Zinc Active site

Trispyrazolylborates are models for tris-histidine active sites in zinc enzymes, e.g., the matrix metalloproteinases involved in breakdown of extracellular matrices. Inhibition of these metalloproteinases may prove valuable in the treatment of, inter alios, cancer and arthritis, so efforts are being made to find appropriate ligands to block the zinc active site. The search has recently moved on from hydroxamates to hydroxypyridinones - l-hydroxy-2-pyridinone is a cyclic analogue of hydroxamic acid. As reported in Section II.B.2 earlier, hydroxypyridinones form stable five-coordinate complexes on reaction with hydrotris(3,5-phenylmethylpyrazolyl)borate zinc hydroxide. Modeling studies suggest that hydroxypyridinonate ligands should be able to access the active site in the enzyme with ease (110). 

Fig. 11. The slowly hydrolyzed substrate glycyl-L-tyrosine binds to carboxypeptidase A in a nonproductive complex where the amino-terminal glycine complexes the active-site ion (large sphere) to form a five-membered chelate, as in Fig. 10. Protein-bound zinc ligands Glu-72, His-69, and His-196 complete the coordinadon polyhedron of pentacoordinate zinc. Active-site residues are indicated by one-letter abbreviadons and sequence numbers E, glutamate H, hisddine R, arginine Y, tyrosine. [Reprinted with permission from Christianson, D. W., Lipscomb, W. N. (1986) Proc. Natl. Acad. Sci. U.S.A. 83,7568-7572.]...

Metabolic Functions. Zinc is essential for the function of many enzymes, either in the active site, ie, as a nondialyzable component, of numerous metahoenzymes or as a dialyzable activator in various other enzyme systems (91,92). WeU-characterized zinc metahoenzymes are the carboxypeptidases A and B, thermolysin, neutral protease, leucine amino peptidase, carbonic anhydrase, alkaline phosphatase, aldolase (yeast), alcohol... 

Catalytic Oxidation. Catalytic oxidation is used only for gaseous streams because combustion reactions take place on the surface of the catalyst which otherwise would be covered by soHd material. Common catalysts are palladium [7440-05-3] and platinum [7440-06-4]. Because of the catalytic boost, operating temperatures and residence times are much lower which reduce operating costs. Catalysts in any treatment system are susceptible to poisoning (masking of or interference with the active sites). Catalysts can be poisoned or deactivated by sulfur, bismuth [7440-69-9] phosphoms [7723-14-0] arsenic, antimony, mercury, lead, zinc, tin [7440-31-5] or halogens (notably chlorine) platinum catalysts can tolerate sulfur compounds, but can be poisoned by chlorine. 

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 4.20 Detailed view of the zinc environment in carboxy-peptidase. The active-site zinc atom is bound to His 69 and Glu 72, which are part of the loop region outside P strand 2. In addition, His 196, which is the last residue of P strand 5, also binds the zinc.

In this structure the loop regions adjacent to the switch point do not provide a binding crevice for the substrate but instead accommodate the active-site zinc atom. The essential point here is that this zinc atom and the active site are in the predicted position outside the switch point for the four central parallel p strands, even though these p strands are only a small part of the total structure. This sort of arrangement, in which an active site formed from parallel p strands is flanked by antiparallel p strands, has been found in a number of other a/p proteins with mixed p sheets. 

An active-site zinc ion stabilizes negative charge development on the oxygen atom of acetaldehyde, leading to an induced partial positive charge on the carbonyl C atom. Transfer of the negatively charged hydride ion to this carbon forms ethanol. 

Two classes of aldolase enzymes are found in nature. Animal tissues produce a Class I aldolase, characterized by the formation of a covalent Schiff base intermediate between an active-site lysine and the carbonyl group of the substrate. Class I aldolases do not require a divalent metal ion (and thus are not inhibited by EDTA) but are inhibited by sodium borohydride, NaBH4, in the presence of substrate (see A Deeper Look, page 622). Class II aldolases are produced mainly in bacteria and fungi and are not inhibited by borohydride, but do contain an active-site metal (normally zinc, Zn ) and are inhibited by EDTA. Cyanobacteria and some other simple organisms possess both classes of aldolase. 

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. 

According to their genetic relationship and their biochemical mechanism of action (3-lactamases are divided into enzymes of the serine-protease type containing an active-site serine (molecular class A, C, and D enzymes) and those of the metallo-protease type (molecular class B enzymes), which contain a complex bound zinc ion. 

Carbonic anhydrase an insight into the zinc binding site and into the active cavity through metal substitution. I. Bertini, C. Luchinat and A. Scozzafava, Struct. Bonding (Berlin), 1982, 48, 46-92 (296). 

Bertini I, Luchinat C, Scozzafava A (1982) Carbonic Anhydrase An Insight into the Zinc Binding Site and into the Active Cavity Through Metal Substitution. 48 45-91 Bertrand P (1991) Application of Electron Transfer Theories to Biological Systems. 75 1-48 Bill E, see Trautwein AX (1991) 78 1-96 Bino A, see Ardon M (1987) 65 1-28 Blanchard M, see Linares C (1977) 33 179-207 Blasse G, see Powell RC (1980) 42 43-96... 

In the effect of active metal, copper was more stable and active than silver and zinc. In the effect of particle size, the smaller particle is the more stable and active. It seems that the catalysts with smaller particle size have more active sites compared with those of larger particle size in same space. Through out the Fig. 3 and Table 2, in the effect of reaction... 

A peptide, once released, is not subject to reuptake like most transmitters, but is broken down by membrane peptidases. There are no known peptide transporters so that reuptake and re-use are not likely. The peptidases are predominantly membrane bound at the synapse and many are metalloproteases in that they have a metal moiety, most often zinc, near the active site. These enzymes are generally selective for particular... 

Bertini, /., Luchinat, C., Scozzafava, A. Carbonic Anhydrase An Insight into the Zinc Binding Site and into the Active Cavity Through Metal Substitution. Vol. 48, pp. 45-91. 

Fig. 2.2 (A) Structure of full-length NS3 including the N-terminal protease domain (bottom) and C-terminal helicase domain (top). The NS4A peptide (purple) is covalently attached to the N-terminus of NS3 (see text). Within the protease domain the N- and C-terminal -barrels are at the right and left, respectively. The zinc atom is visible at the bottom left. [98]. (B) Surface view of the NS3 protease domain showing compound (1) bound at the relatively shallow active site (See also Fig. 2.6) [42].

While PDF was originally proposed to be a zinc-metalloprotease [51], it is now generally accepted that Fe is the physiologically relevant metal ion occupying the active site in vivo [52], The native forms of most PDF enzymes are highly unstable due to propensity to oxidation, rendering them difficult to purify [53, 54], However, the Fe can be suitably replaced by either or Co, both of which provide a stable enzyme and main-... 

X-ray diffraction studies on several forms of the enzyme have demonstrated that the active site is composed of a pseudo-tetrahedral zinc center coordinated to three histidine imidazole groups and either a water molecule [(His)3Zn-OH2]2+ (His = histidine), or a hydroxide anion [(His)3Zn-OH] +, depending upon pH (156,157). On the basis of mechanistic studies, a number of details of the catalytic cycle for carbonic anhydrase have been elucidated, as summarized in Scheme 22... 

The value of the tris(pyrazolyl)hydroborato complexes [TpRR ]ZnOH is that they are rare examples of monomeric four-coordinate zinc complexes with a terminal hydroxide funtionality. Indeed, [TpBut]ZnOH is the first structurally characterized monomeric terminal hydroxide complex of zinc (149). As such, the monomeric zinc hydroxide complexes [TpRR ]ZnOH may be expected to play valuable roles as both structural and functional models for the active site of carbonic anhydrase. Although a limitation of the [TpRR ]ZnOH system resides with their poor solubility in water, studies on these complexes in organic solvents... 

Fig. 42. Comparison of the coordination environment about zinc in the active site of carbonic anhydrase in its deprotonated form with that of [TpRR ]ZnOH. Reprinted with permission from Ref. (151). Copyright 1993 American Chemical Society.

Figure 6.11 Schematic diagrams of the active site zinc of MMP2 in the (A) latent form, (B) active form, and (C) when inhibited by compound 1 of Bernardo et al. (2002).

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