Enzyme, cleft metals

The enzyme consists of a protein chain of 307 a mi no acid residues plus one Zn-+ ton to yield a molecular weight of about 34.600. The molecule is roughly egg-shaped, with a maximum dimension of approximately 5000 pm and a minimum dimension of about 3800 pm (Fig. 19.21a). There is a cleft on one side that contains the zinc ion, the active site. The metal is coordinated approximately letrohedrally to two nitrogen atoms and an oxygen atom from three amino acids (His 69, Clu 72. His 169) in the protein chain ... 

As with carbonic anhydrase the metal is in a cleft that exposes the active site. Interestingly the metal-free enzyme is inactive but the cobalt and nickel analogues are more active. It appears that the transition state complex, where the terminal amino acid side chain is held in place while the peptide bond is hydrolysed, requires six-fold co-ordination. The activation energy required to change from the tetrahedral to octahedral geometries is higher for zinc than the other metals. 

The Walton group has also made models for zinc enzymes but attempted to incorporate another feature common to many of them, positioning the metal ion at the bottom of a constrictive cleft. The approach has the advantage that the only competing substrates ought to be small molecules that can fit inside the cleft. In the case of a compound based on cyclohexane the zinc is bound to acetate, as a model for bicarbonate, in a manner reminiscent of the enzyme. The compound, cis,cis-l,3, 5-tris[ , -3-(2-furyl)acrylideneamino]cyclohexane, has a pocket at its base, as shown in Fig. 4.21, for those metals that prefer a tetrahedral coordination geometry [43],... 

Notice that both structures contain a central metal ion (green) in their active sites, near a large cleft on the right. The similarity of these structures reveals that these enzymes have the same evolutionary origin and have many mechanistic features in common. [Drawn from 1l6V.pdb and ll6H.pdb.]... 

The active site zinc ion (see Fig. 11) is located in a shallow cleft which runs across the surface of the protein to the opening of a pocket in the enzyme surface. Note that the three zinc hgands contributed by the protein are positioned away from the cleft, while the inner sphere water molecule projects out into the cleft. The cleft is hned with several highly polar residues in the vicinity of the metal ion which are beheved to participate in substrate binding and/or catalysis. The pocket adjacent to the metal ion is lined with nonpolar (hydrophobic) residues. Both the cleft and the pocket are filled with water molecules which appear to be arranged in an ice-hke array. 

In the case of some metal-containing enzymes, there are, for example, two globular parts separated by a deep cleft. The metal atom sits inside the cleft. There is a hydrophobic recess near the metal atom and this probably absorbs the substrate, which means that it is responsible for the specificity of the enzyme. 

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