2G1G

Solution structure of the anticodon loop of S. Pombe tRNAi including the naturally occurring N6-threonyl adenine

  • Classification: RNA
  • Mutation(s): No 

  • Deposited: 2006-02-14 Released: 2006-06-20 
  • Deposition Author(s): Lescrinier, E.

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 73 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The naturally occurring N6-threonyl adenine in anticodon loop of Schizosaccharomyces pombe tRNAi causes formation of a unique U-turn motif

Lescrinier, E.Nauwelaerts, K.Zanier, K.Poesen, K.Sattler, M.Herdewijn, P.

(2006) Nucleic Acids Res 34: 2878-2886

  • DOI: 10.1093/nar/gkl081
  • Primary Citation of Related Structures:  
    2G1G

  • PubMed Abstract: 
  • Modified nucleosides play an important role in structure and function of tRNA. We have determined the solution structure of the anticodon stem-loop (ASL) of initiator tRNA of Schizosaccharomyces pombe. The incorporation of N6-threonylcarbamoyladenosine at the position 3' to the anticodon triplet (t6A37) results in the formation of a U-turn motif and enhances stacking interactions within the loop and stem regions (i ...

    Modified nucleosides play an important role in structure and function of tRNA. We have determined the solution structure of the anticodon stem-loop (ASL) of initiator tRNA of Schizosaccharomyces pombe. The incorporation of N6-threonylcarbamoyladenosine at the position 3' to the anticodon triplet (t6A37) results in the formation of a U-turn motif and enhances stacking interactions within the loop and stem regions (i.e. between A35 and t6A37) by bulging out U36. This conformation was not observed in a crystal structure of tRNAi including the same modification in its anticodon loop, nor in the solution structure of the unmodified ASL. A t6A modification also occurs in the well studied anti-stem-loop of lys-tRNA(UUU). A comparison of this stem-loop with our structure demonstrates different effects of the modification depending on the loop sequence.


    Organizational Affiliation

    Laboratory of Medicinal Chemistry, Rega Institute for Medical Research BioMacs, K.U.Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium.



Macromolecules

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-R(*AP*CP*GP*GP*GP*CP*UP*CP*AP*UP*(T6A)P*AP*CP*CP*CP*GP*U)-3'A 17N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 73 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 2G1G Olderado

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2006-02-14 
  • Released Date: 2006-06-20 
  • Deposition Author(s): Lescrinier, E.

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-20
    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: 2022-03-09
    Changes: Data collection, Database references, Derived calculations