Leaving group

Abstract: A mechanism is proposed for the RNA-catalyzed reactions involved in RNA splicing and RNase P hydrolysis of precursor tRNA. The mechanism postulates that chemical catalysis is facilitated by two divalent metal ions 3.9 A apart, as in phosphoryl transfer reactions catalyzed by protein enzymes, such as the 3',5'-exonuclease of Escherichia coli DNA polymerase I. One metal ion activates the attacking water or sugar hydroxyl, while the other coordinates and stabilizes the oxyanion leaving group. Both ions act as Lewis acids and stabilize the expected pentacovalent transition state. The symmetry of a two-metal-ion catalytic site fits well with the known reaction pathway of group I self-splicing introns and can also be reconciled with emerging data on group II self-splicing introns, the spliceosome, and RNase P. The role of the RNA is to position the two catalytic metal ions and properly orient the substrates via three specific binding sites.

Abstract: Alkaline phosphatase was the first zinc enzyme to be discovered in which three closely spaced metal ions (two Zn ions and one Mg ion) are present at the active center. Zn ions at all three sites also produce a maximally active enzyme. These metal ions have center-to-center distances of 3.9 A (Zn1-Zn2), 4.9 A (Zn2-Mg3), and 7.1 A (Zn1-Mg3). Despite the close packing of these metal centers, only one bridging ligand, the carboxyl of Asp51, bridges Zn2 and Mg3. A crystal structure at 2.0-A resolution of the noncovalent phosphate complex, E.P, formed with the active center shows that two phosphate oxygens form a phosphate bridge between Zn1 and Zn2, while the two other phosphate oxygens form hydrogen bonds with the guanidium group of Arg166. This places Ser102, the residue known to be phosphorylated during phosphate hydrolysis, in the required apical position to initiate a nucleophilic attack on the phosphorous. Extrapolation of the E.P structure to the enzyme-substrate complex, E.ROPO4(2-), leads to the conclusion that Zn1 must coordinate the ester oxygen, thus activating the leaving group in the phosphorylation of Ser102. Likewise, Zn2 appears to coordinate the ester oxygen of the seryl phosphate and activate the leaving group during the hydrolysis of the phosphoseryl intermediate. Both of these findings suggest that there may be a significant dissociative character to each of the two displacements at phosphorous catalyzed by alkaline phosphatase. A water molecule (or hydroxide) coordinated to Zn1 following formation of the phosphoseryl intermediate appears to be the nucleophile in the second step of the mechanism. Dissociation of the product phosphate from the E.P intermediate is the slowest, 35 s-1, and therefore the rate-limiting, step of the mechanism at alkaline pH. Since the determination of the initial crystal structure of alkaline phosphatase, two other crystal structures of enzymes involved in phosphate ester hydrolysis have been completed that show a triad of closely spaced zinc ions present at their active centers. These enzymes are phospholipase C from Bacillus cereus (structure at 1.5-A resolution) (43) and P1 nuclease from Penicillium citrinum (structure at 2.8-A resolution) (74). Both enzymes hydrolyze phosphodiesters. Substrates for phospholipase C are phosphatidylinositol and phosphatidylcholine, while P1 nuclease is an endonuclease hydrolyzing single stranded ribo- and deoxyribonucleotides. P1 nuclease also has activity as a phosphomonoesterase against 3'-terminal phosphates of nucleotides. The Zn ions in both enzymes form almost identical trinuclear sites.(ABSTRACT TRUNCATED AT 400 WORDS)

Abstract: Alcohols are relatively common starting materials for chemical reactions, even though they are quite unreactive. For example, reactions that would substitute another functional group (a nucleophile) for OH often fail because the hydroxide group (HO−) is difficult to displace—it is a poor leaving group. Alcohols are usually activated by turning the hydroxide into a better leaving group, either by protonating the alcohol or by converting it into a sulfonate or halide. However, both of these activation methods have some disadvantages ( 1 ). The acidic environment required for protonating the alcohol also protonates and deactivates the incoming nucleophile, especially amines. Conversion of the alcohol into a sulfonate or halide can lead to toxicity problems; many alkyl halides and alkyl sulfonates are mutagenic.

Abstract: Ylides are nucleophiles that bear a unique leaving group, LnM, and can attack aldehydes, ketones, imines, and electron-deficient alkenes. Over the course of the reaction, they react with C═X (X = C, N, O, etc.) double bonds to form betaine or oxetane intermediates, which further eliminate the heteroatom-containing group in one of two ways to give the corresponding olefination or cyclization product. Since the discovery of the Wittig reaction, ylide olefination has developed as one of the most useful approaches in constructing carbon−carbon double bonds. These reactions provide unambiguous positioning of the C−C double bond and good stereoselectivity. Researchers have also widely used ylides for the synthesis of small ring compounds such as epoxides, cyclopropanes, and aziridines. However, the use of ylides to prepare larger cyclic structures was very limited. This Account outlines our recent work on ylide-initiated Michael addition/cyclization reactions. By altering the heteroatoms and the ligands of the ...