Enzyme Architecture: Deconstruction of the Enzyme-Activating Phosphodianion Interactions of Orotidine 5′-Monophosphate Decarboxylase

Goldman, Lawrence M.; Amyes, Tina L.; Goryanova, Bogdana; Gerlt, J.A.; Richard, John P.

doi:10.1021/ja505037v

Cited by 32 publications

(158 citation statements)

References 60 publications

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“… 1 These interactions may be characterized for a particular enzyme in mutagenesis studies, with the aim of determining whether the sum of stabilizing protein–ligand interactions is sufficiently large to account for the observed transition state stabilization. 2 − 4 We are interested in the more general problem of defining paradigms for enzyme architecture, which favor large enzymatic rate accelerations across broad spectra of enzyme-catalyzed reactions. 4 − 9 …”

Section: Introductionmentioning

confidence: 99%

The Activating Oxydianion Binding Domain for Enzyme-Catalyzed Proton Transfer, Hydride Transfer, and Decarboxylation: Specificity and Enzyme Architecture

et al. 2015

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The kinetic parameters for activation of yeast triosephosphate isomerase (ScTIM), yeast orotidine monophosphate decarboxylase (ScOMPDC), and human liver glycerol 3-phosphate dehydrogenase (hlGPDH) for catalysis of reactions of their respective phosphodianion truncated substrates are reported for the following oxydianions: HPO32–, FPO32–, S2O32–, SO42– and HOPO32–. Oxydianions bind weakly to these unliganded enzymes and tightly to the transition state complex (E·S‡), with intrinsic oxydianion Gibbs binding free energies that range from −8.4 kcal/mol for activation of hlGPDH-catalyzed reduction of glycolaldehyde by FPO32– to −3.0 kcal/mol for activation of ScOMPDC-catalyzed decarboxylation of 1-β-d-erythrofuranosyl)orotic acid by HOPO32–. Small differences in the specificity of the different oxydianion binding domains are observed. We propose that the large −8.4 kcal/mol and small −3.8 kcal/mol intrinsic oxydianion binding energy for activation of hlGPDH by FPO32– and S2O32–, respectively, compared with activation of ScTIM and ScOMPDC reflect stabilizing and destabilizing interactions between the oxydianion −F and −S with the cationic side chain of R269 for hlGPDH. These results are consistent with a cryptic function for the similarly structured oxydianion binding domains of ScTIM, ScOMPDC and hlGPDH. Each enzyme utilizes the interactions with tetrahedral inorganic oxydianions to drive a conformational change that locks the substrate in a caged Michaelis complex that provides optimal stabilization of the different enzymatic transition states. The observation of dianion activation by stabilization of active caged Michaelis complexes may be generalized to the many other enzymes that utilize substrate binding energy to drive changes in enzyme conformation, which induce tight substrate fits.

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Section: Introductionmentioning

confidence: 99%

The Activating Oxydianion Binding Domain for Enzyme-Catalyzed Proton Transfer, Hydride Transfer, and Decarboxylation: Specificity and Enzyme Architecture

et al. 2015

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“…This builds on our model for dianion activation: dianions play the active role of providing the necessary binding energy to lock enzymes into their catalytically active conformations, 6d−6f but serve as spectators while substrates GA and NADL are transformed to the transition states for hydride transfer. 10,11,15 …”

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confidence: 99%

Structure–Reactivity Effects on Intrinsic Primary Kinetic Isotope Effects for Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase

2016

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Primary deuterium kinetic isotope effects (1°DKIE) on (kcat/KGA, M–1 s–1) for dianion (X2–) activated hydride transfer from NADL to glycolaldehyde (GA) catalyzed by glycerol-3-phosphate dehydrogenase were determined over a 2100-fold range of enzyme reactivity: (X2–, 1°DKIE); FPO32–, 2.8 ± 0.1; HPO32–, 2.5 ± 0.1; SO42–, 2.8 ± 0.2; HOPO32–, 2.5 ± 0.1; S2O32–, 2.9 ± 0.1; unactivated; 2.4 ± 0.2. Similar 1°DKIEs were determined for kcat. The observed 1°DKIEs are essentially independent of changes in enzyme reactivity with changing dianion activator. The results are consistent with (i) fast and reversible ligand binding; (ii) the conclusion that the observed 1°DKIEs are equal to the intrinsic 1°DKIE on hydride transfer from NADL to GA; (iii) similar intrinsic 1°DKIEs on GPDH-catalyzed reduction of the substrate pieces and the whole physiological substrate dihydroxyacetone phosphate. The ground-state binding interactions for different X2– are similar, but there are large differences in the transition state interactions for different X2–. The changes in transition state binding interactions are expressed as changes in kcat and are proposed to represent changes in stabilization of the active closed form of GPDH. The 1°DKIEs are much smaller than observed for enzyme-catalyzed hydrogen transfer that occurs mainly by quantum-mechanical tunneling.

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“…40 We likewise propose that the transition states for GPDH-catalyzed reactions of the whole substrate DHAP and the pieces GA + X 2 − are similar, and that the intrinsic 1°DKIE on the reaction of the whole substrate is similar to the values of k H / k D . reported for the pieces in Figure 7.…”

Section: Kinetic Isotope Effect On Gpdh-catalyzed Hydride Transfermentioning

confidence: 75%

“…The absence of direct stabilizing interactions between phosphite dianion and the putative transition states for these enzymatic reactions is worth noting; and, in the case of OMPDC the large 8–10 Å separation between the dianion binding site and the catalytic sites precludes strong direct stabilizing interactions. 37, 40, 41 The observation of dianion activation of any one of these enzyme-catalyzed reactions is surprising, while the similarity in the kinetic parameters for dianion activation of the diverse set of reactions catalyzed by TIM, OMPDC and GPDH suggests that there exists a common, generalizable, mechanism for activation of a broad range of enzymatic reactions through protein dianion interactions. 28 …”

Section: Transition State Stabilization From Protein-dianion Binding mentioning

confidence: 99%

“…We have examined the effect of site-directed mutations of TIM, 46–54 OMPDC, 40, 41, 55–57 and GPDH 58–60 on the activity of these enzymes for catalysis of the reactions of the whole substrate and the substrate in pieces. The results of these studies on the reactions of the substrate in pieces have been fully rationalized using Scheme 3.…”

Section: Transition State Stabilization From Protein-dianion Binding mentioning

confidence: 99%

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A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer

2017

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There is no consensus of opinion on the origin of the large rate accelerations observed for enzyme-catalyzed hydride transfer. The interpretation of recent results from studies on hydride transfer reactions catalyzed by alcohol dehydrogenase (ADH) focus on the proposal that the effective barrier height is reduced by quantum-mechanical tunneling through the energy barrier. This interpretation contrasts sharply with the notion that enzymatic rate accelerations are obtained through direct stabilization of the transition state for the nonenzymatic reaction in water. The binding energy of the dianion of substrate for DHAP provides 11 kcal/mol stabilization of the transition state for the hydride transfer reaction catalyzed by glycerol-3-phosphate dehydrogenase (GPDH). We summarize evidence that the binding interactions between (GPDH) and dianion activators are utilized directly for stabilization of the transition state for enzyme-catalyzed hydride transfer. The possibility is considered, and then discounted, that these dianion binding interactions are utilized for the stabilization of a tunnel ready state (TRS) that enables efficient tunneling of the transferred hydride through the energy barrier, and underneath the energy maximum for the transition state. It is noted that the evidence to support the existence of a tunnel-ready state for the hydride transfer reactions catalyzed by ADH is ambiguous. We propose that the rate acceleration for ADH is due to the utilization of the binding energy of the cofactor in the stabilization of the transition state for enzyme-catalyzed hydride transfer.

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Enzyme Architecture: Deconstruction of the Enzyme-Activating Phosphodianion Interactions of Orotidine 5′-Monophosphate Decarboxylase

Cited by 32 publications

References 60 publications

The Activating Oxydianion Binding Domain for Enzyme-Catalyzed Proton Transfer, Hydride Transfer, and Decarboxylation: Specificity and Enzyme Architecture

The Activating Oxydianion Binding Domain for Enzyme-Catalyzed Proton Transfer, Hydride Transfer, and Decarboxylation: Specificity and Enzyme Architecture

Structure–Reactivity Effects on Intrinsic Primary Kinetic Isotope Effects for Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase

A reevaluation of the origin of the rate acceleration for enzyme-catalyzed hydride transfer

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