Blount Kenneth F, Uhlenbeck Olke C
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, USA.
Annu Rev Biophys Biomol Struct. 2005;34:415-40. doi: 10.1146/annurev.biophys.34.122004.184428.
A powerful approach to understanding protein enzyme catalysis is to examine the structural context of essential amino acid side chains whose deletion or modification negatively impacts catalysis. In principle, this approach can be even more powerful for RNA enzymes, given the wide variety and subtlety of functionally modified nucleotides now available. Numerous recent success stories confirm the utility of this approach to understanding ribozyme function. An anomaly, however, is the hammerhead ribozyme, for which the structural and functional data do not agree well, preventing a unifying view of its catalytic mechanism from emerging. To delineate the hammerhead structure-function comparison, we have evaluated and distilled the large body of biochemical data into a consensus set of functional groups unambiguously required for hammerhead catalysis. By examining the context of these functional groups within available structures, we have established a concise set of disagreements between the structural and functional data. The number and relative distribution of these inconsistencies throughout the hammerhead reaffirms that an extensive conformational rearrangement from the fold observed in the crystal structure must be necessary for cleavage to occur. The nature and energetic driving force of this conformational isomerization are discussed.
理解蛋白质酶催化作用的一种有效方法是研究必需氨基酸侧链的结构背景，这些侧链的缺失或修饰会对催化作用产生负面影响。原则上，鉴于现在可用的功能修饰核苷酸种类繁多且微妙，这种方法对RNA酶可能更有效。最近众多成功案例证实了这种方法在理解核酶功能方面的实用性。然而，一个反常的例子是锤头状核酶，其结构和功能数据不太一致，阻碍了对其催化机制形成统一的观点。为了阐明锤头状核酶的结构与功能的比较，我们评估并提炼了大量生化数据，形成了一组锤头状核酶催化作用明确所需的功能基团的共识。通过研究这些功能基团在现有结构中的背景，我们确定了结构数据和功能数据之间一组简洁的分歧。这些不一致在整个锤头状核酶中的数量和相对分布再次证明，从晶体结构中观察到的折叠进行广泛的构象重排对于切割的发生是必要的。本文讨论了这种构象异构化的性质和能量驱动力。
