Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal
(2006) In Nucleic Acids Research 34(16). p.4449-4457- Abstract
- Hepatitis B virus (HBV) replication is initiated by HBV RT binding to the highly conserved encapsidation signal, epsilon, at the 5' end of the RNA pregenome. Epsilon contains an apical stem-loop, whose residues are either totally conserved or show rare non-disruptive mutations. Here we present the structure of the apical stem-loop based on NOE, RDC and H-1 chemical shift NMR data. The H-1 chemical shifts proved to be crucial to define the loop conformation. The loop sequence 5'-CUGUGC-3' folds into a UGU triloop with a CG closing base pair and a bulged out C and hence forms a pseudo-triloop, a proposed protein recognition motif. In the UGU loop conformations most consistent with experimental data, the guanine nucleobase is located on the... (More)
- Hepatitis B virus (HBV) replication is initiated by HBV RT binding to the highly conserved encapsidation signal, epsilon, at the 5' end of the RNA pregenome. Epsilon contains an apical stem-loop, whose residues are either totally conserved or show rare non-disruptive mutations. Here we present the structure of the apical stem-loop based on NOE, RDC and H-1 chemical shift NMR data. The H-1 chemical shifts proved to be crucial to define the loop conformation. The loop sequence 5'-CUGUGC-3' folds into a UGU triloop with a CG closing base pair and a bulged out C and hence forms a pseudo-triloop, a proposed protein recognition motif. In the UGU loop conformations most consistent with experimental data, the guanine nucleobase is located on the minor groove face and the two uracil bases on the major groove face. The underlying helix is disrupted by a conserved non-paired U bulge. This U bulge adopts multiple conformations, with the nucleobase being located either in the major groove or partially intercalated in the helix from the minor groove side, and bends the helical stem. The pseudo-triloop motif, together with the U bulge, may represent important anchor points for the initial recognition of epsilon by the viral RT. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/387893
- author
- Flodell, Sara ; Petersen, Michael ; Girard, Frederic ; Zdunek, Janusz ; Kidd-Ljunggren, Karin LU ; Schleucher, Jurgen and Wijmenga, Sybren
- organization
- publishing date
- 2006
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Nucleic Acids Research
- volume
- 34
- issue
- 16
- pages
- 4449 - 4457
- publisher
- Oxford University Press
- external identifiers
-
- wos:000241277200019
- pmid:16945960
- scopus:33749986531
- ISSN
- 1362-4962
- DOI
- 10.1093/nar/gkl582
- language
- English
- LU publication?
- yes
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Division of Infection Medicine (SUS) (013008000)
- id
- 383dd0de-bdff-48bd-9676-b498db032b1a (old id 387893)
- date added to LUP
- 2016-04-01 11:42:17
- date last changed
- 2022-04-05 03:41:17
@article{383dd0de-bdff-48bd-9676-b498db032b1a, abstract = {{Hepatitis B virus (HBV) replication is initiated by HBV RT binding to the highly conserved encapsidation signal, epsilon, at the 5' end of the RNA pregenome. Epsilon contains an apical stem-loop, whose residues are either totally conserved or show rare non-disruptive mutations. Here we present the structure of the apical stem-loop based on NOE, RDC and H-1 chemical shift NMR data. The H-1 chemical shifts proved to be crucial to define the loop conformation. The loop sequence 5'-CUGUGC-3' folds into a UGU triloop with a CG closing base pair and a bulged out C and hence forms a pseudo-triloop, a proposed protein recognition motif. In the UGU loop conformations most consistent with experimental data, the guanine nucleobase is located on the minor groove face and the two uracil bases on the major groove face. The underlying helix is disrupted by a conserved non-paired U bulge. This U bulge adopts multiple conformations, with the nucleobase being located either in the major groove or partially intercalated in the helix from the minor groove side, and bends the helical stem. The pseudo-triloop motif, together with the U bulge, may represent important anchor points for the initial recognition of epsilon by the viral RT.}}, author = {{Flodell, Sara and Petersen, Michael and Girard, Frederic and Zdunek, Janusz and Kidd-Ljunggren, Karin and Schleucher, Jurgen and Wijmenga, Sybren}}, issn = {{1362-4962}}, language = {{eng}}, number = {{16}}, pages = {{4449--4457}}, publisher = {{Oxford University Press}}, series = {{Nucleic Acids Research}}, title = {{Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal}}, url = {{http://dx.doi.org/10.1093/nar/gkl582}}, doi = {{10.1093/nar/gkl582}}, volume = {{34}}, year = {{2006}}, }