Phosphoryl transfer nucleotidyl

The role of divalent cations in the mechanism of enzyme catalysed phosphoryl and nucleotidyl transfer reactions. A. S. Mildvan and C. M. Grisham, Struct. Bonding (Berlin), 1974,20,1-21 (88),... 

Catalyzed Phosphoryl and Nucleotidyl Transfer Reactions. - H. P. C. Hogenkamp,... 

Studies on the kinetic behaviour of nucleoside and nucleotide complexes are less common than those on structural aspects. This arises because of the rapid rates of the formation and dissociation reactions, requiring NMR or temperature-jump relaxation measurements. The number of species that can coexist in solution also hinders interpretation. The earlier kinetic studies have been reviewed by Frey and Stuehr.127 Two important biological reactions of the nucleotides are phosphoryl and nucleotidyl group transfers. Both reactions are catalytic nucleophilic reactions and they both require the presence of a divalent metal ion, in particular Mg2+. Consequently, one of the main interests has been in understanding the catalytic mechanism of the metal ion involvement. This has mainly involved studies on related non-enzymic reactions.128... 

Phosphoryl and nucleotidyl transfer enzymes are extremely important and widespread in biology. They have in common the catalysis of nucleophilic reactions of phosphorus esters, and the general requirement for divalent metal ions, particularly Mg11, for activity. This requirement has stimulated considerable interest in the catalytic roles of divalent metal ions in these reactions. 

This section emphasizes work done in the last few years. The reader is referred to other sources for reviews of older work236 or more general discussions of nucleophilic reactions at phosphorus.237"245 More general discussions of enzymic phosphoryl and nucleotidyl transfer are available,246 248 and the role of divalent metal ions has been reviewed.249"251... 

Using two enzymes, a mammalian adenylate cyclase and myosin ATPase, as examples the application of phosphorothioate analogues to the study of the mechanism of nucleotidyl and phosphoryl transfer will be described. 

These two examples illustrate the usefulness of the phospho-rothioate analogues of nucleotides as tools for the elucidation of certain aspects of enzymatic nucleotidyl and phosphoryl transfer reactions. 

Contents A. S. Mildvan, C. M. Grisham The Role of Divalent Cations in the Mechanism of Enzyme Catalyzed Phosphoryl and Nucleotidyl Transfer Reactions. - H.P.C.Hogenkamp, G.N.Sando The Enzymatic Reduction of Ribonucleotides. - W. T. Oosterhuis The Electronic State of Iron in Some Natural Iron Compounds. Determination by Mossbauer and ESR Spectroscopy. - A. Trautwein Mossbauer Spectroscopy on Heme Proteins. 

Volume VIII Group Transfer, Part A Nucleotidyl Transfer, Nucleosidyl Transfer, Acyl Transfer, Phosphoryl Transfer... 

This article will consider recent advances in the mechanism of model phosphoryl transfer reactions, magnetic resonance studies of phosphoryl and nucleotidyl transerring enzymes in solution and Xray diffraction studies in the crystalline state which have clarified or at least have suggested the role of the essential divalent cation. 

Phosphoryl and nucleotidyl transfer reactions are nucleophilic displacements on phosphorus 3—6), and like analogous displacements on carbon (7) or on metal ions (5), have been found to take place by mechanisms varying between two extreme or limiting cases 1. In the dissociative or SnI mechanism the initial departure of the leaving nucleophile, yields the planar triply coordinate metaphosphate anion as a reactive chemical intermediate (3, 8), which then combines with the entering ligand on either face of the metaphosphate plane 2. In the associative... 

Enzymes which catalyze the reaction type (a) include phosphodiesterases, phospholipases (C and D), nucleotidyl transferases, nucleases, and pyrophos-phokinases. The type (b) reaction involves mainly phosphokinases and phos-phomutases. The hydrolysis of phosphomonoesters (reaction type c) is catalyzed by phosphatases, nucleotidases, ATPases, and so on. Most phosphatases also catalyze the phosphoryl transfer reaction, type (b), if an alcohol is used as an acceptor. 

Phosphotransferases and nucleotidyltransferases were last reviewed in this series 15 years ago in Volumes VIII and IX. At that time a major mechanistic question was whether these enzymes catalyze their reactions by single-displacement or double-displacement mechanisms. The two mechanisms differed chemically with respect to whether the phosphoryl or nucleotidyl group is transferred directly between two substrates, or whether the group transfer is mediated by a nucleophilic group of the enzyme in a two-step mechanism via a covalent phos-phoenzyme or nucleotidyl-enzyme. 

For a simple Bi Bi reaction, Eq. (1) describes the overall course of group transfer, in which A and B symbolize the group donor and receptor, respectively, and P symbolizes the phosphoryl or nucleotidyl group. 

In this pathway the group donor binds to the active site and reacts with an enzymic nucleophile, transferring the group to the nucleophile, and the first product dissociates. In the second step the acceptor binds to the active site, and the phosphoryl or nucleotidyl group is then transferred to the acceptor from the enzymic nucleophile. 

Two kinds of information about nucleotidyltransferases and phosphotransferases are obtained by use of substrates or substrate analogs with chiral P. The stereochemical course of phosphoryl transfer and nucleotidyl transfer gives important information about the reaction mechanism. If inversion of configuration at phosphorus is observed, it may be concluded that an uneven number of displacements at phosphorus occurs in the reaction mechanism. If retention of configuration at phosphorus is observed, it may be concluded that the mechanism entails an even number of displacements at phosphorus. Inversion corresponds to the single-displacement mechanism of Eq. (2), and retention indicates a mechanism such as that of Eq. (3) or Eqs. (4a) and (4b). 

A few nucleotidyltransferases and phosphotransferases act by mechanisms that include a covalent nucleotidyl-enzyme or phosphoenzyme as a compulsory intermediate. A few more ATP-dependent synthetases act by such mechanisms. However, the overwhelming majority of these enzymes catalyze phosphoryl or nucleotidyl group transfer by mechanisms that entail the direct, one-step transfer of the nucleotidyl group or phosphoryl group between two substrates bound in adjacent subsites at the active site. 

The rationale for the different mechanisms of the other paired reactions [(36a) and (36b) and (37a) and (37b)] is exactly the same. This pattern is followed by all enzymes of this class. That is, nucleophilic catalysis and covalent intermediates, which are necessary and required for the Ping-Pong kinetic pathway to operate, are found only in those cases involving Ping-Pong kinetics. No phosphotransferase or nucleotidyltransferase is known to catalyze phosphoryl or nucleotidyl group transfer by a sequential kinetic pathway via a doubledisplacement mechanism. However, it is not certain that in all cases of double... 

The inference from stereochemical studies is that pseudorotation is not involved in enzymic phosphoryl and nucleotidyl transfer reactions. However, the involvement of pseudorotation has been postulated in several biological reactions involving six-membered-ring phosphorus species. These are discussed in Section 4. 

ATP is the primary source of utilizable energy for biosynthetic reactions, but other purine and pyrimidine nucleoside triphosphates (GTP, UTP, CTP) occur in cells and are formed by phosphoryl transfer from ATP, as described in detail in Chapter 4. These are also high-energy compounds, and their hydrolysis can be coupled to energetically unfavorable reactions. This most commonly takes place through nucleotidyl transfer reactions leading to group-transfer coenzymes (Section II, B, 3). 

Mildvan and Grisham have reviewed the role of bivalent cations in the mechanism of enzyme-catalysed phosphoryl and nucleotidyl transfer reactions. 

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