Computational Characterization of Substrate Binding and Catalysis in S-Adenosylhomocysteine Hydrolase
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- 作者：Yongbo Hu ; Xiaoda Yang ; Daniel H. Yin ; Janaki Mahadevan ; Krzysztof Kuczera ; Richard L. Schowen ; and Ronald T. Borchardt
- 刊名：Biochemistry
- 出版年：2001
- 出版时间：December 18, 2001
- 年：2001
- 卷：40
- 期：50
- 页码：15143 - 15152
- 全文大小：324K
- 年卷期：v.40,no.50(December 18, 2001)
- ISSN：1520-4995
文摘
S-Adenosylhomocysteine (AdoHcy) hydrolase catalyzes the reversible hydrolysis of AdoHcyto adenosine (Ado) and homocysteine (Hcy), playing an essential role in modulating the cellular Hcylevels and regulating activities of a host of methyltransferases in eukaryotic cells. This enzyme exists inan open conformation (active site unoccupied) and a closed conformation (active site occupied with substrateor inhibitor) [Turner, M. A., Yang, X., Yin, D., Kuczera, K., Borchardt, R. T., and Howell, P. L. (2000)Cell Biochem. Biophys. 33, 101-125]. To investigate the binding of natural substrates during catalysis,the computational docking program AutoDock (with confirming calculations using CHARMM) was usedto predict the binding modes of various substrates or inhibitors with the closed and open forms of AdoHcyhydrolase. The results have revealed that the interaction between a substrate and the open form of theenzyme is nonspecific, whereas the binding of the substrate in the closed form is highly specific with theadenine moiety of a substrate as the main recognition factor. Residues Thr57, Glu59, Glu156, Gln181,Lys186, Asp190, Met351, and His35 are involved in substrate binding, which is consistent with the crystalstructure. His55 in the docked model appears to participate in the elimination of water from Ado throughthe interaction with the 5'-OH group of Ado. In the same reaction, Asp131 removes a proton from the 4'position of the substrate after the oxidation-reduction reaction in the enzyme. To identify the residuesthat bind the Hcy moiety, AdoHcy was docked to the closed form of AdoHcy hydrolase. The Hcy tail ispredicted to interact with His55, Cys79, Asn80, Asp131, Asp134, and Leu344 in a strained conformation,which may lower the reaction barrier and enhance the catalysis rate.