Kinemages from Charles Carter's laboratory

1. A tour through five different structural states for E. coli cytidine deaminase. The structures include ligand free enzyme and complexes with inhibitors deazacytidine, (DAC), dihydrozebularine (DHZ), and zebularine (ZEB), and with the product, uridine (URID). These structures are all closely isomorphous, and difference Fouriers between observed structure factors for the different states reveal subtle changes in the zinc coordination, which we have described as a "valence buffer", and which we propose accomodates the buildup of negative charge on the hydrolytic water molecule.

References:

Xiang, Shibin, Short, Steven A., Wolfenden, Richard, and Carter, Charles W., Jr.: Transition State Selectivity for a Single OH Group During Catalysis by Cytidine Deaminase. Biochemistry, 34:4516-4523, 1995.

Xiang, Shibin, Short, Steven A., Wolfenden, Richard, and Carter, Charles W., Jr.: Cytidine Deaminase Complexed to 3-Deazacytidine: A "Valence-Buffer" in Zinc Enzyme Catalysis. Biochemistry, 35:1335-1341, 1996.



2. A comparison between two different crystal polymorphs of E. coli cytidine deaminase. One, the canonical trigonal form, has been studied in twelve different crystal forms, including those represented in the animation of the structural reaction profile, together with other inhibitors and several determinations of the ligand-free enzyme. The other, prepared by "directed crystallogenesis" from conditions identified by a Hampton screen experiment, is grown at elevated temperatures (30 degrees) close to the in vivo temperature of the organism. It has no active-site directed ligands, but has several molecules of cacodylate ion bound to the active sites. This form is asymmetric, with very significant differences between the two monomers. The active site is opened, relative to that in the canonical forms. There is also a significant penetration by water into the crevices between the four, nearly identical domains.

Reference:

Kuyper, Lee, and Carter, C.W., Jr.: Resolving crystal polymorphisms by finding "stationary points" from quantitative analysis of crystal growth response surfaces, J. Cryst. Growth, In press 1996.



3. Comparison of the activated amino acid complex and ligand free forms in tetragonal Tryptophanyl-tRNA synthetase crystals. The concerted changes at the active site and at a remote site appear to be coupled and to be related to coupling of the chemical activation of tryptophan at the active site and anticodon recognition at a remote site on the opposite subunit. Use view 3 to see the coupled changes.