Catalysis 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,... 

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. 

Intermolecular catalysis in hydrolysis of carboxyl amides, carboxyl esters, or phosphodiesters by Co(III) ion untethered to the substrate was accomplished when 3,3, 3"-triaminotripropylamine (trpn AD) or 1,4,7,10-tetraazacyclodode-cane (cyclen AE) was employed as the chelating ligand of the Co(III) ion (88— 90). In particular, parameter values for the hydrolysis of formylmorpholine catalyzed by [Co(cyclen)(OH2)] were measured at 60°C in D2O (AF, AG). Inspite of the exchange-inertness (91) of Co(III), the carboxylate or phosphate anion coordinated to the Co(in) ion complexed by cyclen or trpn dissociated readily without affecting the overall rate of the catalytic process. 

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. 

Better acceleration rates and catalysis of more complex reactions were obtained by direct selection. In this strategy, selection is not based on a binding event rather it is based directly on the desired catalytic event For example, if the to-be-catalysed reaction is phosphodiester hydrolysis, the RNA library is immobilized on solid support. The selection event is thus directly tailored to hydrolysis active molecules cleave their covalent linkage to the solid support and thus dissociate from it The catalytic event thus enables spatial separation of active and inactive molecules. Direct selection has therefore allowed to isolate catalysts for numerous RNA-modilying reactions, from hydrolysis and ligation to RNA alkylation, acylation, phosphorylation and many others (see below). 

En me Mechanism. Staphylococcal nuclease (SNase) accelerates the hydrolysis of phosphodiester bonds in nucleic acids (qv) some 10 -fold over the uncatalyzed rate (r93 and references therein). Mutagenesis studies in which Glu43 has been replaced by Asp or Gin have shown Glu to be important for high catalytic activity. The enzyme mechanism is thought to involve base catalysis in which Glu43 acts as a general base and activates a water molecule that attacks the phosphodiester backbone of DNA. To study this mechanistic possibiUty further, Glu was replaced by two unnatural amino acids. 

The hydrolysis of adenosine 3. 5 -cyclic monophosphate (cAMP) by the cobalt complexes (215) was considered here earlier,187 as was the Ce(IV)-catalysed hydrolysis of phospho monoesters in nucleotides.189 A review (ca 100 references) on current data on the mechanism of cleavage-transesterification of RNA has appeared.258 In this review special attention was focused on the two crucial steps in the hydrolysis of RNA, i.e. cleavage-transesterification and hydrolysis of the cyclic phosphodiester (Scheme 14). The catalysis of various amines for the hydrolysis of RNA has been looked at and ethylenediamine and propane-1,3-diamine are highly active under physiological conditions because they exist as the catalytically active monocation forms.259... 

Prior to the X-ray analysis, the stereochemical course of the hydrolysis of the Sp diastereomer of thymidine 3 -(4-nitrophenyl [ 0, 0]phosphate) 5 -(4-nitrophenyl phosphate) in H2 0 was determined (26). This synthetic oligonucleotide analog is not a good substrate, and the Sp diastereomer of thymidine 3 -[ 0, 0, 0]phosphate 5 -(4-nitrophenyl phosphate) was obtained as product (recall that on double-stranded DNA the oligonucleotide products contain S -phosphate groups). The simplest explanation for this inversion of configuration is that the enzyme catalyzes the direct attack of water on the phosphodiester backbone of double-stranded DNA, presumably by general basic catalysis. 

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