Intramolecular General Acid Catalysis of Phosphate Transfer. Nucleophilic Attack by Oxyanions on the PO32- Group

Kirby, Anthony J.; Dutta-Roy, Neil; Silva, Davi Da; Goodman, Jonathan M.; Lima, Marcelo F.; Roussev, Christo D.; Nome, Faruk

doi:10.1021/ja0502876

Cited by 38 publications

(57 citation statements)

References 25 publications

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“…Negatively charged nucleophiles are unlikely to react with phosphate monoesters in the dianion form. However, this has been observed in cases where, as in the PTP1B reaction, proton transfer is present or the phosphate moiety is neutral or monoanionic (78).…”

Section: Changes Accompanying Conversion Of Tsa2 (Pdb Entrymentioning

confidence: 99%

Insights into the Reaction of Protein-tyrosine Phosphatase 1B

Brandão

Hengge

Johnson

2010

Journal of Biological Chemistry

132

175

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Catalysis by protein-tyrosine phosphatase 1B (PTP1B) occurs through a two-step mechanism involving a phosphocysteine intermediate. We have solved crystal structures for the transition state analogs for both steps. Together with previously reported crystal structures of apo-PTP1B, the Michaelis complex of an inactive mutant, the phosphoenzyme intermediate, and the product complex, a full picture of all catalytic steps can now be depicted. The transition state analog for the first catalytic step comprises a ternary complex between the catalytic cysteine of PTP1B, vanadate, and the peptide DADEYL, a fragment of a physiological substrate. The equatorial vanadate oxygen atoms bind to the P-loop, and the apical positions are occupied by the peptide tyrosine oxygen and by the PTP1B cysteine sulfur atom. The vanadate assumes a trigonal bipyramidal geometry in both transition state analog structures, with very similar apical O-O distances, denoting similar transition states for both phosphoryl transfer steps. Detailed interactions between the flanking peptide and the enzyme are discussed.The phosphorylation of tyrosine residues by protein-tyrosine kinases and the reverse action by protein-tyrosine phosphatases (PTPs) 4 is a common mechanism for the control of biological pathways (1-3). Protein-tyrosine phosphatase 1B (PTP1B) is a biomedically important phosphatase with several roles, including negative regulation of insulin signaling by dephosphorylation of the insulin receptor tyrosine kinase (4). Knock-out studies show that loss of PTP1B is associated with an increased insulin sensitivity and suppression of weight gain in mice (5). As a result, this enzyme has been considered a significant target for treatment of type 2 diabetes and obesity (6, 7). PTP1B also down-regulates cell growth by dephosphorylating the epidermal growth factor receptor (8). Overexpression has been observed in human breast and ovarian cancer, where it is believed to suppress potential tumors by antagonizing signaling of oncogenic factors (9, 10). Other PTPs are known virulence factors for a number of human diseases (11-13).Reactions catalyzed by PTPs take place by a ping-pong mechanism ( Fig. 1) (2). In the first step, a nucleophilic cysteine thiolate attacks the phosphate ester moiety of the substrate, resulting in formation of a phosphoenzyme intermediate with release of the peptidyl tyrosine. The second step occurs via attack of water on the phosphoenzyme intermediate and yields the final products inorganic phosphate and the regenerated enzyme. The central binding site for the substrate is the P-loop, a region at the bottom of a pocket that includes the nucleophilic cysteine and backbone amide groups oriented in a horseshoe fashion. The amide protons in the P-loop, together with a conserved arginine residue, hydrogen-bond to the phosphoryl group of the substrate and orient it for nucleophilic attack, providing transition state (TS) stabilization. Substrate binding is followed by conformational changes that culminate with closure of the activ...

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Section: Changes Accompanying Conversion Of Tsa2 (Pdb Entrymentioning

confidence: 99%

Insights into the Reaction of Protein-tyrosine Phosphatase 1B

Brandão

Hengge

Johnson

2010

Journal of Biological Chemistry

132

175

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“…It was found that three anions, HOO − , MeOO − , and N 3 − each with an adjacent electron donating group, react particularly fast. The α‐effect has been studied for more than 50 years by experimental and theoretical chemists, and its origin has been rationalized by many theories, but still without a definitive answer. Theories that have been put forward for this effect include: (1) transition state (TS) stabilization, (2) destabilization of the ground state, (3) different solvent effects for normal and α‐Nu, and (4) thermodynamic stability of the product .…”

Section: Introductionmentioning

confidence: 99%

The α-effect exhibited in gas-phase S_N2@N and S_N2@C reactions

et al. 2013

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In order to explore the existence of α-effect in gas-phase S(N)2@N reactions, and to compare its similarity and difference with its counterpart in S(N)2@C reactions, we have carried out a theoretical study on the reactivity of six α-oxy-Nus (FO(-), ClO(-), BrO(-), HOO(-), HSO(-), H2NO(-)) in the S(N)2 reactions toward NR2Cl (R = H, Me) and RCl (R = Me, i-Pr) using the G2(+)M theory. An enhanced reactivity induced by the α-atom is found in all examined systems. The magnitude of the α-effect in the reactions of NR2Cl (R = H, Me) is generally smaller than that in the corresponding S(N)2 reaction, but their variation trend with the identity of α-atom is very similar. The origin of the α-effect of the S(N)2@N reactions is discussed in terms of activation strain analysis and thermodynamic analysis, indicating that the α-effect in the S(N)2@N reactions largely arises from transition state stabilization, and the "hyper-reactivity" of these α-Nus is also accompanied by an enhanced thermodynamic stability of products from the n(N) → σ*(O-Y) negative hyperconjugation. Meanwhile, it is found that the reactivity of oxy-Nus in the S(N)2 reactions toward NMe2Cl is lower than toward i-PrCl, which is different from previous experiments, that is, the S(N)2 reactions of NH2Cl is more facile than MeCl.

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“…These results were proposed to be related to impairment of WPD-loop movement. Previous research has explored the relationships in model systems between distance and positioning between proton donor and acceptor and the efficiency of acid catalysis 26,27. Such factors are even more important for proton transfer than for nucleophilic attack 28.…”

Section: Introductionmentioning

confidence: 99%

Impaired Acid Catalysis by Mutation of a Protein Loop Hinge Residue in a YopH Mutant Revealed by Crystal Structures

et al. 2008

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Catalysis by the Yersinia protein-tyrosine phosphatase YopH is significantly impaired by the mutation of the conserved Trp354 residue to Phe. Though not a catalytic residue, this Trp is a hinge residue in a conserved flexible loop (the WPD-loop) that must close during catalysis. To learn why this seemingly conservative mutation reduces catalysis by 2 orders of magnitude, we have solved high-resolution crystal structures for the W354F YopH in the absence and in the presence of tungstate and vanadate. Oxyanion binding to the P-loop in W354F is analogous to that observed in the native enzyme. However, the WPD-loop in the presence of oxyanions assumes a half-closed conformation, in contrast to the fully closed state observed in structures of the native enzyme. This observation provides an explanation for the impaired general acid catalysis observed in kinetic experiments with Trp mutants. A 1.4 Å structure of the W354F mutant obtained in the presence of vanadate reveals an unusual divanadate species with a cyclic [VO] 2 core, which has precedent in small molecules but has not been previously reported in a protein crystal structure.

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Intramolecular General Acid Catalysis of Phosphate Transfer. Nucleophilic Attack by Oxyanions on the PO₃²^- Group

Cited by 38 publications

References 25 publications

Insights into the Reaction of Protein-tyrosine Phosphatase 1B

Insights into the Reaction of Protein-tyrosine Phosphatase 1B

The α-effect exhibited in gas-phase S_N2@N and S_N2@C reactions

Impaired Acid Catalysis by Mutation of a Protein Loop Hinge Residue in a YopH Mutant Revealed by Crystal Structures

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Intramolecular General Acid Catalysis of Phosphate Transfer. Nucleophilic Attack by Oxyanions on the PO32- Group

Cited by 38 publications

References 25 publications

Insights into the Reaction of Protein-tyrosine Phosphatase 1B

Insights into the Reaction of Protein-tyrosine Phosphatase 1B

The α-effect exhibited in gas-phase SN2@N and SN2@C reactions

Impaired Acid Catalysis by Mutation of a Protein Loop Hinge Residue in a YopH Mutant Revealed by Crystal Structures

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Intramolecular General Acid Catalysis of Phosphate Transfer. Nucleophilic Attack by Oxyanions on the PO₃²^- Group

The α-effect exhibited in gas-phase S_N2@N and S_N2@C reactions