Hermann Johannes C, Marti-Arbona Ricardo, Fedorov Alexander A, Fedorov Elena, Almo Steven C, Shoichet Brian K, Raushel Frank M
Department of Pharmaceutical Chemistry, University of California, San Francisco, MC 2550 1700 4th Street, San Francisco, California 94158-2330, USA.
Nature. 2007 Aug 16;448(7155):775-9. doi: 10.1038/nature05981. Epub 2007 Jul 1.
With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (10(5) M(-1 )s(-1)). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function.
随着许多基因组被测序，生物学领域面临的一个紧迫挑战是预测基因所编码蛋白质的功能。当蛋白质与其他已知活性的蛋白质无关时，基于生物信息学推断其功能就会出现问题。因此，直接通过研究蛋白质结构来确定其功能将很有帮助。在此，我们通过对接数千种候选代谢物的高能中间形式，预测了来自海栖热袍菌（Thermotoga maritima）的一种活性未知的酶Tm0936的功能。对接命中列表主要由腺嘌呤类似物组成，这些类似物似乎会发生C6-脱氨反应。其中四种，包括5-甲硫基腺苷和S-腺苷高半胱氨酸（SAH），被作为底物进行测试，其中三种具有可观的催化速率常数（10⁵ M⁻¹ s⁻¹）。我们确定了Tm0936与SAH脱氨产物S-肌苷高半胱氨酸形成的复合物的X射线晶体结构，该结构与预测结构非常吻合。脱氨产物可通过海栖热袍菌在一条以前未被描述的SAH降解途径中进一步代谢。基于结构与潜在底物的高能形式进行对接，可能是一种用于注释酶功能的有用工具。
