| Abstract
| - The cytidine deaminase substrate analog inhibitor 3-deazacytidinebinds with its 4-amino groupinserted into a site previously identified as a probable binding sitefor the leaving ammonia group. Bindingto this site shifts the pyrimidine ring significantly further from theactivated water molecule than theposition it occupies in either of two complexes with compounds capableof hydrogen bonding at the3-position of the ring [Xiang et al. (1995) Biochemistry34, 4516−4523]. Difference Fourier mapsbetweenthe deazacytidine, dihydrozebularine, and zebularine−hydrateinhibitor complexes suggest that the ringitself moves successively toward the activated water, leaving the aminogroup behind in this site as thesubstrate complex approaches the transition state. They alsoreveal systematic changes in a single zinc−sulfur bond distance. These correlate with chemical changesexpected as the substrate approaches thetetrahedral transition state, in which the zinc-activated hydroxylgroup develops maximal negative chargeand forms a short hydrogen bond to the neighboring carboxylate group ofGlu 104. Empirical bondvalence relationships suggest that the Zn−Sγ132bond functions throughout the reaction as a “valencebuffer” that accommodates changing negative charge on the hydroxylgroup. Similar structural featuresin alcohol dehydrogenase suggest that analogous mechanisms may be ageneral feature of catalysis byzinc enzymes.
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