Metals sequence similarities

Although they often share little sequence similarity and have quite different specificiities, many restriction enzymes have similar three-dimensional structures as well as mechanisms of action. This is true for the EcoRI, BamHl (Fig. 26-5),83/90 EcoRV,91/91a and C/r 101 enzymes,84 and presumably many others. The specifically shaped and tightly packed active sites in the enzyme-substrate complexes ensure specificity. For example, the EcoRV endonuclease cleaves DNA at its recognition site at least a million times faster than at any other DNA sequence.91 As mentioned in Chapter 12, restriction endonucleases require a metal ion, preferably Mg2+, and probably act via a hydroxyl ion generated from Mg2+-OH2 at the active site. Three conserved active site residues, Asp 91, Glu 111, and Lys 113, in the EcoRI endonuclease interact with the DNA near the cleavage site. Lys 113 is replaced by Glu 113 in the BamHl enzyme.83 90... 

Sequence Similarities in Metal and Anion Binding Sites0... 

We open with a brief report of the early discovery of the occurrence and isolation of these proteins and the elucidation of their function and homology, followed by a brief discussion of some problems in their isolation and the determination of their activity. We then consider various aspects of their three-dimensional structures and their significance. We summarize studies on the implications of their sequence similarities, and also on the binding of metal ions, especially calcium(H), and consider their implications. Then follows a brief discussion of lactose synthase, an enzyme of which a-lactalbumin and galactosyltransferase are essential components. We then examine the evidence concerning the evolution of the two proteins, about which there are conflicting views (see Section X,B). Some conclusions and predictions of future directions are made. 

Purple acid phosphatases (PAPs) catalyze the hydrolysis of phosphate monoesters with mildly acidic pH optima (5-7) utilizing a binuclear metal center containing a ferric ion and a divalent metal ion. PAPs are also characterized by their purple color, the result of a tyrosine (Tyr) to Fe3+ charge transfer transition at about 560nm.113 All known mammalian PAPs are monomeric and have a binuclear Fe3+-Fe2+ center, whereas the kidney bean and soybean enzymes are dimeric and have an Fe3 + -Zn2+ center in each subunit. The X-ray structures for kidney bean PAP114 and the PAP115 from rat bone reveal that despite a sequence similarity of only 18%, they share very similar catalytic sites. The structure of the kidney bean PAP shows the two metal ions at a distance of 3.1 A, with a monodentate bridging Asp-164. These and other residues involved in metal coordination can be seen in Fig. 21. 

In addition to PTPs, serine/threonine phosphatases, which are metal-dependent enzymes and share no sequence similarities to PTPs, have also been subject of ABPP studies by the functionalization of the natural product microcystin that will be discussed in the natural product section (Section 9.17.3.3.5).97 108... 

In substrates where a halogen is located ortho to nitrogen, ring closure to benzimidazoles can be achieved by palladium(0)-catalysed or copper-catalysed sequences similar formation of benzothiazoles from orf/20-haloarylamine-thioamides, does not require a metal catalyst. ... 

The crystal structures for kidney bean PAP and the PAP from rat bone reveal that despite a sequence similarity of only 18%, the plant and mammalian enzymes share very similar catalytic sites. All PAPs that have been sequenced share a conserved set of active-site residues, and all structures have a similar metal center geometry. These are typified by the kidney bean PAP, in which the two metal ions are separated by 3.1 A with monodentate bridging Asp carboxylate. These and other residues involved in metal coordination can be seen in Figure 9. In addition to the metal ligands, most PAPs have two histidine residues in the region of the metal center that have been shown to be important for substrate positioning and, potentially, as a general acid in catalysis. 

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