Catalytic zinc enzymes

Chewier, B., Schalk, C., D Orchymont, H., Rondeau, J.-M., Moras, D., Tarnus, C. Crystal structure of Aeromonas proteolytica ami-nopeptidase a prototypical member of the co-catalytic zinc enzyme family. Structure, 1994, 2, 283-291. 

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. 

As an illustration, we briefly discuss the SCC-DFTB/MM simulations of carbonic anhydrase II (CAII), which is a zinc-enzyme that catalyzes the interconversion of CO2 and HCO [86], The rate-limiting step of the catalytic cycle is a proton transfer between a zinc-bound water/hydroxide and the neutral/protonated His64 residue close to the protein/solvent interface. Since this proton transfer spans at least 8-10 A depending on the orientation of the His 64 sidechain ( in vs. out , both observed in the X-ray study [87]), the transfer is believed to be mediated by the water molecules in the active site (see Figure 7-1). To carry out meaningful simulations for the proton transfer in CAII, therefore, it is crucial to be able to describe the water structure in the active site and the sidechain flexibility of His 64 in a satisfactory manner. 

The first zinc enzyme to be discovered was carbonic anhydrase in 1940, followed by car-boxypeptidase A some 14 years later. They both represent the archetype of mono-zinc enzymes, with a central catalytically active Zn2+ atom bound to three protein ligands, and the fourth site occupied by a water molecule. Yet, despite the overall similarity of catalytic zinc sites with regard to their common tetrahedral [(XYZ)Zn2+-OH2] structure, these mononuclear zinc enzymes catalyse a wide variety of reactions, as pointed out above. The mechanism of action of the majority of zinc enzymes centres around the zinc-bound water molecule,... 

Coordination motifs in catalytic sites of some typical mononuclear zinc enzymes... 

Several zinc enzymes that catalyse the hydrolysis of phosphoesters have catalytic sites, which contain three metal ions in close proximity (3-7 A from each other). These include (Figure 12.11) alkaline phosphatase, phospholipase C and nuclease PI. In phospholipase C and nuclease PI, which hydrolyse phosphatidylcholine and single-stranded RNA (or DNA), respectively, all three metal ions are Zn2+. However, the third Zn2+ ion is not directly associated with the dizinc unit. In phospholipase C, the Zn-Zn distance in the dizinc centre is 3.3 A, whereas the third Zn is 4.7 and 6.0 A from the other two Zn2+ ions. All three Zn2+ ions are penta-coordinate. Alkaline phosphatase, which is a non-specific phos-phomonoesterase, shows structural similarity to phospholipase C and PI nuclease however,... 

The structure and mechanism of catalysis of FTase were well defined in the late 1990s from several X-ray crystallography and elegant biochemical studies [24,26-30]. The enzyme is a heterodimer of a and P subunits [31,32]. The P subunit contains binding sites for both the farnesyl pyrophosphate and the CAAX protein substrates. A catalytic zinc (Zn " ) identified in the active site of the P subunit participates in the binding and activation of the CAAX protein substrates [28]. The Zn " is coordinated to the enzyme in a distorted tetrahedral geometry and surrounded by hydrophobic pockets [24,27]. Upon binding of the CAAX peptide, the thiol of the cysteine displaces water and is activated for a nucleophilic attack via thiolate on the C-1 carbon atom of farnesyl pyrophosphate [30]. 

Sharma and Reed, 1976)]. In proteins the coordination number 4 is most common, where the zinc ion is typically coordinated in tetrahedral or distorted tetrahedral fashion. The coordination polyhedron of structural zinc is dominated by cysteine thiolates, and the metal ion is typically sequestered from solvent by its molecular environment the coordination polyhedron of catalytic zinc is dominated by histidine ligands, and the metal ion is exposed to bulk solvent and typically binds a solvent molecule (Vallee and Auld, 1990). The inner-sphere coordination number of catalytic zinc may increase to 5 during the course of enzymatic turnover, and several five-coordinate zinc enzyme—substrate, enzyme product, and enzyme-inhibitor complexes have been studied by high-resolution X-ray crystallographic methods (reviewed by Matthews, 1988 Christianson and Lipscomb, 1989). The coordination polyhedron of zinc in five coordinate examples may tend toward either trigonal bipyramid or octahedral-minus-one geometry. 

Four examples of catalytic or regulatory zinc proteins are reviewed here, and the discussion of metalloprotein function is set within the context of the metal ion and its coordination polyhedron. In the zinc enzymes carbonic anhydrase (carbonate dehydratase) II and carboxypeptidase A, the coordination polyhedron of the metal ion changes as the... 

II aldolases FucA and RhuA from E. coli have been crystallized solution of their spatial structures confirmed a close similarity in their overall fold [14]. Both enzymes are homotetramers in which subunits are arranged in C4 symmetry. The active site is assembled in deep clefts at the interface between adjacent subunits, and the catalytic zinc ion is tightly coordinated by three His residues. From X-ray... 

The active site of LADH contains an Asp-His-Zn triad (see Figure 11). This pattern is quite common in zinc-enzymes. The aspartate affects the structure, electronic properties and energetics of the active site and thus the catalytic activity. Indeed, Asp49 is conserved in all mammalian ADHs . 

The MMP enzyme family is part of the superfamily of metzincins. The metzincin superfamily is distinguished by a conserved zinc binding motif for the catalytic zinc and a Met-turn region [4]. The MMPs are unique in that they also contain a second structural zinc, however this zinc may be absent in the intact full-length enzyme [5]. The presence of one to four structural calcium ions has been detected in the MMPs that have been characterized to date. The importance of the zinc ions and at least one of the structural calcium ions to enzymatic activity has been proven [6]. 

Several crystal structures of the enzyme in the presence of the coenzyme and substrate or substrate analogues have served as important indicators of the role of the coenzyme in the enzymic reaction. A crystal structure of the enzyme in the presence of NAD+ and p-bromobenzyl alcohol as substrate revealed that the oxygen of the alcohol is directly bound to the catalytic zinc, thus putting the carbon 1 of the alcohol 3.5 A from carbon 4 of the nicotinamide ring the substrate is thus positioned ideally for direct transfer of hydrogen. The position of the alcohol is close to where the water molecule is bound in the free enzyme, but it was not possible to establish whether this had been displaced on binding of the substrate.1364... 

It was originally assumed that in LADH the zinc existed in an octahedral form with six bonds available for coordination, until in 1967 Vallee and co-workers showed that the enzyme contained two different types of zinc atom.13773 Loss of two zinc atoms from the enzyme resulted in loss of catalytic activity but maintained the tertiary structure. It was postulated from this that one metal ion per subunit played a role maintaining the tertiary structure, while the other zinc functioned in a catalytic role. Only two of the zinc ions in the liver enzyme interact with the inhibitors 1,10-phenanthroline and 2,2 -bipyridyl, thus demonstrating the different chemical reactivities of the zinc ions.1378 It was also shown that one zinc per subunit could be selectively exchanged or removed by dialysis. This modified enzyme containing one zinc per subunit did not bind 1,10-phenanthroline, hence the catalytic zinc is removed first during dialysis.1379 The second zinc atom can be selectively removed in preference to the catalytic zinc, by carboxymethylation followed by dialysis.1377 ... 

The UV spectra of these complexes are very similar to those found in tetrahedral complexes of Co11 known to have a somewhat distorted geometry, suggesting a similar geometry in the cobalt enzyme.1383 Tetrahedral mercaptide complexes of the type [Co(SPh)4]2- were also shown to have similar absorption characteristics to those of [(LADH)Co2Co2j. This work is in complete agreement with the X-ray crystallographic studies of the native LADH, already mentioned, which shows distorted tetrahedral coordination of both the catalytic and non-catalytic zinc atoms of the enzyme. 

Each subunit is made up of two unequal domains. The active site is at the bottom of a hydrophobic pocket, about 25 A from the protein surface. The non-catalytic zinc, some 25 A away, is near the surface, but is not exposed to solvent. Both sites are on the larger domain, while the smaller domain provides the site for the coenzyme. Formation of the enzyme-NAD(H) complex induces major conformational changes,543 in which there is a rotation of the catalytic domain resulting in a narrowing of the active-site cleft. 

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