Catalytic groups, active site

Figure 21 Haloacetamide-derived probes as potent tools for the labeling of arginine deaminase PAD4. The probe design is based on arginine as a natural substrate that is converted into a F/CI reactive group. Active site labeling occurs via a nucleophilic substitution of the halogene by the catalytically active cysteine of PAD4.

Discussions of OH groups in the context of catalysis normally focus on their role as active centers in a number of reactions. The work by Haag et al. (94) constitutes a classic example the authors estahhshed a linear relationship between the concentration of aluminum in HZSM-5 (which imphes an equal concentration of bridging hydroxyls) and the activity for cracking of -hexane. It was concluded that aU protonic acid sites in the zeohte are characterized by the same turnover frequency. Many other correlations between catalytic properties of materials and the strength and/or density of their Bronsted acid sites are well estabHshed. We will not discuss this aspect in detail and recommend instead a number of recently pubhshed reviews (59,60,87). Two more points are worth mentioning. One point is that the cooperative action of Bronsted and Lewis acid sites has been demonstrated. The second is that, of course, OH groups must not necessarily be involved in a catalytic conversion in fact, they can even block the catalyt-icaUy active sites. 

Catalysis in a single fluid phase (liquid, gas or supercritical fluid) is called homogeneous catalysis because the phase in which it occurs is relatively unifonn or homogeneous. The catalyst may be molecular or ionic. Catalysis at an interface (usually a solid surface) is called heterogeneous catalysis, an implication of this tenn is that more than one phase is present in the reactor, and the reactants are usually concentrated in a fluid phase in contact with the catalyst, e.g., a gas in contact with a solid. Most catalysts used in the largest teclmological processes are solids. The tenn catalytic site (or active site) describes the groups on the surface to which reactants bond for catalysis to occur the identities of the catalytic sites are often unknown because most solid surfaces are nonunifonn in stmcture and composition and difficult to characterize well, and the active sites often constitute a small minority of the surface sites. 

In order for the cyclooxygenase to function, a source of hydroperoxide (R—O—O—H) appears to be required. The hydroperoxide oxidizes a heme prosthetic group at the peroxidase active site of PGH synthase. This in turn leads to the oxidation of a tyrosine residue producing a tyrosine radical which is apparendy involved in the abstraction of the 13-pro-(5)-hydrogen of AA (25). The cyclooxygenase is inactivated during catalysis by the nonproductive breakdown of an active enzyme intermediate. This suicide inactivation occurs, on average, every 1400 catalytic turnovers. 

Oxidation of P-nicotinamide adenine dinucleotide (NADH) to NAD+ has attracted much interest from the viewpoint of its role in biosensors reactions. It has been reported that several quinone derivatives and polymerized redox dyes, such as phenoxazine and phenothiazine derivatives, possess catalytic activities for the oxidation of NADH and have been used for dehydrogenase biosensors development [1, 2]. Flavins (contain in chemical structure isoalloxazine ring) are the prosthetic groups responsible for NAD+/NADH conversion in the active sites of some dehydrogenase enzymes. Upon the electropolymerization of flavin derivatives, the effective catalysts of NAD+/NADH regeneration, which mimic the NADH-dehydrogenase activity, would be synthesized [3]. 

Figure 4.8 The active site in all a/p barrels is in a pocket formed by the loop regions that connect the carboxy ends of the p strands with the adjacent a helices, as shown schematically in (a), where only two such loops are shown, (b) A view from the top of the barrel of the active site of the enzyme RuBisCo (ribulose bisphosphate carboxylase), which is involved in CO2 fixation in plants. A substrate analog (red) binds across the barrel with the two phosphate groups, PI and P2, on opposite sides of the pocket. A number of charged side chains (blue) from different loops as welt as a Mg ion (yellow) form the substrate-binding site and provide catalytic groups. The structure of this 500 kD enzyme was determined to 2.4 A resolution in the laboratory of Carl Branden, in Uppsala, Sweden. (Adapted from an original drawing provided by Bo Furugren.)...

The enzyme provides a general base, a His residue, that can accept the proton from the hydroxyl group of the reactive Ser thus facilitating formation of the covalent tetrahedral transition state. This His residue is part of a catalytic triad consisting of three side chains from Asp, His, and Ser, tvhich are close to each other in the active site, although they are far apart in the amino acid sequence of the polypeptide chain (Figure 11.6). 

Many enzymes (see Chapters 14 to 16) derive at least some of their catalytic power from oligomeric associations of monomer subunits. This can happen in several ways. The monomer may not constitute a complete enzyme active site. Formation of the oligomer may bring ail the necessary catalytic groups together to form an active enzyme. For example, the active sites of bacterial glutamine synthetase are formed from pairs of adjacent subunits. The dissociated monomers are inactive. 

The first hint that two active-site carboxyl groups—one proto-nated and one ionized—might be involved in the catalytic activity of the aspartic proteases came from studies of the pH dependence of enzymatic activity. If an ionizable group in an enzyme active site is essential for activity, a plot of enzyme activity versus pH may look like one of the plots at right. 

Rubisco exists in three forms an inactive form designated E a carbamylated, but inactive, form designated EC and an active form, ECM, which is carbamylated and has Mg at its active sites as well. Carbamylation of rubisco takes place by addition of COg to its Lys ° e-NHg groups (to give e—NH—COO derivatives). The COg molecules used to carbamylate Lys residues do not become substrates. The carbamylation reaction is promoted by slightly alkaline pH (pH 8). Carbamylation of rubisco completes the formation of a binding site for the Mg that participates in the catalytic reaction. Once Mg binds to EC, rubisco achieves its active CM form. Activated rubisco displays a Ai, for CO2 of 10 to 20... 

Uncovering of the three dimentional structure of catalytic groups at the active site of an enzyme allows to theorize the catalytic mechanism, and the theory accelerates the designing of model systems. Examples of such enzymes are zinc ion containing carboxypeptidase A 1-5) and carbonic anhydrase6-11. There are many other zinc enzymes with a variety of catalytic functions. For example, alcohol dehydrogenase is also a zinc enzyme and the subject of intensive model studies. However, the topics of this review will be confined to the model studies of the former hydrolytic metallo-enzymes. 

The metabolic breakdown of triacylglycerols begins with their hydrolysis to yield glycerol plus fatty acids. The reaction is catalyzed by a lipase, whose mechanism of action is shown in Figure 29.2. The active site of the enzyme contains a catalytic triad of aspartic acid, histidine, and serine residues, which act cooperatively to provide the necessary acid and base catalysis for the individual steps. Hydrolysis is accomplished by two sequential nucleophilic acyl substitution reactions, one that covalently binds an acyl group to the side chain -OH of a serine residue on the enzyme and a second that frees the fatty acid from the enzyme. 

Threonine peptidases (and some cysteine and serine peptidases) have only one active site residue, which is the N-terminus of the mature protein. Such a peptidase is known as an N-terminal nucleophile hydrolase or Ntn-hydrolase. The amino group of the N-terminal residue performs the role of the general base. The catalytic subunits of the proteasome are examples of Ntn-hydrolases. 

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