2KHY

Specifier Domain of B. subtilis tyrS T box leader RNA

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2009-04-14 Released: 2010-02-16 
  • Deposition Author(s): Wang, J., Henkin, T.M.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA.

Wang, J., Henkin, T.M., Nikonowicz, E.P.

(2010) Nucleic Acids Res 38: 3388-3398

  • DOI: 10.1093/nar/gkq020
  • Primary Citation of Related Structures:  
    2KHY

  • PubMed Abstract: 

    • Gram-positive bacteria utilize a tRNA-responsive transcription antitermination mechanism, designated the T box system, to regulate expression of many amino acid biosynthetic and aminoacyl-tRNA synthetase genes. The RNA transcripts of genes controlled by this mechanism contain 5' untranslated regions, or leader RNAs, that specifically bind cognate tRNA molecules through pairing of nucleotides in the tRNA anticodon loop with nucleotides in the Specifier Loop domain of the leader RNA ...

    Gram-positive bacteria utilize a tRNA-responsive transcription antitermination mechanism, designated the T box system, to regulate expression of many amino acid biosynthetic and aminoacyl-tRNA synthetase genes. The RNA transcripts of genes controlled by this mechanism contain 5' untranslated regions, or leader RNAs, that specifically bind cognate tRNA molecules through pairing of nucleotides in the tRNA anticodon loop with nucleotides in the Specifier Loop domain of the leader RNA. We have determined the solution structure of the Specifier Loop domain of the tyrS leader RNA from Bacillus subtilis. Fifty percent of the nucleotides in the Specifier Loop domain adopt a loop E motif. The Specifier Sequence nucleotides, which pair with the tRNA anticodon, stack with their Watson-Crick edges rotated toward the minor groove and exhibit only modest flexibility. We also show that a Specifier Loop domain mutation that impairs the function of the B. subtilis glyQS T box RNA disrupts the tyrS loop E motif. Our results suggest a mechanism for tRNA-Specifier Loop binding in which the phosphate backbone kink created by the loop E motif causes the Specifier Sequence bases to rotate toward the minor groove, which increases accessibility for pairing with bases in the anticodon loop of tRNA.

    Related Citations: 
    • Specificity of tRNA-mRNA interactions in Bacillus subtilis tyrS antitermination.
      Grundy, F.J., Hodil, S.E., Rollins, S.M., Henkin, T.M.
      (1997) J Bacteriol 179: 2587
    Organizational Affiliation: 

    Department of Biochemistry and Cell Biology, Rice University, Houston, TX 77251-1892, USA.



Macromolecules
Find similar nucleic acids by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (38-MER)A 38N/A
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the least restraint violations 
  • OLDERADO: 2KHY Olderado

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-04-14 
  • Released Date: 2010-02-16 
    • Deposition Author(s): Wang, J., Henkin, T.M.

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations