Prevalence and Significance of the Product Inhibition of Enzymes

Frieden, Earl; Walter, Charles

doi:10.1038/198834a0

Cited by 36 publications

(23 citation statements)

References 13 publications

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“…The curvilinear functions displayed by the curves were consistent with the presence of a slow, tight-binding inhibitor [24]. This type of kinetic behavior is usually due to a process characterized by the rapid formation of reactant-enzyme complex, followed by a slower dissociation of the product-enzyme complex [25]. The steady states of the product formation curves exhibited a trend of slow rise after the inflection point ( Figure 5A ), which showed that the enzyme was slowly becoming inhibited by the accumulation of product.…”

Section: Resultsmentioning

confidence: 59%

Computational and Experimental Insights into the Mechanism of Substrate Recognition and Feedback Inhibition of Protoporphyrinogen Oxidase

et al. 2013

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Protoporphyrinogen IX oxidase (PPO; EC 1.3.3.4) is an essential enzyme catalyzing the last common step in the pathway leading to heme and chlorophyll biosynthesis. Great interest in PPO inhibitors arises from both its significance to agriculture and medicine. However, the discovery of PPO inhibitors with ultrahigh potency and selectivity is hampered due to lack of structural and mechanistic understanding about the substrate recognition, which remains a longstanding question central in porphyrin biology. To understand the mechanism, a novel binding model of protogen (protoporphyrinogen IX, the substrate) was developed through extensive computational simulations. Subsequently, amino acid residues that are critical for protogen binding identified by computational simulations were substituted by mutagenesis. Kinetic analyses of these mutants indicated that these residues were critical for protogen binding. In addition, the calculated free energies of protogen binding with these mutants correlated well with the experimental data, indicating the reasonability of the binding model. On the basis of this novel model, the fundamental mechanism of substrate recognition was investigated by performing potential of mean force (PMF) calculations, which provided an atomic level description of conformational changes and pathway intermediates. The free energy profile revealed a feedback inhibition mechanism of proto (protoporphyrin IX, the product), which was also in agreement with experimental evidence. The novel mechanistic insights obtained from this study present a new starting point for future rational design of more efficient PPO inhibitors based on the product-bound PPO structure.

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Section: Resultsmentioning

confidence: 59%

Computational and Experimental Insights into the Mechanism of Substrate Recognition and Feedback Inhibition of Protoporphyrinogen Oxidase

et al. 2013

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“…No significant difference was found between 3 h (1.05 ± 0.00 mg FA/g) and 6 h (1.02 ± 0.03 mg FA/g) of extraction, which might be due to the accumulation of products inhibiting enzyme activity or the depletion of the substrates. In a study conducted by Frieden and Walter on the product inhibition of enzymes, it was reported that the products of almost all enzyme‐catalyzed reactions may act as suppressants when present in high enough concentrations relative to the enzyme and substrate. Consequently, a period of 3 h was chosen and used throughout the experiments.…”

Section: Resultsmentioning

confidence: 99%

Optimization of enzyme‐assisted extraction of ferulic acid from sweet corn cob by response surface methodology

2019

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BACKGROUND: Sweet corn cob (SCC), an agricultural by-product of the corn-processing industry, contains more than 80% insoluble bound ferulic acid (FA). Extraction of these bound phenolics can be achieved through chemical or enzymatic hydrolysis; however, the shift towards greener chemistry has raised awareness about the use of enzymatic hydrolysis. In the present study, the ability of ferulic acid esterase (FAE) and xylanase (XY) to catalyze the hydrolysis of FA from SCC was investigated. Response surface methodology (RSM), based on a five-level, four-factor central composite rotatable design (CCRD), was used to establish the optimum conditions for enzymatic hydrolysis of FA from SCC. Sweet corn cob was treated with a combination of FAE and XY at various concentrations (FAE: 0.00 to 0.04 U/g; XY: 0.00 to 18 093.5 U/g), temperatures (45 to 65 ∘ C), and pH levels (pH 4.5 to 6.5). RESULTS: The optimum extraction conditions predicted by the model were: FAE concentration of 0.02 U/g, XY concentration of 3475.3 U/g, extraction pH of 4.5, and an extraction temperature of 45 ∘ C.CONCLUSION: Under these conditions, the experimental yield of FA was 1.69 ± 0.02 g kg −1 of SCC, which is in agreement with the value predicted by the model.

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“…Inhibition of an enzyme by its product, a phenomenon termed “product inhibition” in enzymology, has been recognized for over a century (Frieden and Walter, 1963). Product inhibition often provides negative feedback inhibition and has been manipulated by nature and chemists to produce selective enzyme inhibitors.…”

Section: Discussionmentioning

confidence: 99%

OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function

et al. 2012

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SUMMARY Ubiquitylation entails the concerted action of E1, E2 and E3 enzymes. We recently reported that OTUB1, a deubiquitylase, inhibits the DNA damage response independently of its isopeptidase activity. OTUB1 does so by blocking ubiquitin transfer by UBC13, the cognate E2 enzyme for RNF168. OTUB1 also inhibits E2s of the UBE2D and UBE2E families. Here we elucidate the structural mechanism by which OTUB1 binds E2s to inhibit ubiquitin transfer. OTUB1 recognizes ubiquitin-charged E2s through contacts with both donor ubiquitin and the E2 enzyme. Surprisingly, free ubiquitin associates with the canonical distal ubiquitin-binding site on OTUB1 to promote formation of the inhibited E2 complex. Lys48 of donor ubiquitin lies near the OTUB1 catalytic site and the C-terminus of free ubiquitin, a configuration that mimics the products of Lys48-linked ubiquitin chain cleavage. OTUB1 therefore co-opts Lys48-linked ubiquitin chain recognition to suppress ubiquitin conjugation and the DNA damage response.

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Prevalence and Significance of the Product Inhibition of Enzymes

Cited by 36 publications

References 13 publications

Computational and Experimental Insights into the Mechanism of Substrate Recognition and Feedback Inhibition of Protoporphyrinogen Oxidase

Computational and Experimental Insights into the Mechanism of Substrate Recognition and Feedback Inhibition of Protoporphyrinogen Oxidase

Optimization of enzyme‐assisted extraction of ferulic acid from sweet corn cob by response surface methodology

OTUB1 Co-opts Lys48-Linked Ubiquitin Recognition to Suppress E2 Enzyme Function

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