Mechanism and Catalysis of Nucleophilic Substitution in Phosphate Esters

Thatcher, Robert J.; Kluger, Ronald

doi:10.1016/s0065-3160(08)60019-2

Cited by 278 publications

(299 citation statements)

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“…for phosphoryl transfer reactions, which ATP and GTP hydrolysis are examples of, are usually described by a structure somewhere between dissociative and associative extremes (6). In the fully dissociative mechanism, reactions proceed via a metaphosphate intermediate, which is subsequently attacked by the nucleophile.…”

mentioning

confidence: 99%

The Mechanism of GTP Hydrolysis by Ras Probed by Fourier Transform Infrared Spectroscopy

Du¹,

Frei²,

Kim³

2000

Journal of Biological Chemistry

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Ras plays a central role in cell signaling pathways that control cell proliferation, differentiation, and metabolism (1-3). The signal is transmitted by the Ras-GTP complex, and hydrolysis of GTP to GDP turns the signal off. The intrinsic GTP hydrolysis rate is rather low, and it is greatly enhanced by GTPase-activating proteins. Numerous studies have been devoted to the mechanism of GTP hydrolysis by Ras in the presence or absence of GTPase-activating protein. Despite extensive structural, kinetic, and site-directed mutagenesis data, no consensus regarding key mechanistic aspects of catalysis by Ras has thus far been reached (4).Much of the debate has recently centered on the nature of the transition state for GTP hydrolysis (4, 5). The transition states for phosphoryl transfer reactions, which ATP and GTP hydrolysis are examples of, are usually described by a structure somewhere between dissociative and associative extremes (6). In the fully dissociative mechanism, reactions proceed via a metaphosphate intermediate, which is subsequently attacked by the nucleophile. In contrast, a fully associative mechanism involves a trigonal bipyramidal intermediate, followed by the departure of the leaving group. Between these two limits exist concerted pathways featuring trigonal bipyramidal transition states with no distinct intermediate. For GTP hydrolysis by Ras, several distinct models have been developed to explain the biochemical and mutagenesis data (4,5,7,8). While some groups have been looking for a general base that activates the water molecule in the active site to render it a better nucleophile (8 -10), others emphasized the contribution from transition state stabilization by Ras (7, 11). An underlying feature common to these models is the assumption that the transition state of the GTP hydrolysis is associative in nature. It is based on the observation that the ␥-phosphoryl group is surrounded by positive charges capable of neutralizing the negative charges accumulating on the ␥-phosphoryl oxygens in an associative transition state (7,(12)(13)(14). Evidence supporting an associative mechanism includes the following: (i) an observed linear free energy relationship between the rates of GTP hydrolysis by Ras mutants and the pK a values of the ␥-PO 3 2Ϫ group of GTP bound to these mutants (5); (ii) the observation that the catalytically important residues interact extensively with the transition state analog GDP-AlF 4 Ϫ in the crystal structures of Ras-GDP-AlF 4 Ϫ -GTPase-activating protein (15), G i␣1 -GDP-AlF 4 Ϫ (16), and transducin ␣-GDP-AlF 4 Ϫ (17). This assumption has been strongly challenged by Maegley et al. (4), who argued that the transition state is more likely dissociative in nature based on the following: (i) a wealth of physical organic data that implicates a dissociative, metaphosphate-like transition state in solution reactions of phosphate monoesters, acyl phosphates, phosphorylated amines (6), and phosphoanhydride (18); and (ii) the fact that the localization of positively charged side chains a...

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mentioning

confidence: 99%

The Mechanism of GTP Hydrolysis by Ras Probed by Fourier Transform Infrared Spectroscopy

Du¹,

Frei²,

Kim³

2000

Journal of Biological Chemistry

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“…In this way, a pentavalent trigonal bipyramidal intermediate is formed, where the nucleophile and the leaving group are located on the apical positions (see Figure 6). [105][106][107][108] In OPCs with more than a potential leaving group, the intermediate structure influences which group will be replaced, determining the product stereochemistry. In OPCs, it is common a competition between a alcoxy and a thioalkyl leaving group, the former being more electronegative and the latter being more polarizable, less basic and, therefore, a better leaving group.…”

Section: Mechanism Of Action Of Opcsmentioning

confidence: 99%

“…20, No. 3, 2009 effects, the most electronegative substituents tend to occupy the apical positions in trigonal bipyramidal structures, 107,109,110 which would make them the preferable leaving groups. However, the possibility of occurrence of pseudorotations around the phosphorus atom and the possible existence of steric hindrances may result in a less electronegative group occupying an apical position in the intermediate, so becoming the preferable leaving group.…”

Section: Mechanism Of Action Of Opcsmentioning

confidence: 99%

Organophosphorus compounds as chemical warfare agents: a review

Delfino¹,

Ribeiro²,

Figueroa‐Villar³

2009

J. Braz. Chem. Soc.

228

178

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Os agentes de guerra química constituem uma das maiores ameaças do mundo moderno. Dentre estes, destacam-se os agentes neurotóxicos, em virtude de sua alta letalidade e periculosidade. Eles são compostos organofosforados que atuam pela inibição da enzima acetilcolinesterase, a qual é fundamental no processo de transmissão de impulsos nervosos. Existem várias formas de tratamento para a intoxicação por organofosforados, mas nenhuma delas é eficaz contra todos os agentes conhecidos ou contra todos os seus efeitos. Esta revisão tem como foco o uso de compostos organofosforados como agentes neurotóxicos de guerra química. Após uma breve introdução histórica, será feita uma discussão sobre as principais características estruturais e biológicas da acetilcolinesterase, seguida por uma revisão das propriedades dos compostos organofosforados e da sua aplicação como agentes de guerra química. Por fim, serão discutidas as formas de tratamento contra estes agentes, com ênfase nas oximas usadas para reativar a acetilcolinesterase inibida.Chemical warfare agents constitute one of the greatest threats in the modern world. Among them, the neurotoxic agents are of special interest due to their high lethality and danger. Neurotoxic agents are organophosphorus compounds that act by inhibiting the enzyme acetylcholinesterase, which is fundamental for the control of transmission of nervous impulses. There are several ways of treating intoxication by organophosphorus compounds, but none of them is efficient against all the known neurotoxic agents or against all of their effects. This review focus on the use of organophosphorus compounds as neurotoxic chemical warfare agents. After a brief historical introduction, it will be done a discussion about the structural and biological characteristics of acetylcholinesterase, followed by a review of the properties of organophosphorus compounds and their application as chemical warfare agents. Finally, the ways of treatment against intoxication with these agents will be discussed, with emphasis on the oximes used for reactivating the inhibited acetylcholinesterase.

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“…The catalytic cycles of enzymes such as protein kinases, G proteins, and ATPases are crucial to the ability of these molecules to regulate themselves and other proteins. Detailed understanding of the regulatory mechanisms employed by such enzymes is lacking, however, because the mechanism of phosphoryl transfer is still poorly understood (Thatcher & Kluger, 1989).…”

mentioning

confidence: 99%

“…(2) The reaction could proceed by a double-displacement mechanism, through one phosphoenzyme intermediate, in which one of the transfers does not result in inversion (Thatcher & Kluger, 1989). (3) The production of the phosphoenzyme could be a side reaction and not an intermediate in catalysis.…”

mentioning

confidence: 99%

Crystallization of acetate kinase from Methanosarcina thermophila and prediction of its fold

Buss

Ingram‐Smith

Ferry³

et al. 1997

Protein Science

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Abstract:The unique biochemical properties of acetate kinase present a classic conundrum in the study of the mechanism of enzyme-catalyzed phosphoryl transfer. Large, single crystals of acetate kinase from Methanosarcina thennophila were grown from a solution of ammonium sulfate in the presence of ATP. The crystals diffract to beyond 1.7 8, resolution. Analysis of X-ray data from the crystals is consistent with a space group of C2 and unit cell dimensions a = 181 A, b = 67 8,, c = 83 A, p = 103". Diffraction data have been collected from the crystals at 110 and 277 K. Data collected at 277 K extend to lower resolution, but are more reproducible. The orientation of a noncrystallographic twofold axis of symmetry has been determined. Based on an analysis of the predicted amino acid sequences of acetate kinase from several organisms, we hypothesize that acetate kinase is a member of the sugar kinase/actin/hsp70 structural family.

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Mechanism and Catalysis of Nucleophilic Substitution in Phosphate Esters

Cited by 278 publications

References 286 publications

The Mechanism of GTP Hydrolysis by Ras Probed by Fourier Transform Infrared Spectroscopy

The Mechanism of GTP Hydrolysis by Ras Probed by Fourier Transform Infrared Spectroscopy

Organophosphorus compounds as chemical warfare agents: a review

Crystallization of acetate kinase from Methanosarcina thermophila and prediction of its fold

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