Sigel Roland K O, Sashital Dipali G, Abramovitz Dana L, Palmer Arthur G, Butcher Samuel E, Pyle Anna Marie
Department of Chemistry, Winterthurerstrasse 190, University of Zürich, CH-8057 Zürich, Switzerland.
Nat Struct Mol Biol. 2004 Feb;11(2):187-92. doi: 10.1038/nsmb717. Epub 2004 Jan 25.
Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5 gamma in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg(2+) binding to a minor groove shelf in the D5 bulge. Another distinct metal ion-binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site.
结构域5（D5）是II组内含子核酶的核心部分。这个高度保守的发夹结构的许多碱基和骨架取代基参与催化作用，并且对于与其他内含子结构域的结合至关重要。我们报道了来自II组内含子ai5γ的34个核苷酸的D5发夹在不存在和存在二价金属离子情况下的溶液结构。D5的凸起区域呈现出一种新颖的折叠方式，其中G26采取顺式构象并向下翻转进入螺旋1的大沟，靠近催化性AGC三联体的大沟面。G26附近的骨架发生扭结，使相邻A-U对的碱基平面暴露于溶剂中，并导致凸起处的碱基进行插入堆积。金属离子滴定显示Mg(2+)与D5凸起处的一个小沟平台有强烈结合。沿着催化三联体的小沟侧观察到另一个独特的金属离子结合位点，其方式与核酶活性位点中的金属离子结合一致。
