Topological enzymes

Figure 2.11 Beta sheets are usuaiiy represented simply by arrows in topology diagrams that show both the direction of each (3 strand and the way the strands are connected to each other along the polypeptide chain. Such topology diagrams are here compared with more elaborate schematic diagrams for different types of (3 sheets, (a) Four strands. Antiparallel (3 sheet in one domain of the enzyme aspartate transcarbamoylase. The structure of this enzyme has been determined to 2.8 A resolution in the laboratory of William Lipscomb, Harvard University, (b) Five strands. Parallel (3 sheet in the redox protein flavodoxin, the structure of which has been determined to 1.8 A resolution in the laboratory of Martha Ludwig, University of Michigan, (c) Eight strands. Antiparallel barrel in the electron carrier plastocyanln. This Is a closed barrel where the sheet is folded such that (3 strands 2 and 8 are adjacent. The structure has been determined to 1.6 A resolution in the laboratory of Hans Freeman in Sydney, Australia. (Adapted from J. Richardson.)...

Figure 2.15 The Greek key motif is found in antiparallel p sheets when four adjacent p strands are arranged in the pattern shown as a topology diagram in (a). The motif occurs in many p sheets and is exemplified here by the enzyme Staphylococcus nuclease (b). The four p strands that form this motif are colored red and blue.

Figure 4.1 Alpha/beta domains are found in many proteins. They occur in different classes, two of which are shown here (a) a closed barrel exemplified by schematic and topological diagrams of the enzyme trlosephosphate isomerase and (b) an open twisted sheet with helices on both sides, as in the coenzymebinding domain of some dehydrogenases. Both classes are built up from p-a-p motifs that are linked such that the p strands are parallel. Rectangles represent a helices, and arrows represent p strands in the topological diagrams, [(a) Adapted from J. Richardson, (b) Adapted from B. Furugren.j...

Figure 4.14 Examples of different types of open twisted a/p structures. Both schematic and topological diagrams are given. In the topological diagrams, arrows denote strands of p sheet and rectangles denote a helices, (a) The FMN-binding redox protein flavodoxln. (b) The enzyme adenylate kinase, which catalyzes the reaction AMP +...

Figure 4.19 Schematic and topological diagrams for the structure of the enzyme carboxypeptidase. The central region of the mixed p sheet contains four adjacent parallel p strands (numbers 8, 5, 3, and 4), where the strand order is reversed between strands 5 and 3. The active-site zinc atom (yellow circle) is bound to side chains in the loop regions outside the carboxy ends of these two p strands. The first part of the polypeptide chain is red, followed by green, blue, and brown. (Adapted from J. Richardson.)...

Figure 5.30 Schematic diagrams of the structure of the enzyme pectate lyase C, which has a three-sheet parallel P-helix topology.

Adapted from Hatefi, Y, 1985. The mitochondrial electron tran.sport chain and oxidative pho.sphorylation. sy.stem. Annual Review of Biochemistry 54 1015-1069 and DePierre, J., and Ern.ster, L., 1977. Enzyme topology of intracellular membrane.s. Annual Review of Biochemistry 46 201-262. 

Topoisomerase enzymes control and modify the topologic states of DNA. The mechanisms of these enzymes involve DNA cleavage and strand passage through the break, followed by religation of the cleaved DNA. Two main forms of topoisomerase exist. The type... 

Deoxyribonucleic acid (DNA) topoisomerases (topos) are ubiquitous enzymes that can manipulate DNA by changing the number of topological links between two strands of the same or different DNA molecules [1]. These enzymes are involved in many cellular processes, such as replication, recom-... 

The HlV-1 protease is responsible for processing the protein precursors to the enzymes (integrase, protease and reverse transcriptase) and the structural proteins of the HIV-1 virus. Maw and Hall found that topological indices provide rehable QSAR models for the IC50 data of 32 HIV-1 protease inhibitors [29]. The best QSAR model, with r = 0.86, s=0.60 and q = 0.79, was obtained with the shape index Ka, the connechvity index the sum of HE-state indices for ah groups that act as... 

The 12-transmembrane-spanning domain topology of the adenylyl cyclase enzymes is similar to that found in the ABC family of transporters (see Ch. 5), which includes the cystic fibrosis transmembrane rectifier and the P-glyco-protein. However, there is currently no convincing evidence of a transporter or channel function for mammalian adenylyl cyclases. The structural similarity may indicate that these functionally divergent protein families are derived in an evolutionary sense from related proteins. 

G. Bellucci, G. Berti, R. Bianchini, P. Cetera, E. Mastrorilli, Stereoselectivity of the Epoxide Hydrolase Catalyzed Hydrolysis of the Stereoisomeric 3-ieri-Buty 1-1,2-epoxycyclohexane. Further Evidence for the Topology of the Enzyme Active Site ,. /. Org. Chem. 1982, 47, 3105 - 3112. 

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