DEAMINASE COMPLEXED TO 3-DEAZACYTIDINE - A VALENCE BUFFER IN ZINC ENZYME CATALYSIS

The cytidine deaminase substrate analog inhibitor 3-deazacytidine bind s with its 4-amino group inserted into a site previously identified as a probable binding site for the leaving ammonia group. Binding to thi s site shifts the pyrimidine ring significantly further from the activ ated water molecule than the position it occupies in either of two com plexes with compounds capable of hydrogen bonding at the 3-position of the ring [Xiang et al. (1995) Biochemistry 34, 4516-4523]. Difference Fourier maps between the deazacytidine, dihydrozebularine, and zebula rine-hydrate inhibitor complexes suggest that the ring itself moves su ccessively toward the activated water, leaving the amino group behind in this site as the substrate complex approaches the transition state. They also reveal systematic changes in a single zinc-sulfur bond dist ance. These correlate with chemical changes expected as the substrate approaches the tetrahedral transition state, in which the zinc-activat ed hydroxyl group develops maximal negative charge and forms a short h ydrogen bond to the neighboring carboxylate group of Glu 104. Empirica l bond valence relationships suggest that the Zn-S(gamma)132 bond func tions throughout the reaction as a ''valence buffer'' that accommodate s changing negative charge on the hydroxyl group. Similar structural f eatures in alcohol dehydrogenase suggest that analogous mechanisms may be a general feature of catalysis by zinc enzymes.