3D structures of enzymes

The ENZYME database at http //www.expasy.ch/enzyme/ provides information on EC number, name, catalytic activity, and hyperlinks to sequence data of enzymes. The 3D structures of enzymes can be accessed via Enzyme Structures Database at http //www.biochem.ucl.ac.uk/bsm/enzyme/index.html. Some other enzyme databases are listed in Table 7.1. 

Significant progress in QSAR resulted from Hansch analyses of enzyme inhibitors [432, 456, 668 — 670], especially from the systematic work of Hansch and his group on dihydrofolate reductase and on cysteine and serine proteases. Most of our current knowledge of the quantitative aspects of ligand-protein interactions has been derived from QSAR equations, aided by the interpretation of the 3D structures of enzymes and their inhibitor complexes with molecular graphics [38, 288, 671 — 676]. 

Three subclasses Bl, B2 and B3 can be distinguished on the basis of the sequences. Bl and B3 enzymes are optimally active with 2 Zn2+ions, while the B2 enzymes are inhibited by the second Zn2+. These B2 enzymes also exhibit a very narrow activity spectrum and only hydrolyse carbapenems. The 3D structures of representative members of each subfamily have been... 

Both enzymes belong to the family of a,p-hydrolases." The active site of MeHNL is located inside the protein and connected to the outside through a small channel, which is covered by the bulky amino acid tryptophane 128." It was possible to obtain the crystal structure of the complex with the natural substrate acetone cyanohydrin with the mutant SerSOAla of MeHNL. This complex allowed the determination of the mode of substrate binding in the active site." A summary of 3D structures of known HNLs was published recently." " ... 

Fig. 4 Energy-minimized 3D structures of compounds 3-7, which showed potential inhibitory activities against the enzyme tyrosinase [43]...

The majority of enzyme substrates contain flexible moieties. As the 3D structure of the substrate to be analyzed (the conformation) has a reasonable impact on the outcome of the method, a precise protocol is used to build it. Each substrate is subjected to a conformational search followed by energy minimization by means of a software developed at Molecular Discovery Ltd. The population of conformers is... 

Although the current software package was prepared to work with the five most important human cytochromes, this procedure can be adopted to work with any CYP structure and applied to humans, bacteria, fish and plant CYPs. There are more than 120 P450 families, and more than 1000 P450 enzymes. All these structures can in theory be imported, processed and used for the prediction of the site of metabolism. The procedure is totally automated and does not require user assistance. It only requires the availability of the 3D structure of the enzyme and input of the compound(s) to be evaluated. 

To help the reader gain a better understanding of the three-dimensional structure of the catalytic site of an esterase, Fig. 3.8 presents the 3D structure of human butyrylcholinesterase (EC 3.1.1.8) obtained by homology modeling [42], The overall structure of the enzyme is shown in Fig. 3.8, a, while Fig. 3.8,b shows a closeup of the active site with the catalytic triad highlighted and the close spatial relationship of the Ser-His-Glu residues revealed. 

Fig. 3.8. The 3D structure of butyrylcholinesterase obtained from leho.pdb [42]. a) Structure of the enzyme, with the Ser-His-Glu catalytic triad shown in blue, b) Closeup of the catalytic triad, revealing the close spatial proximity of the three catalytic residues. 

Almost all enzymes are proteins. They provide templates whereby reactants (substrates) can bind and are favorably oriented to react and generate the products. The locations where the substrates bind are known as active sites. Because of the specific 3D structures of the active sites, the functions of enzymes are specific that is, each particular type of enzyme catalyzes specific biochemical reactions. Enzymes speed up reactions, but they are not consumed and do not become part of the products. Enzymes are grouped into six functional classes by the International Union of Biochemists (Table 2.2). 

The 3D structures of several aminoglycoside-enzyme complexes have been described recently by X-ray methods [35,36]. Interestingly, in some cases, the 3D structure of the antibiotic in the enzyme binding site significantly... 

In another process, which does not require any knowledge of the 3D structure of the enzyme, every single position is randomized separately in a systematic manner 45,46). Thus, in the case of an enzyme composed of N amino acids, libraries each containing about 300 clones are produced and screened. In still another strategy, hot spots are first identified by the epPCR screening process, and these are subsequently randomized separately 47,48). 

In collaboration with Gunter Schneider s group at the Karolinska Institute in Stockholm, the 3D structures of transaldolase and of several of its mutant derivatives have been solved. For the first time, a Schiff base intermediate of an aldolase was analyzed crystallographically. The structure of FSA was solved too, and it was found that the enzyme forms a decameric structure out of two pentamer rings. 

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