2RVO

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

Summary for 2RVO

• Entry DOI: 10.2210/pdb2rvo/pdb
• NMR Information: BMRB: 11607
• Descriptor: RNA (34-MER) (1 entity in total)
• Functional Keywords: rna, line, retrotransposon
• Biological source: Danio rerio (zebrafish)
• Total number of polymer chains: 1
• Total formula weight: 10859.50

Authors

Otsu, M.,Norose, N.,Arai, N.,Terao, R.,Kajikawa, M.,Okada, N.,Kawai, G. (deposition date: 2016-02-03, release date: 2017-02-08, Last modification date: 2024-05-15)

Primary citation

Otsu, M.,Kajikawa, M.,Okada, N.,Kawai, G.
Solution structure of a reverse transcriptase recognition site of a LINE RNA from zebrafish.
J. Biochem., 162:279-285, 2017

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 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.

PubMed: 28431120
DOI: 10.1093/jb/mvx026

Experimental method

SOLUTION NMR