1VS3

Crystal Structure of the tRNA Pseudouridine Synthase TruA From Thermus thermophilus HB8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of tRNA pseudouridine synthase TruA from Thermus thermophilus HB8.

Dong, X.Bessho, Y.Shibata, R.Nishimoto, M.Shirouzu, M.Kuramitsu, S.Yokoyama, S.

(2006) RNA Biol 3: 115-122

  • DOI: 10.4161/rna.3.3.3286
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The pseudouridine synthase (Psi synthase) TruA catalyzes the conversion of uridine to pseudouridine at positions 38, 39 and/or 40 in the anticodon stem-loop (ASL) of tRNA. We have determined the crystal structure of TruA from Thermus thermophilus HB8 ...

    The pseudouridine synthase (Psi synthase) TruA catalyzes the conversion of uridine to pseudouridine at positions 38, 39 and/or 40 in the anticodon stem-loop (ASL) of tRNA. We have determined the crystal structure of TruA from Thermus thermophilus HB8 at 2.25 A resolution. TruA and the other (Psi synthases have a completely conserved active site aspartate, which suggests that the members of this enzyme family share a common catalytic mechanism. The T. thermophilus TruA structure reveals the remarkably flexible structural features in the tRNA-binding cleft, which may be responsible for the primary tRNA interaction. In addition, the charged residues occupying the intermediate positions in the cleft may lead the tRNA to the active site for catalysis. Based on the TruB-tRNA complex structure, the T. thermophilus TruA structure reveals that the tRNA probably makes the melting base pairs move into the cleft, and suggests that a conformational change of the substrate tRNA is necessary to facilitate access to the active site aspartate residue, deep within the cleft.


    Organizational Affiliation

    RIKEN Genomic Sciences Center, Tsurumi, Yokohama, Japan.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA pseudouridine synthase AA, B249Thermus thermophilus HB8Mutation(s): 0 
Gene Names: truATTHA1631
EC: 5.4.99.12
Find proteins for Q5SHU9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SHU9 
Go to UniProtKB:  Q5SHU9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.53α = 90
b = 91.53β = 90
c = 163.99γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2019-11-06
    Changes: Data collection, Database references