Catalytic Versatility and Backups in Enzyme Active Sites: The Case of Serum Paraoxonase 1

Ben‐David, Moshe; Elias, Mikael; Filippi, Jean Jacques; Duñach, Élisabet; Silman, Israel; Sussman, Joel L.; Tawfik, Dan S.

doi:10.1016/j.jmb.2012.02.042

Cited by 153 publications

(211 citation statements)

References 52 publications

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“…Work on arylsulfatase (38), alkaline phosphatase (39), and paraoxonase (40) has revealed that the dominant factor for efficient catalysis is not shape complementarity to the substrate. More important is the ability of these enzymes to exploit electrostatic preorganization of the active site for the native substrate to stabilize the transition state of promiscuous reactions.…”

Section: Discussionmentioning

confidence: 99%

Electrostatic transition state stabilization rather than reactant destabilization provides the chemical basis for efficient chorismate mutase catalysis

Burschowsky

Eerde

Ökvist

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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For more than half a century, transition state theory has provided a useful framework for understanding the origins of enzyme catalysis. As proposed by Pauling, enzymes accelerate chemical reactions by binding transition states tighter than substrates, thereby lowering the activation energy compared with that of the corresponding uncatalyzed process. This paradigm has been challenged for chorismate mutase (CM), a well-characterized metabolic enzyme that catalyzes the rearrangement of chorismate to prephenate. Calculations have predicted the decisive factor in CM catalysis to be ground state destabilization rather than transition state stabilization. Using X-ray crystallography, we show, in contrast, that a sluggish variant of Bacillus subtilis CM, in which a cationic active-site arginine was replaced by a neutral citrulline, is a poor catalyst even though it effectively preorganizes chorismate for the reaction. A series of high-resolution molecular snapshots of the reaction coordinate, including the apo enzyme, and complexes with substrate, transition state analog and product, demonstrate that an active site, which is only complementary in shape to a reactive substrate conformer, is insufficient for effective catalysis. Instead, as with other enzymes, electrostatic stabilization of the CM transition state appears to be crucial for achieving high reaction rates.pericyclic reaction | catalysis | enzyme mechanism | near attack conformation | X-ray crystal structures

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Section: Discussionmentioning

confidence: 99%

Electrostatic transition state stabilization rather than reactant destabilization provides the chemical basis for efficient chorismate mutase catalysis

Burschowsky

Eerde

Ökvist

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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“…Human paraoxonase-1 (PON1) is a calcium-dependent lactonase that is produced by the liver and almost exclusively associated with HDL [7] . Although hydrolysis of homocysteine thiolactone might represent a major physiologic function of PON1 [8] , several further substrates have been described including other lactones [9] , organophosphates and lipid peroxides [7] . Interestingly, some previous studies proved that PON1 is predominantly associated to the smaller and denser HDL3 subfractions, and PON1 activity of HDL2 was only 4% of that in HDL3 [10] .…”

Section: Introductionmentioning

confidence: 99%

HDL subfraction distribution and HDL function in untreated dyslipidemic patients

Harangi¹,

Szentpéteri²,

Nádró³

et al. 2017

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Aim:The protective role of high-density lipoprotein (HDL) against atherosclerosis is well known. However, both structural and functional changes of the HDL particles may affect its protective efficacy. Increased levels of HDL-associated myeloperoxidase (MPO) and decreased HDL-linked paraoxonase-1 (PON1) activity have been reported in dyslipidemic patients. Some changes in HDL subfraction distributions were also studied previously, but data on structural and functional changes in dyslipidemia are not complete. Therefore, the authors aimed to evaluate these qualitative and quantitative markers of HDL in dyslipidemic patients and healthy control subjects. Methods: Anthropometric parameters, serum levels of lipoproteins and MPO, as well as PON1 activities were investigated in 81 untreated dyslipidemic patients and in 32 healthy gender-matched controls. Additionally, HDL subfractions were detected by an electrophoretic method on polyacrylamide gel (Lipoprint). Results: Significantly higher glucose, hemoglobin A1c, total cholesterol, low-density lipoprotein-cholesterol, triglyceride, lipoprotein(a), apolipoprotein B, C-reactive protein, and MPO levels were found in patients compared to the healthy subjects. There were no significant differences in PON1 paraoxonase and arylesterase activities between the two study groups, but MPO/PON1 ratio was significantly higher in patients. There was a shift towards the smaller HDL subfractions, but only the intermediate HDL ratio was significantly lower in patients compared to controls. Conclusion:The results highlight the importance of HDL-associated pro-and antioxidant enzymes suggesting the possible clinical benefit of MPO/PON1 calculation and confirm that quantification of HDL-C level alone provides limited data regarding HDL's cardioprotective effect. Calculation of MPO/PON1 ratio may be a useful cardiovascular marker in dyslipidemia. Key words:High-density lipoprotein, subfraction, paraoxonase, myeloperoxidase, dyslipidemia ABSTRACTArticle history:

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“…In recent studies, it has been shown that the flexibility of active-site loops leads to differential conformational sampling and active site reshaping, allowing alternative substrates to be utilized (47,48). The examination of a designed aldolase has further indicated that backbone flexibility would enable exploration of potential sites for introducing catalytic residues (49).…”

Section: Mechanisms Of Specificity and Promiscuitymentioning

confidence: 99%

Enzyme Promiscuity: Engine of Evolutionary Innovation

Pandya

Farelli

Dunaway‐Mariano

et al. 2014

Journal of Biological Chemistry

132

106

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Catalytic promiscuity and substrate ambiguity are keys to evolvability, which in turn is pivotal to the successful acquisition of novel biological functions. Action on multiple substrates (substrate ambiguity) can be harnessed for performance of functions in the cell that supersede catalysis of a single metabolite. These functions include proofreading, scavenging of nutrients, removal of antimetabolites, balancing of metabolite pools, and establishing system redundancy. In this review, we present examples of enzymes that perform these cellular roles by leveraging substrate ambiguity and then present the structural features that support both specificity and ambiguity. We focus on the phosphatases of the haloalkanoate dehalogenase superfamily and the thioesterases of the hotdog fold superfamily.In the 1990s, a series of studies on the evolution of catalysis in protein fold families helped define contemporary understanding of enzymes as potentially promiscuous catalysts; the analyses of these enzyme superfamilies suggested that certain folds showed higher variability than expected with regard to the chemistries that can be catalyzed or the substrates that can be acted on (1-11). To summarize, the current model holds that enzyme families grow as a result of gene duplication coupled with the acquisition of an advantageous new function. Because the backbone folds, and thus, the catalytic scaffolds are inherited, so is the chemical trait that underlies the intrinsic catalytic functions of all family members. In enzyme families, evidence can be found for low level intrinsic activity associated with one or more extant members, co-existing with the high level of activity unique to the subject enzyme (see for instance, the enolase and alkaline phosphatase enzyme superfamilies (12, 13)). The ability to carry out such alternate chemistry is termed catalytic promiscuity. The plausible link between catalytic promiscuity and evolvability has been explored in previous publications (for recent coverage and reviews of this topic, see Refs. 14 -17).The most commonly encountered observation of promiscuity involves the catalysis of one type of chemistry with many different substrates. Jensen (18) referred to this trait as "substrate ambiguity," and this is the name we will use. Herein, we examine the selective advantage associated with activity toward multiple substrates by highlighting specific examples of enzymes for which the level of substrate ambiguity runs high to fulfill specific roles in the cell. We use as examples enzymes from the haloalkanoate dehalogenase (HAD) 3 superfamily and the thioesterases of the hotdog fold superfamily. In addition, we dissect the architectures of enzymes from these families to discover underlying structural sources of specificity and substrate ambiguity. Screening to Assess Substrate AmbiguityIn vitro enzyme activity measurements carried out with a structurally diverse library of potential substrates allow one to generate a substrate specificity profile for the enzyme of interest. However, the mo...

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Catalytic Versatility and Backups in Enzyme Active Sites: The Case of Serum Paraoxonase 1

Cited by 153 publications

References 52 publications

Electrostatic transition state stabilization rather than reactant destabilization provides the chemical basis for efficient chorismate mutase catalysis

Electrostatic transition state stabilization rather than reactant destabilization provides the chemical basis for efficient chorismate mutase catalysis

HDL subfraction distribution and HDL function in untreated dyslipidemic patients

Enzyme Promiscuity: Engine of Evolutionary Innovation

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