Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA

Experimental Data Snapshot

  • Resolution: 3.90 Å
  • R-Value Free: 0.350 
  • R-Value Work: 0.298 

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How U38, 39, and 40 of Many tRNAs Become the Targets for Pseudouridylation by TruA.

Hur, S.Stroud, R.M.

(2007) Mol Cell 26: 189-203

  • DOI: https://doi.org/10.1016/j.molcel.2007.02.027
  • Primary Citation of Related Structures:  
    2NQP, 2NR0, 2NRE

  • PubMed Abstract: 

    Translational accuracy and efficiency depend upon modification of uridines in the tRNA anticodon stem loop (ASL) by a highly conserved pseudouridine synthase TruA. TruA specifically modifies uridines at positions 38, 39, and/or 40 of tRNAs with highly divergent sequences and structures through a poorly characterized mechanism that differs from previously studied RNA-modifying enzymes. The molecular basis for the site and substrate "promiscuity" was studied by determining the crystal structures of E. coli TruA in complex with two different leucyl tRNAs in conjunction with functional assays and computer simulation. The structures capture three stages of the TruA*tRNA reaction, revealing the mechanism by which TruA selects the target site. We propose that TruA utilizes the intrinsic flexibility of the ASL for site promiscuity and also to select against intrinsically stable tRNAs to avoid their overstabilization through pseudouridylation, thereby maintaining the balance between the flexibility and stability required for its biological function.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
tRNA pseudouridine synthase AE [auth A],
F [auth B],
G [auth C],
H [auth D]
270Escherichia coli K-12Mutation(s): 0 
Gene Names: truA
Find proteins for P07649 (Escherichia coli (strain K12))
Explore P07649 
Go to UniProtKB:  P07649
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07649
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
leucyl tRNAA [auth E],
B [auth F],
C [auth G],
D [auth H]
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.90 Å
  • R-Value Free: 0.350 
  • R-Value Work: 0.298 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.033α = 90
b = 149.292β = 90
c = 291.991γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Refinement description