2RVO

Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 11 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish.

Otsu, M.Kajikawa, M.Okada, N.Kawai, G.

(2017) J. Biochem. 162: 279-285

  • DOI: 10.1093/jb/mvx026

  • PubMed Abstract: 
  • Long interspersed nuclear element (LINE) is known to be transposed by reverse transcription using its RNA transcript. Recognition of the 3' stem-loop of LINE RNA by its reverse transcriptase (RT) is an important step of the retrotransposition. Our pr ...

    Long interspersed nuclear element (LINE) is known to be transposed by reverse transcription using its RNA transcript. Recognition of the 3' stem-loop of LINE RNA by its reverse transcriptase (RT) is an important step of the retrotransposition. Our previous study revealed that the second G residue (G8) in the GGAUA loop of a 17mer LINE RNA from eel, UnaL2-17, is recognized by its RT and the U residue (U10) in the same loop is required to maintain the loop structure (Baba S, Kajikawa M, Okada N, Kawai G. Solution structure of an RNA stem-loop derived from the 3' conserved region of eel LINE UnaL2. RNA 2004;10:1380-1387). ZfL2-2, a LINE from zebrafish, has the same 3' stem-loop with UnaL2 and ZfL2-1 has similar but distinct 3' stem-loop with an insertion which can form an additional stem-loop. Here, we determined the solution structure of the 34mer RT recognition site of the LINE RNA (ZfL2-1-34). It was found that ZfL2-1-34 forms a hairpin with an internal loop, the tertiary structure of which is superimposed with that of ZfL2-2. It is noted that A10 and the inserted stem-loop, starting with A12, in ZfL2-1-34 located at the positions corresponding to those of G8 and U10, respectively, in UnaL2-17. These results strongly suggest that the two LINEs share the similar recognition mechanism and the A10 in ZfL2-1-34 is the determinant recognized by its RT.


    Organizational Affiliation

    Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
RNA (34-MER)A34Danio rerio
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 11 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Database references