1ALN
CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE COMPLEXED WITH 3-DEAZACYTIDINE
Summary for 1ALN
| Entry DOI | 10.2210/pdb1aln/pdb |
| Descriptor | CYTIDINE DEAMINASE, ZINC ION, 3-DEAZACYTIDINE, ... (4 entities in total) |
| Functional Keywords | cytidine deaminase, valence buffer, zinc enzyme, substrate, hydrolase |
| Biological source | Escherichia coli |
| Total number of polymer chains | 1 |
| Total formula weight | 31877.42 |
| Authors | Xiang, S.,Carter, C.W. (deposition date: 1997-06-02, release date: 1997-09-17, Last modification date: 2024-05-22) |
| Primary citation | Xiang, S.,Short, S.A.,Wolfenden, R.,Carter Jr., C.W. Cytidine deaminase complexed to 3-deazacytidine: a "valence buffer" in zinc enzyme catalysis. Biochemistry, 35:1335-1341, 1996 Cited by PubMed Abstract: The cytidine deaminase substrate analog inhibitor 3-deazacytidine binds with its 4-amino group inserted into a site previously identified as a probable binding site for the leaving ammonia group. Binding to this site shifts the pyrimidine ring significantly further from the activated water molecule than the position it occupies in either of two complexes 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 zebularine--hydrate inhibitor complexes suggest that the ring itself moves successively 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 distance. These correlate with chemical changes expected as the substrate approaches the tetrahedral transition state, in which the zinc-activated hydroxyl group develops maximal negative charge and forms a short hydrogen bond to the neighboring carboxylate group of Glu 104. Empirical bond valence relationships suggest that the Zn-S gamma 132 bond functions throughout the reaction as a "valence buffer" that accommodates changing negative charge on the hydroxyl group. Similar structural features in alcohol dehydrogenase suggest that analogous mechanisms may be a general feature of catalysis by zinc enzymes. PubMed: 8634261DOI: 10.1021/bi9525583 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.3 Å) |
Structure validation
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