Trends in Biochemical Sciences
ReviewThe Limits of Enzyme Specificity and the Evolution of Metabolism
Section snippets
Many Metabolic Enzymes Are Not Strictly Substrate-Specific
It is now well appreciated that a substantial fraction of metabolic enzymes can catalyze reactions of different types and/or with different substrates 1, 2. The former behavior is termed catalytic promiscuity [3], the latter is usually called substrate promiscuity [4] (because these terms may be equivocal, Box 1 explains the definition of ‘promiscuity’ used here and compares it to a stricter definition accepted by evolutionary biochemists). Although this paper is essentially concerned with
Substrate Specificity, Discrimination, and Binding Energy
In contrast to catalytic efficiency, which can be gauged in reference to an absolute scale of ‘catalytic perfection’ 10, 11, specificity is a relative concept because it requires comparison between given alternative substrates. In fact, specificity is formally defined as the ability of an enzyme to discriminate between two potential substrates, in the presence of both compounds 12, 13. In a biological context, specificity entails acting on a single substrate in preference to a multitude of
Theoretical and Empirical Limits of Substrate Specificity
That substrate specificity is inherently limited was first glimpsed by Pauling 60 years ago [15] in relation to the process of aminoacyl-tRNA synthesis. He focused in particular on the case of isoleucyl-tRNA synthetase that must distinguish between isoleucine and valine. The two amino acids differ only by one methyl group, and the difference in binding energy between them could therefore not be greater than the energy provided by the terminal CH3 group of L-Ile. This has been estimated to be
Detrimental Activities with Alternative Substrates May Be Redressed by Repair Enzymes
An opposite scenario arises when the activity of a metabolic enzyme with an alternative substrate is seriously detrimental to fitness. In fact, every such reaction may generate a product that is useless for the cell (a metabolic dead-end, implying a waste of resources) or that is even toxic [44], and this is expected to elicit strong evolutionary pressure to improve the specificity of the enzyme. However, as discussed, there are limits to such an improvement. Preventing access of the enzyme to
When Does Activity with Alternative Substrates Depend on Neutral Drift?
In a final scenario, the alternative reaction catalyzed by an enzyme might have no significant (positive or negative) effects on the system fitness, and thus it would be invisible to natural selection and essentially subject to neutral drift. This is often assumed as the ‘default’ case [11], but positive proof is scarce. We have seen above that some reactions which, based on the discrimination factor, would appear very negligible, do become liabilities because the promiscuous enzyme and the
Substrate Promiscuity Contributes to Underground Metabolism
As seen in the sections above, enzymes have an unavoidable tendency to act on alternative, available substrates. Even when (perhaps not very often) this tendency is restrained to near the minimum level allowed by chemistry, and even in the presence of ‘repair’ systems, these enzymes will generate alternative products, many of which will be nonstandard metabolites. Substrate promiscuity must be hence considered as a major contribution to the complexity of the metabolome – together with catalytic
Concluding Remarks
The results and arguments reviewed here show that, although perfect substrate specificity is essentially unattainable, metabolic enzymes are often much less selective than they could be. Furthermore, enzyme activities with alternative substrates are subject to distinct selective pressures. They can be fostered by natural selection until they reach levels that are most useful for fitness, or repressed to levels at which they are no longer harmful. When deleterious side-reactions cannot be
References (76)
- et al.
Catalytic promiscuity and the evolution of new enzymatic activities
Chem. Biol.
(1999) - et al.
Enzyme promiscuity: mechanism and applications
Trends Biotechnol.
(2007) Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency?
Curr. Opin. Chem. Biol.
(2014)An evolutionary biochemist’s perspective on promiscuity
Trends Biochem. Sci.
(2015)Enzyme evolution: innovation is easy, optimization is complicated
Curr. Opin. Struct. Biol.
(2018)The role of induced fit and conformational changes of enzymes in specificity and catalysis
Bioorg. Chem.
(1988)The BRENDA enzyme information system – from a database to an expert system
J. Biotechnol.
(2017)- et al.
Principles of protein stability derived from protein engineering experiments
Curr. Opin. Struct. Biol.
(1993) - et al.
The quest for molecular quasi-species in ligand-activity space and its application to directed enzyme evolution
FEBS Lett.
(2010) - et al.
Structure and functioning mechanism of transketolase
Biochim. Biophys. Acta
(2014)
Inherent properties of adenylosuccinate lyase could explain S-Ado/SAICAr ratio due to homozygous R426H and R303C mutations
Biochim. Biophys. Acta
Yeast and rat Coq3 and Escherichia coli UbiG polypeptides catalyze both O-methyltransferase steps in coenzyme Q biosynthesis
J. Biol. Chem.
Lysine biosynthesis of Thermococcus kodakarensis with the capacity to function as an ornithine biosynthetic system
J. Biol. Chem.
D-Aspartate: an endogenous NMDA receptor agonist enriched in the developing brain with potential involvement in schizophrenia
J. Pharm. Biomed. Anal.
Proofreading of noncognate acyl adenylates by an acyl-coenzyme a ligase
Chem. Biol.
Escherichia coli D-malate dehydrogenase, a generalist enzyme active in the leucine biosynthesis pathway
J. Biol. Chem.
Broad specificity of human phosphoglycerate kinase for antiviral nucleoside analogs
Biochem. Pharmacol.
Nucleotide triphosphate promiscuity in Mycobacterium tuberculosis dethiobiotin synthetase
Tuberculosis
Underground metabolism: network-level perspective and biotechnological potential
Curr. Opin. Biotechnol.
Specificity and promiscuity at the branch point in gentamicin biosynthesis
Chem. Biol.
Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis
Mol. Syst. Biol.
Shining a light on enzyme promiscuity
Curr. Opin. Struct. Biol.
Network context and selection in the evolution to enzyme specificity
Science
Tracing the repertoire of promiscuous enzymes along the metabolic pathways in archaeal organisms
Life (Basel)
Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis
Biochemistry
Completing the folate biosynthesis pathway in Plasmodium falciparum: p-aminobenzoate is produced by a highly divergent promiscuous aminodeoxychorismate lyase
Biochem. J.
Substrate and catalytic promiscuity of secondary metabolite enzymes: O-prenylation of hydroxyxanthones with different prenyl donors by a bisindolyl benzoquinone C- and N-prenyltransferase
RSC Adv.
The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters
Biochemistry
Structure and Mechanism in Protein Science – A Guide to Enzyme Catalysis and Protein Folding
Specificity of non-Michaelis-Menten enzymes: necessary information for analyzing metabolic pathways
J. Phys. Chem. B
The probability of errors in the process of synthesis of protein molecules
Festschrift fur Prof Dr Arthur Stoll
Synthetic and editing mechanisms of aminoacyl-tRNA synthetases
Top. Curr. Chem.
Testing the limits of protein-ligand binding discrimination with transition-state analogue inhibitors
Acc. Chem. Res.
Increased promiscuity of human galactokinase following alteration of a single amino acid residue distant from the active site
Chembiochem
Evolution of substrate specificity in a recipient’s enzyme following horizontal gene transfer
Mol. Biol. Evol.
Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme
Mol. Biol. Evol.
Nit1 is a metabolite repair enzyme that hydrolyzes deaminated glutathione
Proc. Natl. Acad. Sci. U. S. A.
Enzyme promiscuity: a mechanistic and evolutionary perspective
Annu. Rev. Biochem.
Cited by (50)
On the evolution of natural product biosynthesis
2023, Advances in Microbial PhysiologyDiffusion control in biochemical specificity
2022, Biophysical JournalThe physical logic of protein machines
2024, Journal of Statistical Mechanics: Theory and ExperimentMultifacetedProtDB: a database of human proteins with multiple functions
2024, Nucleic Acids ResearchStudy of two glycosyltransferases related to polysaccharide biosynthesis in Rhodococcus jostii RHA1
2024, Biological Chemistry