Nucleic Acids Research Advance Access originally published online on August 31, 2006
Nucleic Acids Research 2006 34(16):4449-4457; doi:10.1093/nar/gkl582
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Nucleic Acids Research, 2006, Vol. 34, No. 16 4449-4457
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
Solution structure of the apical stem–loop of the human hepatitis B virus encapsidation signal
Department of Medical Biochemistry and Biophysics, Umeå University 901 87 Umeå, Sweden 1 Biophysical Chemistry, University of Nijmegen, Toernooiveld 1 6225ED Nijmegen, The Netherlands 2 Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark 5230 Odense M, Denmark 3 Department of Infectious Diseases, Lund University 221 85 Lund, Sweden
*To whom correspondence should be addressed. Tel: +31 24 3653384/2678; Fax: +31 24 3652112; Email: s.wijmenga{at}nmr.ru.nl
Received June 2, 2006. Revised July 21, 2006. Accepted July 26, 2006.
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 1H chemical shift NMR data. The 1H 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.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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