Oxygen Chiral Phosphate Esters

Gerlt, J.A.; Coderre, Jeffrey A.; Mehdi, Shujaath

doi:10.1002/9780470123010.ch4

Cited by 14 publications

(3 citation statements)

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“…Cleavage of phosphodiester bonds is thought to be done by a general acid–base catalysis, where the general base activates the nucleophile by deprotonation and the general acid facilitates product formation by protonating the leaving group. Perhaps because of the stability of nucleic acid phosphodiester bonds, the cleavage reaction is usually of the associative S N 2 type (Gerlt et al 1983). The reaction can be divided into three stages: nucleophilic attack, the formation of a highly negatively charged penta-covalent intermediate and the breakage of the scissile bond.…”

Section: Nucleolytic Reactionsmentioning

confidence: 99%

“…In the cleaved product, the stereo configuration of the phosphorus is inverted in this one-step reaction. Although phosphate in nucleic acid is achiral, due to two chemically indistinguishable non-bridging oxygen atoms, the stereo inversion is evident when one of the non-bridging oxygen is replaced by a heavy isotope or sulfur (Eckstein, 1985; Gerlt et al 1983). Hence, the two non-bridging oxygens are referred to as pro-Sp and pro-Rp.…”

Section: Nucleolytic Reactionsmentioning

confidence: 99%

See 1 more Smart Citation

Nucleases: diversity of structure, function and mechanism

Yang

2010

Quart. Rev. Biophys.

561

624

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Nucleases cleave the phosphodiester bonds of nucleic acids and may be endo or exo, DNase or RNase, topoisomerases, recombinases, ribozymes, or RNA splicing enzymes. In this review, I survey nuclease activities with known structures and catalytic machinery and classify them by reaction mechanism and metal-ion dependence and by their biological function ranging from DNA replication, recombination, repair, RNA maturation, processing, interference, to defense, nutrient regeneration or cell death. Several general principles emerge from this analysis. There is little correlation between catalytic mechanism and biological function. A single catalytic mechanism can be adapted in a variety of reactions and biological pathways. Conversely, a single biological process can often be accomplished by multiple tertiary and quaternary folds and by more than one catalytic mechanism. Two-metal-ion-dependent nucleases comprise the largest number of different tertiary folds and mediate the most diverse set of biological functions. Metal-ion-dependent cleavage is exclusively associated with exonucleases producing mononucleotides and endonucleases that cleave double- or single-stranded substrates in helical and base-stacked conformations. All metal-ion-independent RNases generate 2',3'-cyclic phosphate products, and all metal-ion-independent DNases form phospho-protein intermediates. I also find several previously unnoted relationships between different nucleases and shared catalytic configurations.

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Section: Nucleolytic Reactionsmentioning

confidence: 99%

Section: Nucleolytic Reactionsmentioning

confidence: 99%

Nucleases: diversity of structure, function and mechanism

Yang

2010

Quart. Rev. Biophys.

561

624

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“…In TMC reactions, two divalent metal ions are positioned on opposite ends of the scissile phosphate bond, at the interface between the protein or ribozyme catalyst and the substrate. The metal ions facilitate an S N 2-type reaction, in which the nucleophilic “attacking” oxygen replaces the “leaving” oxygen in the broken P–O bond of the phosphate on the opposite side. , Similar Mg 2+ ion selectivity has been found among many TMC enzymes; but in spite of numerous studies and detailed structural information, − the factors determining the functional competence − of different metal ions remain poorly understood.…”

Section: Introductionmentioning

confidence: 99%

Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis

2014

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Most phosphate-processing enzymes require Mg2+ as a cofactor to catalyze nucleotide cleavage and transfer reactions. Ca2+ ions inhibit many of these enzymatic activities, despite Ca2+ and Mg2+ having comparable binding affinities and overall biological abundances. Here we study the molecular details of the calcium inhibition mechanism for phosphodiester cleavage, an essential reaction in the metabolism of nucleic acids and nucleotides, by comparing Ca2+- and Mg2+ catalyzed reactions. We study the functional roles of the specific metal ion sites A and B in enabling the catalytic cleavage of an RNA/DNA hybrid substrate by B. halodurans ribonuclease (RNase) H1 using hybrid quantum-mechanics/molecular mechanics (QM/MM) free energy calculations. We find that Ca2+ substitution of either of the two active-site Mg2+ ions substantially increases the height of the reaction barrier and thereby abolishes the catalytic activity. Remarkably, Ca2+ at the A site is inactive also in Mg2+-optimized active-site structures along the reaction path, whereas Mg2+ substitution recovers activity in Ca2+-optimized structures. Geometric changes resulting from Ca2+ substitution at metal ion site A may thus be a secondary factor in the loss of catalytic activity. By contrast, at metal ion site B geometry plays a more important role, with only a partial recovery of activity after Mg2+ substitution in Ca2+-optimized structures. Ca2+-substitution also leads to a change in mechanism, with deprotonation of the water nucleophile requiring a closer approach to the scissile phosphate, which in turn increases the barrier. As a result, Ca2+ is less efficient in activating the water. As a likely cause for the different reactivities of Mg2+ and Ca2+ ions in site A, we identify differences in charge transfer to the ions and the associated decrease in the pKa of the oxygen nucleophile attacking the phosphate group.

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Chiral Phosphorothioates: Stereochemical Analysis of Enzymatic Substitution at Phosphorus

Frey

1989

Advances in Enzymology - And Related Areas of Molecular Biology

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Oxygen Chiral Phosphate Esters

Cited by 14 publications

References 122 publications

Nucleases: diversity of structure, function and mechanism

Nucleases: diversity of structure, function and mechanism

Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis

Chiral Phosphorothioates: Stereochemical Analysis of Enzymatic Substitution at Phosphorus

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