Catalysis cyclic phosphate formation

Recently the related cyclization of the phenyl ester of c/j-tetrahydrofuran-3,4-diol monophosphate to the corresponding five-membered phosphate with loss of phenol has been shown to be subject to general catalysis by imidazole132. This reaction serves as a model for the first step in the action of ribonuclease which leads to the formation of the nucleoside 2 ,3 -cyclic phosphate. The actual details of the transition state leading to the cyclic phosphate as catalyzed by the enzyme are presently the subject of some debate. One possibility is the in-line mechanism (53)... 

In the author s own laboratory the Cu(II)-catalyzed hydrolysis of the phosphate ester derived from 2-[4(5)-imidazolyl] phenol recently has been investigated146. The pertinent results are (a) the pre-equilibrium formation of a hydrolytically labile Cu(II)-substrate complex (1 1), (b) the occurrence of catalysis with the free-base form of the imidazolyl and phosphate moieties and (c) the extraordinary rate acceleration at pH 6 (104) relative to the uncatalyzed hydrolysis146. The latter recalls the unusual rate enhancement encountered above with five-membered cyclic phosphates and suggests a mechanism in which the metal ion, at the center of a square planar complex or a distorted tetrahedral complex, might induce strain in the P-O ester bonds (60). viz. 

RNase Tl cleaves P-05 ester bonds in ssRNA, specifically at the 3 -P of the guanylic acid residues. As in RNase A (see Fig. 3.3), the catalysis occurs by a two-step mechanism, i.e., the formation of a terminal guanosine 2, 3 -cyclic phosphate intermediate (transesterification step) and the hydrolysis of the cyclic ester to guanosine 3 -monophosphate (hydrolysis step). The transesterification step involves a general acid—base catalysis. 

Ribonuclease A hydrolyzes RNA adjacent to pyrimidine bases. The reaction proceeds through a 2, 3 -phosphate cyclic diester intermediate. Formation and breakdown of the cyclic diester appear to be promoted by concerted general-base and general-acid catalysis by two histidine residues, and by electrostatic interactions with two lysines. These reactions proceed through pentavalent phosphoryl intermediates. The geometry of these intermediates resembles the geometry of vanadate compounds that act as inhibitors of the enzyme. 

Another type of bond that is ubiquitous in nature is phosphodiester bond making up the backbone of DNA or RNA. Enzymes can use more than one amino acid side chain in their active side for simultaneous bifimctional or multifunctional catalysis. Often an add-base catalyst is formed as in the enzyme ribonuclease A. The natural enzyme consists of 124 amino acids and catalyzes the hydrolysis of RNA phosphodiester bonds between the phosphorous atom and the 5 -oxygen atom. The mechanism of ester cleavage proceeds via a 2, 3 cyclo-phosphate intermediate. The histidine 119 and 12 function as acid and base to catalyze the formation of the cyclic intermediate while the lysine stabilizes the pentacoordinated transition state. The hydrolysis of the cyclic intermediate is then again catalyzed by both histidine residues (Figure 26). ... 

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