Crystal Structures of Orotidine Monophosphate Decarboxylase: Does the Structure Reveal the Mechanism of Nature's Most Proficient Enzyme?

Houk, K. N.; Lee, Jeehiun K.; Tantillo, Dean J.; Bahmanyar, Sogole; Hietbrink, Bruce N.

doi:10.1002/1439-7633(20010202)2:2<113::aid-cbic113>3.3.co;2-k

Cited by 21 publications

(45 citation statements)

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“…Five years after the discovery of its remarkable catalytic proficiency, ODCase was crystallized almost simultaneously in four laboratories, from Saccharomyces cerevisiae (71) and from three species of bacteria (72,73,74), in a complex with three different ligands. In most respects, these structures are in very close agreement [for discussion, see (69) and (75)]. ODCase adopts an ␣/␤-barrel fold with a ligand binding site consisting of residues belonging to both subunits of the active homodimer, Figure 9.…”

Section: The Structure Of Omp Decarboxylase-new Mechanistic Insights?mentioning

confidence: 72%

Catalytic Proficiency: The Unusual Case of OMP Decarboxylase

Miller

Wolfenden²

2002

Annu. Rev. Biochem.

274

344

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Enzymes are called upon to differ greatly in the difficulty of the tasks that they perform. The catalytic proficiency of an enzyme can be evaluated by comparing the second-order rate constant (kcat/Km) with the rate of the spontaneous reaction in neutral solution in the absence of a catalyst. The proficiencies of enzymes, measured in this way, are matched by their affinity constants for the altered substrate in the transition state. These values vary from approximately approximately 10(9) M(-1) for carbonic anhydrase to approximately 10(23) M(-1) for yeast orotidine 5'-phosphate decarboxylase (ODCase). ODCase turns its substrate over with a half-time of 18 ms, in a reaction that proceeds in its absence with a half-time of 78 million years in neutral solution. ODCase differs from other decarboxylases in that its catalytic activity does not depend on the presence of metals or other cofactors, or on the formation of a covalent bond to the substrate. Several mechanisms of transition state stabilization are considered in terms of ODCase crystal structures observed in the presence and absence of bound analogs of the substrate, transition state, and product. Very large connectivity effects are indicated by the results of experiments testing how transition state stabilization is affected by the truncation of binding determinants of the substrate and the active site.

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Section: The Structure Of Omp Decarboxylase-new Mechanistic Insights?mentioning

confidence: 72%

Catalytic Proficiency: The Unusual Case of OMP Decarboxylase

Miller

Wolfenden²

2002

Annu. Rev. Biochem.

274

344

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“…The mechanism of catalysis by this enzyme is still under debate, and both covalent and noncovalent mechanisms have been proposed. 33 We claim that the 10 23 M -1 proficiency of ODC ∆SASA values of enzymesubstrate were obtained from the 34 crystal structures of enzymesubstrate complexes available in the PDB database (information on the PDB codes of these X-ray crystal structures and ∆SASA calculated with Grasp is available in Supporting Information). ∆SASA of transition states was obtained by estimation.…”

Section: Survey Of Host-guest Binding Constantsmentioning

confidence: 99%

Why Enzymes Are Proficient Catalysts: Beyond the Pauling Paradigm

2005

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Pauling proposed that "enzymes are molecules that are complementary in structure to the activated complexes of the reactions that they catalyze, ..., [rather than] entering into reactions". This paradigm has dominated thinking in the field. While complementarity of the type proposed by Pauling can account for acceleration up to 11 orders of magnitude, most enzymes exceed that proficiency. Enzymes with proficiencies ((k(cat)/K(M))/k(uncat)) > 10(11) M(-1) achieve over 15 kcal/mol of "transition state binding" not merely by a concatenation of noncovalent effects but by covalent bond formation between enzyme or cofactor and transition state, involving a change in mechanism from that in aqueous solution. Enzymes enter into reactions with substrates and do not merely complement the transition states of the uncatalyzed reactions.

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“…5 High-resolution X-ray crystal structures of OMPDC resulted in a flurry of controversy and activity, because of their failure to lead to a consensus decarboxylation reaction mechanism. 6 This gave rise to provocative statements. For example, it was claimed that "This prof icient enzyme jolted many biochemists' assumptions about the catalytic potential of enzymes..." 7 A second group claimed that "the 10 23 M −1 prof iciency of ODC must arise f rom covalent catalysis, since only 10 11 M −1 prof iciency is possible by noncovalent binding," 8 even though there was no solid experimental evidence to support covalent catalysis by OMPDC.…”

Section: Introductionmentioning

confidence: 99%

Orotidine 5′-Monophosphate Decarboxylase: Probing the Limits of the Possible for Enzyme Catalysis

2018

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The mystery associated with catalysis by what were once regarded as protein black boxes, diminished with the X-ray crystallographic determination of the three-dimensional structures of enzyme-substrate complexes. The report that several high-resolution X-ray crystal structures of orotidine 5'-monophosphate decarboxylase (OMPDC) failed to provide a consensus mechanism for enzyme-catalyzed decarboxylation of OMP to form uridine 5'-monophosphate, therefore, provoked a flurry of controversy. This controversy was fueled by the enormous 10-fold rate acceleration for this enzyme, which had " jolted many biochemists' assumptions about the catalytic potential of enzymes." Our studies on the mechanism of action of OMPDC provide strong evidence that catalysis by this enzyme is not fundamentally different from less proficient catalysts, while highlighting important architectural elements that enable a peak level of performance. Many enzymes undergo substrate-induced protein conformational changes that trap their substrates in solvent occluded protein cages, but the conformational change induced by ligand binding to OMPDC is incredibly complex, as required to enable the development of 22 kcal/mol of stabilizing binding interactions with the phosphodianion and ribosyl substrate fragments of OMP. The binding energy from these fragments is utilized to activate OMPDC for catalysis of decarboxylation at the orotate fragment of OMP, through the creation of a tight, catalytically active, protein cage from the floppy, open, unliganded form of OMPDC. Such utilization of binding energy for ligand-driven conformational changes provides a general mechanism to obtain specificity in transition state binding. The rate enhancement that results from the binding of carbon acid substrates to enzymes is partly due to a reduction in the carbon acid p K that is associated with ligand binding. The binding of UMP to OMPDC results in an unusually large >12 unit decrease in the p K = 29 for abstraction of the C-6 substrate hydrogen, due to stabilization of an enzyme-bound vinyl carbanion, which is also an intermediate of OMPDC-catalyzed decarboxylation. The protein-ligand interactions operate to stabilize the vinyl carbanion at the enzyme active site compared to aqueous solution, rather than to stabilize the transition state for the concerted electrophilic displacement of CO by H that avoids formation of this reaction intermediate. There is evidence that OMPDC induces strain into the bound substrate. The interaction between the amide side chain of Gln-215 from the phosphodianion gripper loop and the hydroxymethylene side chain of Ser-154 from the pyrimidine umbrella of ScOMPDC position the amide side chain to interact with the phosphodianion of OMP. There are no direct stabilizing interactions between dianion gripper protein side chains Gln-215, Tyr-217, and Arg-235 and the pyrimidine ring at the decarboxylation transition state. Rather these side chains function solely to hold OMPDC in the catalytically active closed conformation. The hydrophobic sid...

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Crystal Structures of Orotidine Monophosphate Decarboxylase: Does the Structure Reveal the Mechanism of Nature's Most Proficient Enzyme?

Cited by 21 publications

References 0 publications

Catalytic Proficiency: The Unusual Case of OMP Decarboxylase

Catalytic Proficiency: The Unusual Case of OMP Decarboxylase

Why Enzymes Are Proficient Catalysts: Beyond the Pauling Paradigm

Orotidine 5′-Monophosphate Decarboxylase: Probing the Limits of the Possible for Enzyme Catalysis

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