Solution structure of the apical stem-loop of the human hepatitis B virus encapsidation signal

被引:40
作者
Flodell, Sara
Petersen, Michael
Girard, Frederic
Zdunek, Janusz
Kidd-Ljunggren, Karin
Schleucher, Jurgen
Wijmenga, Sybren [1 ]
机构
[1] Umea Univ, Dept Med Biochem & Biophys, S-90187 Umea, Sweden
[2] Univ Nijmegen, NL-6225 ED Nijmegen, Netherlands
[3] Odense Univ, Nucle Acid Ctr, Dept Phys & Chem, DK-5230 Odense M, Denmark
[4] Lund Univ, Dept Infect Dis, S-22185 Lund, Sweden
关键词
RESIDUAL DIPOLAR COUPLINGS; IRON-RESPONSIVE ELEMENT; REPLICATION INITIATION COMPLEX; RIBOSOME ENTRY SITE; REVERSE-TRANSCRIPTASE; IN-VITRO; RNA ENCAPSIDATION; MOLECULAR-DYNAMICS; NUCLEIC-ACIDS; DNA-SYNTHESIS;
D O I
10.1093/nar/gkl582
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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.
引用
收藏
页码:4449 / 4457
页数:9
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