Carboxyl groups active site

The lone-pair electrons in a carboxylate group are designated syn or antiy as shown in Fig. 18. The proton on another molecule can approach in either of these directions. In the syn conformation (Z-form) the proton is on the same side of the C-0 bond as the other C-0 bond this is the conformation found when carboxyl groups dimerize by forming two hydrogen bonds. On the other hand, in the anti conformation (E-form) the proton is on the opposite side of the C-0 bond from the other C-0 bond. Ab initio quantum chemical studies of formic acid indicate that the syn (Z) conformation is more stable than the anti (E) conformation by about 4.5 kcal mol" implying that the syn lone pairs are more basic (and therefore bind metal ions more readily) than do the anti lone pairs [55]. Carboxylates in active sites of enzymes generally seem to employ the more basic syn lone pairs for metal chelation [56], and it has been estimated that syn protonation is 10 -fold more favorable than anti protonation (since 1.4 kcal mol corresponds approximately to a tenfold increase in rate). The carboxylate ion is therefore a weaker base when constrained to accept a proton in the anti (E) direction. 

The first hint that two active-site carboxyl groups—one proto-nated and one ionized—might be involved in the catalytic activity of the aspartic proteases came from studies of the pH dependence of enzymatic activity. If an ionizable group in an enzyme active site is essential for activity, a plot of enzyme activity versus pH may look like one of the plots at right. 

Results from an array of methods, including X-ray absorption, EXAFS, esr and magnetic circular dichroism, suggest that in all ureases the active sites are a pair of Ni" atoms. In at least one urease,these are 350 pm apart and are bridged by a carboxylate group. One nickel is attached to 2 N atoms with a fourth site probably used for binding to urea. The second nickel has a trigonal bipyramidal coordination sphere. 

Q The enzyme active site contains an aspartic acid, a histidine, and a serine. First, histidine acts as a base to deprotonate the -OH group of serine, with the negatively charged carboxylate of aspartic acid stabilizing the nearby histidine cation that results. Serine then adds to the carbonyl group of the triacylglycerol, yielding a tetrahedral intermediate. 

The HIV-1 protease, like other retroviral proteases, is a homodimeric aspartyl protease (see Fig. 1). The active site is formed at the dimer interface, with the two aspartic acids located at the base of the active site. The enzymatic mechanism is thought to be a classic acid-base catalysis involving a water molecule and what is called a push-pull mechanism. The water molecule is thought to transfer a proton to the dyad of the carboxyl groups of the aspartic acids, and then a proton from the dyad is transferred to the peptide bond that is being cleaved. In this mechanism, a tetrahedral intermediate transiently exists, which is nonconvalent and which is mimicked in most of the currently used FDA approved inhibitors. 

Fig. 8 Superimposition of inhibitors and key active site residues in influenza A virus sialidase cyclopentane-based inhibitor peramivir 34 (brown carbons, PDB - 117f), Neu5Ac2en 4 (green carbons, PDB - lf8b). Note the overlap of the carboxyl and acetamido-methyl groups of the inhibitors, and the alternative conformations of the side-chain of Glu276. To the right is shown peramivir 34 oriented as in the crystal structure...

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