tRNA endonucleases. From structural and mutational analyses of H236A, Y229F, and K265I in vitro, we have demonstrated that they play critical roles in recognizing the splice site and in cleaving the pre-tRNA substrate.

  • Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA-splicing endonuclease
A, B
289Thermoplasma acidophilum DSM 1728Mutation(s): 0 
Gene Names: endA
Find proteins for Q9HIY5 (Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165))
Explore Q9HIY5 
Go to UniProtKB:  Q9HIY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HIY5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.17α = 90
b = 57.17β = 90
c = 459.91γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Source and taxonomy, Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description