Diffraction active-site waters

Blevins and Tulinsky (1985) suggested two functions for the solvent at the chymotrypsin active site (1) solvation of the Asp—His—Ser catalytic triad, and (2) a guiding effect on the substrate in formation of the enzyme-substrate complex, provided by several waters at the end of the specificity site. X-Ray diffraction results have suggested a role of active-site water in determining the kinetics or equilibria of substrate binding for other proteins (Section IV). 

X-ray diffraction studies on several forms of the enzyme have demonstrated that the active site is composed of a pseudo-tetrahedral zinc center coordinated to three histidine imidazole groups and either a water molecule [(His)3Zn-OH2]2+ (His = histidine), or a hydroxide anion [(His)3Zn-OH] +, depending upon pH (156,157). On the basis of mechanistic studies, a number of details of the catalytic cycle for carbonic anhydrase have been elucidated, as summarized in Scheme 22... 

The presence of a covalent acyl-enzyme intermediate in the catalytic reaction of the serine proteases made this class of enzymes an attractive candidate for the initial attempt at using subzero temperatures to study an enzymatic mechanism. Elastase was chosen because it is easy to crystallize, diffracts to high resolution, has an active site which is accessible to small molecules diffusing through the crystal lattice, and is stable in high concentrations of cryoprotective solvents. The strategy used in the elastase experiment was to first determine in solution the exact conditions of temperature, organic solvent, and proton activity needed to stabilize an acyl-enzyme intermediate for sufficient time for X-ray data collection, and then to prepare the complex in the preformed, cooled crystal. Solution studies were carried out in the laboratory of Professor A. L. Fink, and were summarized in Section II,A,3. Briefly, it was shown that the chromophoric substrate -carbobenzoxy-L-alanyl-/>-nitrophenyl ester would react with elastase in both solution and in crystals in 70 30 methanol-water at pH 5.2 to form a productive covalent complex. These... 

Lipases are ester hydrolases acting on triacylglycerols. They achieve their highest catalytic rate at oil-water interfaces. Though they widely differ in size, substrate and catalytic rate and show little sequence similarity, the Ser...His...Asp(Glu) triad in the active site is a structural feature common to serine proteases (cf. Section 3.1.1.) and lipases. Their mechanism of action is not yet fully revealed. X-ray diffraction studies suggest that the putative hydrolytic site is covered by a surface loop and is therefore inaccessible to solvent (Brady et al., 1990 Winkler et al., 1990). Therefore the enzyme... 

The mechanism of the activation of H2O2 by TS-1 and related catalysts has been the subject of much research using spectroscopic and computational techniques. This has centred on the nature of the active site and its mode of reaction with H2O2, solvents and the organic substrates. Work to elucidate the structure of the active site has concentrated on the coordination chemistry of the titanium. X-ray and neutron diffraction studies, coupled with X-ray absorption, infrared and Raman spectroscopies, give evidence that most of the Ti(IV) in calcined TS-1, in the absence of any adsorbate molecules, is in tetrahedral coordination. Upon addition of one molecule of water, one of the Ti-OSi bonds is hydrolysed and the titanium adopts tetrahedral coordination as Ti(0Si)30H. Addition of a further water molecule gives rise to a pentaco-ordinated titanium. ... 

---