Catalytic sites, structure

In spite of the apparent extreme diversity of the / -(l- 4) glycans— from crystalline cellulose to components of bacterial cell walls—the similarity of the environments around their / -(1— 4) glycosidic linkage raises the question of a common catalytic site structure in the various / -(l- 4) glycoside hydrolases. This chapter will review the evidence for and against a general lysozyme type mechanism. 

Following the discovery of the two important factors (the N and micropore contents) that govern the activity of catalysts made by the impregnation of a carbon black with 0.2 wt% Fe as iron acetate and its pyrolysis in NH3 at high temperature, in 2008, we proposed a structure that would replace FeN2/C, the incomplete catalytic site structure depicted in Fig. 10.4 that was previously introduced as a possible part of the most active type of catalytic site. 

The components in catalysts called promoters lack significant catalytic activity tliemselves, but tliey improve a catalyst by making it more active, selective, or stable. A chemical promoter is used in minute amounts (e.g., parts per million) and affects tlie chemistry of tlie catalysis by influencing or being part of tlie catalytic sites. A textural (structural) promoter, on tlie otlier hand, is used in massive amounts and usually plays a role such as stabilization of tlie catalyst, for instance, by reducing tlie tendency of tlie porous material to collapse or sinter and lose internal surface area, which is a mechanism of deactivation. 

Figure 16.21 Structure of one subunit of the core protein of Slndbls virus. The protein has a similar fold to chymotrypsin and other serine proteases, comprising two Greek key motifs separated by an active site cleft. The C-terminus of the protein is bound in the catalytic site, making the coat protein inactive (Adapted from S. Lee et al., Structure 4 531-541, 1996.)...

FIGURE 15.15 (a) The structure of a glycogen phosphorylase monomer, showing the locations of the catalytic site, the PLP cofactor site, the allosteric effector site, the glycogen storage site, the tower helix (residnes 262 throngh 278), and the snbnnit interface. 

The two isozymes are both homodimers, composed of approximately 600 amino acids and possess approximately 60% homology. The three-dimensional structures of COX-1 and COX-2 are very similar. Each one consists of three independent units an epidermal growth factor-like domain, a membrane-binding section and an enzymic domain. The catalytic sites and the residues immediately adjacent are identical but for two small but crucial variations that result in an increase in the volume of the COX-2-active site, enabling it to accept inhibitor-molecules larger than those that could be accommodated in the COX-1 molecule. 

Some enzymes require cofactors to activate catalysis. Typical cofactors are metal atoms, ammonia, and small organic molecules that associate with the enzyme and help to structure the catalytic site. To conduct an enz5anatic reaction, the necessary cofactors must be suppUed along with the substrate and the enzyme. In cell metabolism, a variety of these cofactors act in conjunction with inhibitors to control the metabolic rate. 

The majority of NNRTIs share common conformational properties and structural features that allow them to fit into an asymmetric, hydrophobic pocket about 10 A away from the catalytic site of the HlV-1 RT, where they act as non-competitive inhibitors (Kohlstaedt et al. 1992). However, the NNRTIs select for mutant virus strains with several degrees of dmg resistance. 

The lack of structural similarity between a feedback inhibitor and the substrate for the enzyme whose activity it regulates suggests that these effectors are not isosteric with a substrate but allosteric ( occupy another space ). Jacques Monod therefore proposed the existence of allosteric sites that are physically distinct from the catalytic site. Allosteric enzymes thus are those whose activity at the active site may be modulated by the presence of effectors at an allosteric site. This hypothesis has been confirmed by many lines of evidence, including x-ray crystallography and site-directed mutagenesis, demonstrating the existence of spatially distinct active and allosteric sites on a variety of enzymes. 

Partial oxidations over complex mixed metal oxides are far from ideal for singlecrystal like studies of catalyst structure and reaction mechanisms, although several detailed (and by no means unreasonable) catalytic cycles have been postulated. Successful catalysts are believed to have surfaces that react selectively vith adsorbed organic reactants at positions where oxygen of only limited reactivity is present. This results in the desired partially oxidized products and a reduced catalytic site, exposing oxygen deficiencies. Such sites are reoxidized by oxygen from the bulk that is supplied by gas-phase O2 activated at remote sites. 

The studies of ammonia synthesis over Fe and Re and the hydrodesulfurization of thiophene over Mo, described above, illustrate the importance and success of our approach of studying catalysis over single crystal samples at high pressures. The use of surfaces having a variety of orientations allows the study of reactions that are surface structure sensitive 6Uid provides insight into the nature of the catalytic site. Here we have shown that the ammonia synthesis... 

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