Enzyme architecture: on the importance of being in a protein cage

Richard, John P.; Amyes, Tina L.; Goryanova, Bogdana; Zhai, Xiang

doi:10.1016/j.cbpa.2014.03.001

Cited by 106 publications

(213 citation statements)

References 65 publications

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“…12,27 This strategy should result in a catalyst where the tight loop–substrate interactions are expressed as a large turnover number k cat for the decarboxylation reaction. 10,13 …”

Section: Resultsmentioning

confidence: 99%

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

et al. 2014

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The mechanism for activation of orotidine 5′-monophosphate decarboxylase (OMPDC) by interactions of side chains from Gln215 and Try217 at a gripper loop and R235, adjacent to this loop, with the phosphodianion of OMP was probed by determining the kinetic parameters kcat and Km for all combinations of single, double, and triple Q215A, Y217F, and R235A mutations. The 12 kcal/mol intrinsic binding energy of the phosphodianion is shown to be equal to the sum of the binding energies of the side chains of R235 (6 kcal/mol), Q215 (2 kcal/mol), Y217 (2 kcal/mol), and hydrogen bonds to the G234 and R235 backbone amides (2 kcal/mol). Analysis of a triple mutant cube shows small (ca. 1 kcal/mol) interactions between phosphodianion gripper side chains, which are consistent with steric crowding of the side chains around the phosphodianion at wild-type OMPDC. These mutations result in the same change in the activation barrier to the OMPDC-catalyzed reactions of the whole substrate OMP and the substrate pieces (1-β-d-erythrofuranosyl)orotic acid (EO) and phosphite dianion. This shows that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The 12 kcal/mol intrinsic phosphodianion binding energy of OMP is divided between the 8 kcal/mol of binding energy, which is utilized to drive a thermodynamically unfavorable conformational change of the free enzyme, resulting in an increase in (kcat)obs for OMPDC-catalyzed decarboxylation of OMP, and the 4 kcal/mol of binding energy, which is utilized to stabilize the Michaelis complex, resulting in a decrease in (Km)obs.

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“…12,27 This strategy should result in a catalyst where the tight loop–substrate interactions are expressed as a large turnover number k cat for the decarboxylation reaction. 10,13 …”

Section: Resultsmentioning

confidence: 99%

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

et al. 2014

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“…30 ). It would not be unreasonable to assume that the water-exclusion effect is amplified upon interaction with detergents, lipids let alone with HDL (in themselves acting as "plugs" to exclude solvent).…”

Section: Lack Of Stimulation Of the Paraoxonase Activitymentioning

confidence: 93%

Catalytic Stimulation by Restrained Active-Site Floppiness—The Case of High Density Lipoprotein-Bound Serum Paraoxonase-1

Ben‐David

Sussman

Maxwell

et al. 2015

Journal of Molecular Biology

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“…They are often constructed by the folding of the eight βα front loops into a structured cage for the substrate, whose formation is driven by the development of stabilizing interactions between the substrate and the catalytic front loops. 15 The eight back loops lie at the end of the barrel distant from the front loops, and play an important role in stabilizing this protein fold. 8,11 The TIM-barrel provides a robust framework to support an incredible variety of front loop structures, which are used in construction of the active sites for enzymes found in 21 homologous superfamilies and 76 different sequence families.…”

Section: Introductionmentioning

confidence: 99%

Reflections on the catalytic power of a TIM-barrel

Richard¹,

Zhai²,

Malabanan³

2014

Bioorganic Chemistry

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The TIM-barrel fold is described and its propagation throughout the enzyme universe noted. The functions of the individual front loops of the eponymous TIM-barrel of triosephosphate isomerase are presented in a discussion of: (a) Electrophilic catalysis, by amino acid side chains from loops 1 and 4, of abstraction of an α-carbonyl hydrogen from substrate dihydroxyacetone phosphate (DHAP) or D-glyceraldehyde 3-phosphate (DGAP). (b) The engineering of loop 3 to give the monomeric variant monoTIM and the structure and catalytic properties of this monomer. (c) The interaction between loops 6, 7 and 8 and the phosphodianion of DHAP or DGAP. (d) The mechanism by which a ligand-gated conformational change, dominated by motion of loops 6 and 7, activates TIM for catalysis of deprotonation of DHAP or DGAP. (e) The conformational plasticity of TIM, and the utilization of substrate binding energy to “mold” the distorted active site loops of TIM mutants into catalytically active enzymes. The features of the TIM-barrel fold that favor effective protein catalysis are discussed.

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Enzyme architecture: on the importance of being in a protein cage

Cited by 106 publications

References 65 publications

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

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

Catalytic Stimulation by Restrained Active-Site Floppiness—The Case of High Density Lipoprotein-Bound Serum Paraoxonase-1

Reflections on the catalytic power of a TIM-barrel

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