MgF3− as a Transition State Analog of Phosphoryl Transfer

Graham, Debbie L.; Lowe, Peter N.; Grime, G.W.; Marsh, Michael P.; Rittinger, Katrin; Smerdon, Stephen J.; Gamblin, S.J.; Eccleston, John F.

doi:10.1016/s1074-5521(02)00112-6

Cited by 105 publications

(126 citation statements)

References 27 publications

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“…x is not only a good mimic of the TS for phosphoryl transfer reactions (Graham et al 2002), but also that it can form under the crystallization conditions employed by Lahiri and co-workers. This was then later examined by detailed NMR studies that also provided insight in the molecular mechanism of fluoride inhibition by bPGM (Baxter et al 2006), as well as further (steady and pre-steady state) kinetic analysis of both the reactivity of bPGM and its inhibition by magnesium fluoride, which essentially ruled out the existence of a stable pentavalent phosphorane intermediate in the active site of bPGM (Golicnick et al 2009).…”

Section: B-phosphoglucomutase (Bpgm) : Metal Fluoride Ts Analogs As Pmentioning

confidence: 99%

Why nature really chose phosphate

Kamerlin

Sharma

Prasad

et al. 2013

Quart. Rev. Biophys.

339

448

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Phosphoryl transfer plays key roles in signaling, energy transduction, protein synthesis, and maintaining the integrity of the genetic material. On the surface, it would appear to be a simple nucleophile displacement reaction. However, this simplicity is deceptive, as, even in aqueous solution, the low-lying d-orbitals on the phosphorus atom allow for eight distinct mechanistic possibilities, before even introducing the complexities of the enzyme catalyzed reactions. To further complicate matters, while powerful, traditional experimental techniques such as the use of linear free-energy relationships (LFER) or measuring isotope effects cannot make unique distinctions between different potential mechanisms. A quarter of a century has passed since Westheimer wrote his seminal review, ‘Why Nature Chose Phosphate’ (Science 235 (1987), 1173), and a lot has changed in the field since then. The present review revisits this biologically crucial issue, exploring both relevant enzymatic systems as well as the corresponding chemistry in aqueous solution, and demonstrating that the only way key questions in this field are likely to be resolved is through careful theoretical studies (which of course should be able to reproduce all relevant experimental data). Finally, we demonstrate that the reason that naturereallychose phosphate is due to interplay between two counteracting effects: on the one hand, phosphates are negatively charged and the resulting charge-charge repulsion with the attacking nucleophile contributes to the very high barrier for hydrolysis, making phosphate esters among the most inert compounds known. However, biology is not only about reducing the barrier to unfavorable chemical reactions. That is, the same charge-charge repulsion that makes phosphate ester hydrolysis so unfavorable also makes it possible to regulate, by exploiting the electrostatics. This means that phosphate ester hydrolysis can not only be turned on, but also be turned off, by fine tuning the electrostatic environment and the present review demonstrates numerous examples where this is the case. Without this capacity for regulation, it would be impossible to have for instance a signaling or metabolic cascade, where the action of each participant is determined by the fine-tuned activity of the previous piece in the production line. This makes phosphate esters the ideal compounds to facilitate life as we know it.

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Section: B-phosphoglucomutase (Bpgm) : Metal Fluoride Ts Analogs As Pmentioning

confidence: 99%

Why nature really chose phosphate

Kamerlin

Sharma

Prasad

et al. 2013

Quart. Rev. Biophys.

339

448

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“…12A). [23] The PDB now lists 16 entries for this ligand (PDB ligand: MGF) while a further 3 entries assigned as tbp AlF3 0 have been shown by 19 F NMR to be MgF3 -complexes (SI Table 8). [24] Magnesium is regularly 6-coordinate and gives octahedral complexes with oxygen ligands.…”

Section: Trifluoromagnesates Mgf3 -mentioning

confidence: 99%

Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes

et al. 2017

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Abstract:The 1994 structure of a transition state analog with AlF4 -and GDP complexed to G1α, a small G protein, heralded a new field of research into structure and mechanism of enzymes that manipulate transfer of the phosphoryl (PO3 -) group. The list of enzyme structures that embrace metal fluorides, MFx, as ligands that imitate either the phosphoryl group or a phosphate, is now growing at over 80 per triennium. They fall into three distinct geometrical classes: (i) Tetrahedral complexes, based on BeF3 -, mimic ground state phosphates; (ii) Octahedral complexes, primarily based on AlF4 -, mimic "in-line" anionic transition state for phosphoryl transfer; and (iii) Trigonal bipyramidal complexes, represented by MgF3 -and putative AlF3 0 moieties, additionally mimic the tbp geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding of the behavior and manipulation of phosphate monoesters in molecular biology. This review provides a comprehensive overview of these structures, their uses, and their computational development. It questions the identification of AlF3 0 and MgF4 = as tbp species in protein complexes and discusses the relevance of physical organic chemistry and water-based model studies for understanding phosphoryl group transfer in enzymes. It describes two roles for amino acid side-chains that mediate proton transfers during phosphoryl transfer, based on the analysis of protein/MFx structures. First, they deploy hydrogen bonding to neutral oxygen nucleophiles so as to orientate them for correct orbital overlap with the electrophilic phosphorus center. Secondly, they behave as classical general acid/base catalysts.

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“…Aluminum with fluoride bound to the enzymes was shown to be either AlF 3 or AlF 4 Ϫ compound (53,(55)(56)(57), and their formation also depends on pH in the incubation medium (56). The structural studies further revealed that both AlF 3 and AlF 4 Ϫ possess the planar (trigonal (AlF 3 ) and square (AlF 4 Ϫ )) geometry, in which two oxygen atoms coordinate to the aluminum at apical positions, for example, from the hydrolytic water molecule and the specific aspartate to produce the state superimposable (AlF 3 ) or analogous (AlF 4 Ϫ ) to the trigonal bipyramidal structure of the penta-coordinated phosphorus in the transition state of in-line associative acylphosphate hydrolysis mechanism, which was also predicted for the Ca 2ϩ -ATPase (58).…”

Section: Close Similarities and Differences Between E2p Analogues Andmentioning

confidence: 99%

Distinct Natures of Beryllium Fluoride-bound, Aluminum Fluoride-bound, and Magnesium Fluoride-bound Stable Analogues of an ADP-insensitive Phosphoenzyme Intermediate of Sarcoplasmic Reticulum Ca2+-ATPase

Dankó

Yamasaki

Daiho

et al. 2004

Journal of Biological Chemistry

116

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The structural natures of stable analogues for the ADP-insensitive phosphoenzyme (E2P) of Ca 2؉ -ATPase formed in sarcoplasmic reticulum vesicles, i.e. the enzymes with bound beryllium fluoride (BeF⅐E2), bound aluminum fluoride (AlF⅐E2), and bound magnesium fluoride (MgF⅐E2), were explored and compared with those of actual E2P formed from P i without Ca 2؉ . Changes in trinitrophenyl-AMP fluorescence revealed that the catalytic site is strongly hydrophobic in BeF⅐E2 as in E2P but hydrophilic in MgF⅐E2 and AlF⅐E2; yet, the three cytoplasmic domains are compactly organized in these states. Thapsigargin, which was shown in the crystal structure to fix the transmembrane helices and, thus, the postulated Ca 2؉ release pathway to lumen in a closed state, largely reduced the tryptophan fluorescence in BeF⅐E2 as in E2P, but only very slightly (hence, the release pathway is likely closed without thapsigargin) in MgF⅐E2 and AlF⅐E2 as in dephosphorylated enzyme. Consistently, the completely suppressed Ca 2؉ -ATPase activity in BeF-treated vesicles was rapidly restored in the presence of ionophore A23187 but not in its absence by incubation with Ca 2؉ (over several millimolar concentrations) at pH 6, and, therefore, lumenal Ca 2؉ is accessible to reactivate the enzyme. In contrast, no or only very slow restoration was observed with vesicles treated with MgF and AlF even with A23187. BeF⅐E2 thus has the features very similar to those characteristic of the E2P ground state, although AlF⅐E2 and MgF⅐E2 most likely mimic the transition or product state for the E2P hydrolysis, during which the hydrophobic nature around the phosphorylation site is lost and the Ca 2؉ release pathway is closed. The change in hydrophobic nature is probably associated with the change in phosphate geometry from the covalently bound tetrahedral ground state (BeF 3 ؊ ) to trigonal bipyramidal transition state (AlF 3 or AlF 4 ؊ ) and further to tetrahedral product state (MgF 4 2؊ ), and such change likely rearranges transmembrane helices to prevent access and leakage of lumenal Ca 2؉ .Sarcoplasmic reticulum (SR) 1 Ca 2ϩ -ATPase is a representative member of P-type ion-transporting ATPases and catalyzes Ca 2ϩ transport coupled with ATP hydrolysis (Fig. 1) (Refs. 1 and 2 and, for recent reviews, see Refs. 3-6). In the catalytic cycle, the enzyme is activated by the binding of two Ca 2ϩ ions (E2 to Ca 2 E1, steps 1-2) and then autophosphorylated at Asp 351 by MgATP to form ADP-sensitive phosphoenzyme (E1P, steps 3-4). The subsequent isomeric transition to the ADPinsensitive form (E2P) will result in a reduction in affinity, a change in orientation of the Ca 2ϩ binding sites, and Ca 2ϩ release into lumen (steps 5-6). Finally, hydrolysis takes place and returns the enzyme into an unphosphorylated and Ca 2ϩ -unbound form (E2, steps 7-8). E2P can also be formed from P i in the presence of Mg 2ϩ and the absence of Ca 2ϩ by reversal of its hydrolysis, and the subsequent addition of high concentrations of Ca 2ϩ (from the lumenal side) can readily reverse the Ca 2ϩ ...

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MgF3− as a Transition State Analog of Phosphoryl Transfer

Cited by 105 publications

References 27 publications

Why nature really chose phosphate

Why nature really chose phosphate

Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes

Distinct Natures of Beryllium Fluoride-bound, Aluminum Fluoride-bound, and Magnesium Fluoride-bound Stable Analogues of an ADP-insensitive Phosphoenzyme Intermediate of Sarcoplasmic Reticulum Ca2+-ATPase

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