2NRE

Crystal structure of pseudoudirinde synthase TruA in complex with leucyl tRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.molcel.2007.02.027
  • Primary Citation of Related Structures:  2NQP, 2NR0

  • 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 highl ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
tRNA pseudouridine synthase A
A
270Escherichia coli (strain K12)Gene Names: truA (asuC, hisT, leuK)
EC: 5.4.99.12
Find proteins for P07649 (Escherichia coli (strain K12))
Go to UniProtKB:  P07649
Entity ID: 1
MoleculeChainsLengthOrganism
leucyl tRNAF87N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
F
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4 Å
  • R-Value Free: 0.357 
  • R-Value Work: 0.259 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 80.355α = 90.00
b = 80.355β = 90.00
c = 205.373γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-11-01 
  • Released Date: 2007-05-15 
  • Deposition Author(s): Hur, S., Stroud, R.M.

Revision History 

  • Version 1.0: 2007-05-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance