Phosphodiester hydrolysis

Catalysis, general base (Continued) in phosphodiester hydrolysis by SNase, 190... 

Reactive trajectories, 43-44,45, 88,90-92,215 downhill trajectories, 90,91 velocity of, 90 Relaxation processes, 122 Relaxation times, 122 Reorganization energy, 92,227 Resonance integral, 10 Resonance structures, 58,143 for amide hydrolysis, 174,175 covalent bonding arrangement for, 84 for Cys-His proton transfer in papain, 141 for general acid catalysis, 160,161 for phosphodiester hydrolysis, 191-195,... 

Transition states (Continued) in hydrogen abstraction, 25 in phosphodiester hydrolysis, 190 reactant-like vs product-like, 96 solvation energy of, 211, 213,214 solvent effects on, 46 stabilization of charge distribution, 91, 225-227... 

While formation of a dinucleotide may be represented as the elimination of water between two monomers, the reaction in fact strongly favors phosphodiester hydrolysis. Phosphodiesterases rapidly catalyze the hydrolysis of phosphodiester bonds whose spontaneous hydrolysis is an extremely slow process. Consequently, DNA persists for considerable periods and has been detected even in fossils. RNAs are far less stable than DNA since the 2khydroxyl group of RNA... 

DNA (phosphodiester) hydrolysis has also been examined with [Co(cyclen)(OH2)(OH)]2+ as the active species.1239,1246 Significant rate enhancement of linear1247 and supercoiled1248 double-stranded polydeoxyribonucleotide hydrolysis is observed by immobilizing the Co complex on a polystyrene support. Wider exploration of reactions with DNA follow. 

Also, Chin s dihydroxy-bridged dicobalt(III) complex 10 provides one of the largest rate enhancements ever observed for phosphodiester hydrolysis [36]. Reaction with the activated phosphodiester methyl(p-nitrophenyl)phosphate (MNPP) yields 11. A crystal structure is available for the analogous dimethylphosphate complex in which the Co ions are 2.9 A apart. At pH 7 and 45 °C 11 releases p-nitrophenolate with k = 0.1 s 1 which corresponds to a nearly 10I2-fold rate enhancement over spontaneous hydrolysis of the substrate. The product of the reaction is a methylphosphate-bridged complex. Based on the pH rate profile and on... 

A series of diaquatetraaza cobalt(III) complexes accelerated the hydrolysis of adenylyl(3 -50adenosine (ApA) (304), an enhancement of 10 -fold being observed with the triethylenetetramine complex (303) at pH 7. The pentacoordinated intermediate (305), which is formed with the complex initially acting as an electrophilic catalyst, then suffers general acid catalysis by the coordination water on the Co(III) ion to yield the complexed 1,2-cyclic phosphate (306), the hydrolysis of which occurs via intracomplex nucleophilic attack by the metal-bound hydroxide ion on the phosphorus atom. Neomycin B (307) has also been shown to accelerate the phosphodiester hydrolysis of ApA (304) more effectively than a simple unstructured diamine. 

Phosphodeoxyribomutase, PHOSPHOPENTOMUTASE PHOSPHODIESTERASES See also specific enzyme Phosphodiester hydrolysis,... 

The Co(m)-complex of cyden, Co(m)Cyc, is one of the most effedive synthetic catalysts discovered so far for the hydrolysis of supercoiled DNAs [59]. The hydrolytic nature of DNA cleavage by the Co(m) complexes of polyamines including cyden has been well documented [57, 58]. The mechanism illustrated in 25 has been proposed [57] for the catalytic action of the Co(m) complexes. Given the remarkable enhancement of proteolytic activity of Cu(n)Cyc upon attachment to PCD [49], we tested the activity of Co(m)Cyc in phosphodiester hydrolysis to see if it is also enhanced greatly upon attachment to PCD derivatives [61, 62]. 

Phosphodiester hydrolysis -Elimination Aza-Diels-Alder Allylic rearrangement... 

Janda KD. A bait and switch hapten strategy generates catalytic 70. antibodies for phosphodiester hydrolysis. Proc. Natl. Acad. Sci. 

Sun W, Pertzev A, Nicholson AW. Catalytic mechanism of Escherichia coli ribonuclease 111 kinetic and inhibitor evidence for the involvement of two magnesium ions in RNA phosphodiester hydrolysis. Nucleic Acids Res. 2005 33(3) 807-815. 

In view of the apparent convergent evolution of mechanism in the serine and cysteine protease family, it is interesting that two phosphodiesterases that require Ca + for catalytic activity by virtue of presumed electrophilic catalysis via direct coordination to the anionic phosphoryl oxygens of the substrate have evolved conceptually similar (general basic catalysis) but structurally distinct solutions to the problem of phosphodiester hydrolysis. 

Phosphodiesters hydrolysis (thymidine 5 -monophosphate 4-nitrophenyl ester, 1.6 x 10 )... 

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