Amarasinghe G K, De Guzman R N, Turner R B, Summers M F
Howard Hughes Medical Institute, University of Maryland, Baltimore County 21250, USA.
J Mol Biol. 2000 May 26;299(1):145-56. doi: 10.1006/jmbi.2000.3710.
The genome of the human immunodeficiency virus type-1 (HIV-1) contains a stretch of approximately 120 nucleotides known as the psi-site that is essential for RNA packaging during virus assembly. These nucleotides have been proposed to form four stem-loops (SL1-SL4) that have both independent and overlapping functions. Stem-loop SL2 is important for efficient recognition and packaging of the full-length, unspliced viral genome, and also contains the major splice-donor site (SD) for mRNA splicing. We have determined the structure of the 19-residue SL2 oligoribonucleotide by heteronuclear NMR methods. The structure is generally consistent with the most recent of two earlier secondary structure predictions, with residues G1-G2-C3-G4 and C6-U7 forming standard Watson Crick base-pairs with self-complementary residues C16-G17-C18-C19 and A12-G13, respectively. However, residue A15, which is located near the center of the stem, does not form a predicted bulge, and residues A5 and U14 do not form an expected Watson-Crick base-pair. Instead, these residues form a novel A5-U14-A15 base-triple that appears to be stabilized by hydrogen bonds from A15-H61 and -H62 to A5-N1 and U14-O2, respectively; from A5-H61 to U14-O2, and from C16-H42 to U14-O2'. A kink in the backbone allows the aromatic rings of the sequential U14-A15 residues to be approximately co-planar, adopting a stable "platform motif" that is structurally similar to the A-A (adenosine) platforms observed in the P4-P6 ribozyme domain of the Tetrahymena group I intron. Platform motifs generally function in RNA by mediating long-range interactions, and it is therefore possible that the A-U-A base-triple platform mediates long-range interactions that either stabilize the psi-RNA or facilitate splicing and/or packaging. Residue G8 of the G8-G9-U10-G11 tetraloop is stacked above the U7-A12 base-pair, and the remaining tetraloop residues are disordered and available for potential interactions with either other RNA or protein components.
人类免疫缺陷病毒1型（HIV-1）的基因组包含一段约120个核苷酸的区域，称为ψ位点，这对于病毒组装过程中的RNA包装至关重要。这些核苷酸被认为可形成四个茎环（SL1-SL4），它们具有独立和重叠的功能。茎环SL2对于全长未剪接病毒基因组的有效识别和包装很重要，并且还包含用于mRNA剪接的主要剪接供体位点（SD）。我们通过异核核磁共振方法确定了19个残基的SL2寡核糖核苷酸的结构。该结构总体上与两个早期二级结构预测中最新的预测一致，其中残基G1-G2-C3-G4和C6-U7分别与自身互补残基C16-G17-C18-C19和A12-G13形成标准的沃森-克里克碱基对。然而，位于茎中心附近的残基A15并未形成预测的凸起，并且残基A5和U14也未形成预期的沃森-克里克碱基对。相反，这些残基形成了一个新的A5-U14-A15碱基三联体，似乎通过分别从A15-H61和-H62到A5-N1和U14-O2的氢键得以稳定；从A5-H61到U14-O2，以及从C16-H42到U14-O2'。主链中的一个扭结使得连续的U14-A15残基的芳香环大致共面，形成一个稳定的“平台基序”，其结构类似于在嗜热四膜虫I组内含子的P4-P6核酶结构域中观察到的A-A（腺苷）平台。平台基序通常在RNA中通过介导长程相互作用发挥作用，因此A-U-A碱基三联体平台可能介导长程相互作用，从而稳定ψ-RNA或促进剪接和/或包装。G8-G9-U10-G11四环的残基G8堆积在U7-A12碱基对上方，其余四环残基无序，可用于与其他RNA或蛋白质成分进行潜在的相互作用。
