Wilson Timothy J, McLeod Aileen C, Lilley David M J
Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, UK.
EMBO J. 2007 May 16;26(10):2489-500. doi: 10.1038/sj.emboj.7601698. Epub 2007 Apr 26.
A guanine (G638) within the substrate loop of the VS ribozyme plays a critical role in the cleavage reaction. Replacement by any other nucleotide results in severe impairment of cleavage, yet folding of the substrate is not perturbed, and the variant substrates bind the ribozyme with similar affinity, acting as competitive inhibitors. Functional group substitution shows that the imino proton on the N1 is critical, suggesting a possible role in general acid-base catalysis, and this in accord with the pH dependence of the reaction rate for the natural and modified substrates. We propose a chemical mechanism for the ribozyme that involves general acid-base catalysis by the combination of the nucleobases of guanine 638 and adenine 756. This is closely similar to the probable mechanism of the hairpin ribozyme, and the active site arrangements for the two ribozymes appear topologically equivalent. This has probably arisen by convergent evolution.
VS核酶底物环内的鸟嘌呤（G638）在切割反应中起关键作用。被任何其他核苷酸取代都会导致切割严重受损，但底物的折叠不受干扰，并且变体底物以相似的亲和力结合核酶，起到竞争性抑制剂的作用。官能团取代表明N1上的亚氨基质子至关重要，这表明其在一般酸碱催化中可能发挥作用，这与天然和修饰底物反应速率的pH依赖性一致。我们提出了一种核酶的化学机制，该机制涉及鸟嘌呤638和腺嘌呤756的核碱基组合进行的一般酸碱催化。这与发夹核酶的可能机制非常相似，并且两种核酶的活性位点排列在拓扑上似乎是等效的。这可能是由趋同进化产生的。
