Active site structural features

This chapter summarizes (i) the intellectual problem associated with understanding the rates of these reactions, i.e., the required reduction in the kinetic barrier for proton transfer from carbon to an active site general base so that kcat will not be limited by the rate of this overall reaction (ii) the active site structural features that allow the necessary reduction in kinetic barrier and (iii) specific enzymatic examples of how these strategies are employed. 

Gliubich F, Gazerro M, Zanotti G, Delbono S, Bombieri G, Bemi R (1996) Active site structural features for chemically modified forms of rhodanese. J Biol Chem 271(35) 21054-21061 Li S, Hall MB (2001) Modeling the active sites of metalloenzymes. 4. predictions of the unready states of [NiPe] desulfovibrio gigas hydrogenase from density functional theory. Inorg Chem 40(l) 18-24... 

Physical studies of the hydroxylase have established the structural nature of the diiron core in its three oxidation states, Hox, Hmv, and Hred. Although the active site structures of hydroxylase from M. tri-chosporium OB3b and M. capsulatus (Bath) are similar, some important differences are observed for other features of the two MMO systems. The interactions with the other components, protein B and reductase, vary substantially. More structural information is necessary to understand how each of the components affects the others with respect to its physical properties and role in the hydroxylation mechanism and to reconcile the different properties seen in the two MMO systems. The kinetic behavior of intermediates in the hydroxylation reaction cycle and the physical parameters of intermediate Q appear similar. The reaction of Q with substrate, however, varies. The participation of radical intermediates is better established with the M. triehosporium... 

The active site of DHFR illustrates several features that are common to enzyme active sites. Some of the salient features of active site structure that relate to enzyme catalysis and ligand (e.g., inhibitor) interactions have been enumerated by Copeland (2000) ... 

These systems are also described as normal copper proteins due to their conventional ESR features. In the oxidized state, their color is light blue (almost undetectable) due to weak d-d transitions of the single Cu ion. The coordination sphere around Cu, which has either square planar or distorted tetrahedral geometry, contains four ligands with N and/or 0 donor atoms [ 12, 22]. Representative examples of proteins with this active site structure (see Fig. 1) and their respective catalytic function include galactose oxidase (1) (oxidation of primary alcohols) [23,24], phenylalanine hydroxylase (hydroxy-lation of aromatic substrates) [25,26], dopamine- 6-hydroxylase (C-Hbond activation of benzylic substrates) [27] and CuZn superoxide dismutase (disproportionation of 02 superoxide anion) [28,29]. 

A remarkable feature of the active site structure in bovine SOD is the presumably deprotonated imidazole ring of His 61 that bridges the two metal ions ... 

The situation with respect to selectivity is less clear. Some examples of selective oxidation catalysts used in commercial practice are listed in Table 1. A consistent feature is that many oxidation catalysts are not highly dispersed when viewed on the atomic scale. Hence particle sizes tend to be large, even for supported precious metal catalysts.1,4 7 This feature, in turn, has led to descriptions of active site structures on these catalysts that are extensions of bulk structures. 

About 70 different lipases are commercially available. Most of these are presumably serine hydrolases containing a serine residue in their active site and featuring presumably the triad Ser. .. His. Asp. The crystal structures of the 13 different lipases have been determined 84 87. ... 

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