Enzymes with structure

Molybdopterin is a component of four enzyme families all of which contain Mo(VI) the xanthine oxidase and the sulfite oxidase families with one molybdopterin and the DMSO family with two molybdopterins. There are a number of tungsten-containing enzymes with structures analogous... 

Many attempts have been made to correlate the enantioselective properties of enzymes with structure and/or process conditions [61, 70-73]. Attempts to correlate the effect of a particular medium on the enantioselectivity of an enzyme-catalyzed reaction with physico-chemical descriptors of the solvent have also been reported by a number of groups [22, 59, 64, 74]. Correlations with solvent size [75], dielectric constant [59], polarizability, electron pair acceptance index [76], logP [17],... 

By following the example of nature (copying enzymes with structures that have a similar mode of action (zeozymes)... 

The observations on the histidine operons described above clearly show that all the enzymes with amino acid sequences determined by the histidine operon are not synthesized in equimolecular amounts. But the rate at which each of the proteins is synthesized is determined by the position of the cistron within the operon. The amount of protein synthesized decreases the further the cistron is from the operator gene. Furthermore, mutations that interfere with the biosynthesis of one enzyme of the histidine pathway lead to a reduction of the rate of synthesis of all the enzymes with structures dictated by cistrons distal to the mutated cistron. 

The stereospecificity of many of the antibiotics indicates that they interact at several points, like the substrates of enzymes, with structures that themselves contain asymmetric centres. Antibiotics which are highly selective in their action presumably react with structural entities in sensitive cells which do not exist, or are inaccessible, in cells that are resistant. 

An impressive example of the application of structure-based methods was the design of a inhibitor of the HIV protease by a group of scientists at DuPont Merck [Lam et al. 1994 This enzyme is crucial to the replication of the HIV virus, and inhibitors have bee shown to have therapeutic value as components of anti-AIDS treatment regimes. The star1 ing point for their work was a series of X-ray crystal structures of the enzyme with number of inhibitors boimd. Their objective was to discover potent, novel leads whid were orally available. Many of the previously reported inhibitors of this enzyme possessei substantial peptide character, and so were biologically unstable, poorly absorbed am rapidly metabolised. 

The eight-stranded a/p-barrel stmcture is one of the largest and most regular of all domain stmctures. A minimum of about 200 residues are required to form this structure. It has been found in many different proteins, most of which are enzymes, with completely different amino acid sequences and... 

Brick, R, Bhat, T.N., Blow, D.M. Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. /. Mol. Biol. 208 83-98, 1988. 

Regulation of enzyme activity is achieved in a variety of ways, ranging from controls over the amount of enzyme protein produced by the cell to more rapid, reversible interactions of the enzyme with metabolic inhibitors and activators. Chapter 15 is devoted to discussions of enzyme regulation. Because most enzymes are proteins, we can anticipate that the functional attributes of enzymes are due to the remarkable versatility found in protein structures. 

This enzyme is of wide occurrence in bacteria where it is concerned with the reduction of nitrate and CO2 as well as sulphur. Methods for its estimation depend on measuring some activity of hydrogenase by (a) dye reduction (benzyl viologen or methylene blue), (b) isotopic exchange and (c) evolution of molecular hydrogen. Interpretation of quantitative results is difficult due to the complex relationship between the enzyme cell structure and the particular method selected. ... 

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 class A enzymes have Mx values around 30,000. Their substrate specificities are quite variable and a large number of enzymes have emerged in response to the selective pressure exerted by the sometimes abusive utilization of antibiotics. Some of these new enzymes are variants of previously known enzymes, with only a limited number of mutations (1 4) but a significantly broadened substrate spectrum while others exhibit significantly different sequences. The first category is exemplified by the numerous TEM variants whose activity can be extended to third and fourth generation cephalosporins and the second by the NMCA and SME enzymes which, in contrast to all other SXXK (3-lactamases, hydrolyse carbapenems with high efficiency. Despite these specificity differences, the tertiary structures of all class A (3-lactamases are nearly superimposable. 

P-Lactamases are enzymes that hydrolyze the P-lactam ring of P-lactamantibiotics (penicillins, cephalosporins, monobactams and carbapenems). They are the most common cause of P-lactam resistance. Most enzymes use a serine residue in the active site that attacks the P-lactam-amid carbonyl group. The covalently formed acylester is then hydrolyzed to reactivate the P-lacta-mase and liberates the inactivated antibiotic. Metallo P-lactamases use Zn(II) bound water for hydrolysis of the P-lactam bond. P-Lactamases constitute a heterogeneous group of enzymes with differences in molecular structures, in substrate preferences and in the genetic localizations of the encoding gene (Table 1). 

Hen egg-white lysozyme catalyzes the hydrolysis of various oligosaccharides, especially those of bacterial cell walls. The elucidation of the X-ray structure of this enzyme by David Phillips and co-workers (Ref. 1) provided the first glimpse of the structure of an enzyme-active site. The determination of the structure of this enzyme with trisaccharide competitive inhibitors and biochemical studies led to a detailed model for lysozyme and its hexa N-acetyl glucoseamine (hexa-NAG) substrate (Fig. 6.1). These studies identified the C-O bond between the D and E residues of the substrate as the bond which is being specifically cleaved by the enzyme and located the residues Glu 37 and Asp 52 as the major catalytic residues. The initial structural studies led to various proposals of how catalysis might take place. Here we consider these proposals and show how to examine their validity by computer modeling approaches. 

The concept of electrostatic complimentarity is somewhat meaningless without the ability to estimate its contribution to AAg. Thus, it is quite significant that the electrostatic contribution to AAthat should be evaluated by rigorous FEP methods can be estimated with a given enzyme-substrate structure by rather simple electrostatic models (e.g., the PDLD model). It is also significant that calculated electrostatic contributions to A A g seem to account for its observed value (at least for the enzymes studied in this book). This indicates that simple calculations of electrostatic free energy can provide the correlation between structure and catalytic activity (Ref. 10). 

Fibrinolytic effecting protease enzyme with glycoprotein structure relative mol mass ca. 30000. Isolation from the poison secretion (venom) of Agkistrodon rhodostoma (malayan pit viper) with chromatographic purification. 

Sjbberg B-M (1997) Ribonucleotide Reductases - A Group of Enzymes with Different Metallosites and a Similar Reaction Mechanism. 88 139-174 Slebodnick C, Hamstra BJ, Pecoraro VL (1997) Modeling the Biological Chemistry of Vanadium Structural and Reactivity Studies Elucidating Biological Function. 89 51-108 Smit HHA, see Thiel RC (1993) 81 1-40... 

Each of these compounds, 53-56, was shown to be a very effective competitive inhibitor of the enzyme with respect to the fructose 1,6-diphosphate, whereas several other analogs, including acyclic structures, had no effect. These and other results suggest that the furanose form of the sugar diphosphate is the active form in the enzymatic reaction (105). More recent studies using rapid quenching techniques and C-nmr measurements have confirmed this hypothesis and indicate that the enzyme uses the a anomer 52 much more rapidly than the 3 anomer 50 and probably uses the a anomer exclusively (106). 

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