The Catalytic Mechanism

Catalytic reaction schemes for laccase and ceruloplasmin have been formulated on the basis of the mechanistic studies and the state of characterization of the copper redox centers at this time. They are outlined in the reviews on laccase by Reinhammar (10) and on ceruloplasmin by Ryden (26). The degree of correctness of these reaction schemes is rather limited due to the fact that the structure and spatial arrangement of the copper centers were unknown at this time. 

A tentative catalytic mechanism of ascorbate oxidase has been proposed based on the refined X-ray structure and on spectroscopic and mechanistic studies of ascorbate oxidase and the related laccase. The results of these studies have been discussed in detail (74). The X-ray structure determinations of the fully reduced and peroxide derivatives define two important intermediate states during the catalytic cycle. A proposal for the catalytic mechanism incorporating this new information is given in Messerschmidt et al. (150) and presented in Fig. 14. This scheme should be valid in principle also for laccase due to the close similarities of both blue oxidases. 

Although the reduction of ribonucleotides to the corresponding 2 -deoxyribonucleotides is catalyzed by enzyme systems differing in their cofactor requirements and/or in the level of phosphorylation of the substrates, the overall reduction process is very similar in all systems. For all the systems NADPH is the ultimate reductant, the hydrogen is transferred by thioredoxin reductase to thioredoxin, which in turn is oxidized by ribonucleotide reductase with the concomitant production of a 2 -deoxyribonucleotide. In these systems the thioredoxin-thiore-doxin reductase reducing system can be replaced by dithiols such as dihydrolipoate or dithiothreitol. 

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Verschueren K H G, Seljee F, Rozeboom J, Kalk K H and Dijkstra B W 1993 Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase Nature 363 693-8... 

The subtilisin mutants described here illustrate the power of protein engineering as a tool to allow us to identify the specific roles of side chains in the catalytic mechanisms of enzymes. In Chapter 17 we shall discuss the utility of protein engineering in other contexts, such as design of novel proteins and the elucidation of the energetics of ligand binding to proteins. 

All the residues involved in important functions in the catalytic mechanism are strictly conserved in all homologous GTPases with one notable exception. Ras does not have the arginine in the switch 1 region that stabilizes the transition state. The assumption that the lack of this catalytically important residue was one reason for the slow rate of GTP hydrolysis by Ras was confirmed when the group of Alfred Wittinghofer, Max-Planck Institute,... 

In summary, structural studies of Ras and Gq with GTP-yS and a transition state analog have illuminated the catalytic mechanism of their GTPase activity, as well as the mechanism by which GTP hydrolysis is stimulated by GAP and RGS. In addition, these structural studies have shown how tumor-causing mutations affect the function of Ras and Gq. 

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. 

Catalysts which enhance the burning rate of composite propellants are generally believed to accelerate the decomposition of ammonium perchlorate, but the catalytic mechanism is still not very clear. The important observed aspects of this catalysis can be summarized as follows ... 

Abstract This review provides an overview of the development of viral protease inhibitors as antiviral drugs. We concentrate on HlV-1 protease inhibitors, as these have made the most significant advances in the recent past. Thus, we discuss the biochemistry of HlV-1 protease, inhibitor development, clinical use of inhibitors, and evolution of resistance. Since many different viruses encode essential proteases, it is possible to envision the development of a potent protease inhibitor for other viruses if the processing site sequence and the catalytic mechanism are known. At this time, interest in developing inhibitors is Umited to viruses that cause chronic disease, viruses that have the potential to cause large-scale epidemics, or viruses that are sufQciently ubiquitous that treating an acute infection would be... 

Amaya ME, Watts AG, Damager 1, Wehenkel A, Nguyen T, Buschiazzo A, Paris G, Frasch AC, Withers SG, Alzari PM (2004) Structural insights into the catalytic mechanism of Trypanosoma cmzi tran.s-sialidase. Structure 12 775-784... 

Spectroscopic studies have been instrumental in elucidating the catalytic mechanism of Ni-Fe hydrogenases. A great deal of controversy concerning this mechanism arises from the fact that, as the as the X-ray crystallographic analysis has shown, there are at least three potential redox-active species at the enzyme s active site the thiolate ligands (75) and the Fe (65) and Ni (9) ions. 

Proteases, which originally catalyze the amidic carbon-nitrogen bond breaking, also catalyze ester hydrolysis. However, in this case, the catalytic mechanism is hkely very similar and consists in the preliminary attack of the active site serine on the carbonyl carbon atom [103]. 

Cu and Ag on Si(lll) surfaces. In the last example, we come back to surfaces. It is well known (44-46) that Cu catalyzes the formation of dimethyl-dichlorosilane from methylchloride and solid silicon, which is a crucial technological step in the synthesis of silicone polymers. Even today, the details of the catalytic mechanism are unclear. Cu appears to have unique properties for example, the congener Ag shows no catalytic activity. Thus, the investigation of the differences between Cu and Ag on Si surfaces can help in understanding the catalytic process. Furthermore, the bonding of noble metal atoms to Si surfaces is of great importance in the physics and chemistry of electronic devices. 

In this article are discussed the results of those studies which have become available over the past 15 years and which permit some generalizations on the catalytic mechanism of glycoside hydrolases from widely differing sources and with different sugar and aglycon specificities. It will be seen that, with few exceptions, the data support a mechanism almost identical to that proposed by Phillips and his group for lysozyme. ... 

Catalysis by enzymes that proceeds via a unique reaction mechanism typically occurs when the transition state intermediate forms a covalent bond with the enzyme (covalent catalysis). The catalytic mechanism of the serine protease chymotrypsin (Figure 7-7) illustrates how an enzyme utilizes covalent catalysis to provide a unique reaction pathway. 

Figure 2 Scheme of the catalytic mechanism of type I BVMOs. Phenylacetone... 

Messerschmidt A, L Prade, R Wever (1997) Implications for the catalytic mechanism of the vanadium-containing enzyme chloroperoxodase from the fungus Curvularia inaequalis hy X-ray structures of the native and peroxide form. Biol Chem 378 309-315. 

V) and selectivity ( av 3.9). It appears fairly well accepted that in the very best cofacial porphyrin catalysts, bimetaUic cooperativity plays a critical role. The catalytic mechanism remains to be adequately elucidated, complicating rational improvement of these fascinating compounds. Cofacial porphyrins remain too unstable and prohibitively expensive for practical applications. 

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