Enzyme Promiscuous Activity: How to Define it and its Evolutionary Aspects

Author(s): Valentina De Luca, Luigi Mandrich*

Journal Name: Protein & Peptide Letters

Volume 27 , Issue 5 , 2020

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Graphical Abstract:


Enzymes are among the most studied biological molecules because better understanding enzymes structure and activity will shed more light on their biological processes and regulation; from a biotechnological point of view there are many examples of enzymes used with the aim to obtain new products and/or to make industrial processes less invasive towards the environment. Enzymes are known for their high specificity in the recognition of a substrate but considering the particular features of an increasing number of enzymes this is not completely true, in fact, many enzymes are active on different substrates: this ability is called enzyme promiscuity. Usually, promiscuous activities have significantly lower kinetic parameters than to that of primary activity, but they have a crucial role in gene evolution. It is accepted that gene duplication followed by sequence divergence is considered a key evolutionary mechanism to generate new enzyme functions. In this way, promiscuous activities are the starting point to increase a secondary activity in the main activity and then get a new enzyme. The primary activity can be lost or reduced to a promiscuous activity. In this review we describe the differences between substrate and enzyme promiscuity, and its rule in gene evolution. From a practical point of view the knowledge of promiscuity can facilitate the in vitro progress of proteins engineering, both for biomedical and industrial applications. In particular, we report cases regarding esterases, phosphotriesterases and cytochrome P450.

Keywords: Enzyme promiscuity, hydrolases, carboxylesterases, phosphotriesterases, cytochrome P450, mutagenesis, kinetic parameters, enzyme evolution.

Northrop, J.H.; Kunitz, M. Isolation of protein crystals possessing trypsin activity. Science, 1888, 1931(73), 262-263.
Smyth, D.G.; Stein, W.H.; Moore, S. The sequence of amino acid residues in bovine pancreatic ribonuclease: Revisions and confirmations. J. Biol. Chem., 1963, 238, 227-234.
[PMID: 13989651]
Blake, C.C.F.; Koenig, D.F.; Mair, G.A.; North, A.C.T.; Phillips, D.C.; Sarma, V.R. Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution. Nature, 1965, 206(4986), 757-761.
[http://dx.doi.org/10.1038/206757a0] [PMID: 5891407]
Nelson, J.W.; Breaker, R.R. The lost language of the RNA World. Sci. Signal., 2017, 10(483), eaam8812
[http://dx.doi.org/10.1126/scisignal.aam8812] [PMID: 28611182]
O’Brien, P.J.; Herschlag, D. Catalytic promiscuity and the evolution of new enzymatic activities. Chem. Biol., 1999, 6(4), R91-R105.
[http://dx.doi.org/10.1016/S1074-5521(99)80033-7] [PMID: 10099128]
Bornscheuer, U.T.; Kazlauskas, R.J. Catalytic promiscuity in biocatalysis: Using old enzymes to form new bonds and follow new pathways. Angew. Chem. Int. Ed. Engl., 2004, 43(45), 6032-6040.
[http://dx.doi.org/10.1002/anie.200460416] [PMID: 15523680]
Khersonsky, O.; Tawfik, D.S. Enzyme promiscuity: A mechanistic and evolutionary perspective. Annu. Rev. Biochem., 2010, 79, 471-505.
[http://dx.doi.org/10.1146/annurev-biochem-030409-143718] [PMID: 20235827]
Manco, G.; Adinolfi, E.; Pisani, F.M.; Ottolina, G.; Carrea, G.; Rossi, M. Overexpression and properties of a new thermophilic and thermostable esterase from Bacillus acidocaldarius with sequence similarity to hormone-sensitive lipase subfamily. Biochem. J., 1998, 332(Pt 1), 203-212.
[http://dx.doi.org/10.1042/bj3320203] [PMID: 9576869]
Mandrich, L.; Manco, G.; Rossi, M.; Floris, E.; Jansen-van den Bosch, T.; Smit, G.; Wouters, J.A. Alicyclobacillus acidocaldarius thermophilic esterase EST2's activity in milk and cheese models. Appl. Environ. Microbiol., 2006, 72(5), 3191-3197.
[http://dx.doi.org/10.1128/AEM.72.5.3191-3197.2006] [PMID: 16672457]
Kim, T.D. Bacterial Hormone-Sensitive Lipases (bHSLs): Emerging enzymes for biotechnological applications. J. Microbiol. Biotechnol., 2017, 27(11), 1907-1915.
[http://dx.doi.org/10.4014/jmb.1708.08004] [PMID: 29032653]
Manco, G.; Giosuè, E.; D’Auria, S.; Herman, P.; Carrea, G.; Rossi, M. Cloning, overexpression, and properties of a new thermophilic and thermostable esterase with sequence similarity to hormone-sensitive lipase subfamily from the archaeon Archaeoglobus fulgidus. Arch. Biochem. Biophys., 2000, 373(1), 182-192.
[http://dx.doi.org/10.1006/abbi.1999.1497] [PMID: 10620337]
De Santi, C.; Tutino, M.L.; Mandrich, L.; Giuliani, M.; Parrilli, E.; Del Vecchio, P.; de Pascale, D. The hormone-sensitive lipase from Psychrobacter sp. TA144: New insight in the structural/functional characterization. Biochimie, 2010, 92(8), 949-957.
[http://dx.doi.org/10.1016/j.biochi.2010.04.001] [PMID: 20382198]
Furlong, C.E.; Marsillach, J.; Jarvik, G.P.; Costa, L.G. Paraoxonases-1, -2 and -3: What are their functions? Chem. Biol. Interact., 2016, 259(Pt B), 51-62.
[http://dx.doi.org/10.1016/j.cbi.2016.05.036] [PMID: 27238723]
Carr, P.D.; Ollis, D.L. Alpha/beta hydrolase fold: An update. Protein Pept. Lett., 2009, 16(10), 1137-1148.
[http://dx.doi.org/10.2174/092986609789071298] [PMID: 19508187]
Holmquist, M. Alpha/Beta-hydrolase fold enzymes: Structures, functions and mechanisms. Curr. Protein Pept. Sci., 2000, 1(2), 209-235.
[http://dx.doi.org/10.2174/1389203003381405] [PMID: 12369917]
Nardini, M.; Dijkstra, B.W. Alpha/beta hydrolase fold enzymes: The family keeps growing. Curr. Opin. Struct. Biol., 1999, 9(6), 732-737.
[http://dx.doi.org/10.1016/S0959-440X(99)00037-8] [PMID: 10607665]
Svendsen, A. Lipase protein engineering. Biochim. Biophys. Acta, 2000, 1543(2), 223-238.
[http://dx.doi.org/10.1016/S0167-4838(00)00239-9] [PMID: 11150608]
Tjoelker, L.W.; Eberhardt, C.; Unger, J.; Trong, H.L.; Zimmerman, G.A.; McIntyre, T.M.; Stafforini, D.M.; Prescott, S.M.; Gray, P.W. Plasma platelet-activating factor acetylhydrolase is a secreted phospholipase A2 with a catalytic triad. J. Biol. Chem., 1995, 270(43), 25481-25487.
[http://dx.doi.org/10.1074/jbc.270.43.25481] [PMID: 7592717]
Spiegel, S.; Foster, D.; Kolesnick, R. Signal transduction through lipid second messengers. Curr. Opin. Cell Biol., 1996, 8(2), 159-167.
[http://dx.doi.org/10.1016/S0955-0674(96)80061-5] [PMID: 8791422]
Bencharit, S.; Edwards, C.C.; Morton, C.L.; Howard-Williams, E.L.; Kuhn, P.; Potter, P.M.; Redinbo, M.R. Multisite promiscuity in the processing of endogenous substrates by human carboxylesterase 1. J. Mol. Biol., 2006, 363(1), 201-214.
[http://dx.doi.org/10.1016/j.jmb.2006.08.025] [PMID: 16962139]
Becker, A.; Böttcher, A.; Lackner, K.J.; Fehringer, P.; Notka, F.; Aslanidis, C.; Schmitz, G. Purification, cloning, and expression of a human enzyme with Acyl coenzyme A: Cholesterol acyltransferase activity, which is identical to liver carboxylesterase. Arterioscler. Thromb., 1994, 14(8), 1346-1355.
[http://dx.doi.org/10.1161/01.ATV.14.8.1346] [PMID: 8049197]
Ma, J.; Li, Q.; Song, B.; Liu, D.; Zheng, B.; Zhang, Z.; Feng, Y. Ring-opening polymerization of ε-caprolactone catalyzed by a novel thermophilic esterase from the archaeon Archaeoglobus fulgidus. J. Mol. Catal., B Enzym., 2009, 56, 151-157.
Ding, Y.; Xiang, X.; Gu, M.; Xu, H.; Huang, H.; Hu, Y. Efficient lipase-catalyzed Knoevenagel condensation: Utilization of biocatalytic promiscuity for synthesis of benzylidene-indolin-2-ones. Bioprocess Biosyst. Eng., 2016, 39(1), 125-131.
[http://dx.doi.org/10.1007/s00449-015-1496-2] [PMID: 26546230]
Udatha, D.B.; Madsen, K.M.; Panagiotou, G.; Olsson, L. Multiple nucleophilic elbows leading to multiple active sites in a single module esterase from Sorangium cellulosum. J. Struct. Biol., 2015, 190(3), 314-327.
[http://dx.doi.org/10.1016/j.jsb.2015.04.009] [PMID: 25907516]
Wagner, U.G.; DiMaio, F.; Kolkenbrock, S.; Fetzner, S. Crystal structure analysis of EstA from Arthrobacter sp. Rue61a-an insight into catalytic promiscuity. FEBS Lett., 2014, 588(7), 1154-1160.
[http://dx.doi.org/10.1016/j.febslet.2014.02.045] [PMID: 24613918]
Alcaide, M.; Tornés, J.; Stogios, P.J.; Xu, X.; Gertler, C.; Di Leo, R.; Bargiela, R.; Lafraya, A.; Guazzaroni, M.E.; López-Cortés, N.; Chernikova, T.N.; Golyshina, O.V.; Nechitaylo, T.Y.; Plumeier, I.; Pieper, D.H.; Yakimov, M.M.; Savchenko, A.; Golyshin, P.N.; Ferrer, M.; Ferrer, M. Single residues dictate the co-evolution of dual esterases: MCP hydrolases from the α/β hydrolase family. Biochem. J., 2013, 454(1), 157-166.
[http://dx.doi.org/10.1042/BJ20130552] [PMID: 23750508]
Harel, M.; Aharoni, A.; Gaidukov, L.; Brumshtein, B.; Khersonsky, O.; Meged, R.; Dvir, H.; Ravelli, R.B.; McCarthy, A.; Toker, L.; Silman, I.; Sussman, J.L.; Tawfik, D.S. Structure and evolution of the serum paraoxonase family of detoxifying and anti-atherosclerotic enzymes. Nat. Struct. Mol. Biol., 2004, 11(5), 412-419.
[http://dx.doi.org/10.1038/nsmb767] [PMID: 15098021]
Benning, M.M.; Kuo, J.M.; Raushel, F.M.; Holden, H.M. Three-dimensional structure of the binuclear metal center of phosphotriesterase. Biochemistry, 1995, 34(25), 7973-7978.
[http://dx.doi.org/10.1021/bi00025a002] [PMID: 7794910]
Holm, L.; Sander, C. An evolutionary treasure: Unification of a broad set of amidohydrolases related to urease. Proteins, 1997, 28(1), 72-82.
[http://dx.doi.org/10.1002/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L] [PMID: 9144792]
Aubert, S.D.; Li, Y.; Raushel, F.M. Mechanism for the hydrolysis of organophosphates by the bacterial phosphotriesterase. Biochemistry, 2004, 43(19), 5707-5715.
[http://dx.doi.org/10.1021/bi0497805] [PMID: 15134445]
Seibert, C.M.; Raushel, F.M. Structural and catalytic diversity within the amidohydrolase superfamily. Biochemistry, 2005, 44(17), 6383-6391.
[http://dx.doi.org/10.1021/bi047326v] [PMID: 15850372]
Elias, M.; Tawfik, D.S. Divergence and convergence in enzyme evolution: Parallel evolution of paraoxonases from quorum-quenching lactonases. J. Biol. Chem., 2012, 287(1), 11-20.
[http://dx.doi.org/10.1074/jbc.R111.257329] [PMID: 22069329]
Draganov, D.I.; Teiber, J.F.; Speelman, A.; Osawa, Y.; Sunahara, R.; La Du, B.N. Human paraoxonases (PON1, PON2, and PON3) are lactonases with overlapping and distinct substrate specificities. J. Lipid Res., 2005, 46(6), 1239-1247.
[http://dx.doi.org/10.1194/jlr.M400511-JLR200] [PMID: 15772423]
Mandrich, L.; Cerreta, M.; Manco, G. An engineered version of human PON2 opens the way to understand the role of its post-translational modification in modulating catalytic activity. PLoS One, 2015, 10(12), e0144579
[http://dx.doi.org/10.1371/journal.pone.0144579] [PMID: 26656916]
Shim, H.; Raushel, F.M. Self-assembly of the binuclear metal center of phosphotriesterase. Biochemistry, 2000, 39(25), 7357-7364.
[http://dx.doi.org/10.1021/bi000291o] [PMID: 10858282]
Dumas, D.P.; Caldwell, S.R.; Wild, J.R.; Raushel, F.M. Purification and properties of the phosphotriesterase from Pseudomonas diminuta. J. Biol. Chem., 1989, 264(33), 19659-19665.
[PMID: 2555328]
Caldwell, S.R.; Newcomb, J.R.; Schlecht, K.A.; Raushel, F.M. Limits of diffusion in the hydrolysis of substrates by the phosphotriesterase from Pseudomonas diminuta. Biochemistry, 1991, 30(30), 7438-7444.
[http://dx.doi.org/10.1021/bi00244a010] [PMID: 1649628]
Pedroso, M.M.; Ely, F.; Mitić, N.; Carpenter, M.C.; Gahan, L.R.; Wilcox, D.E.; Larrabee, J.L.; Ollis, D.L.; Schenk, G. Comparative investigation of the reaction mechanisms of the organophosphate-degrading phosphotriesterases from Agrobacterium radiobacter (OpdA) and Pseudomonas diminuta (OPH). J. Biol. Inorg. Chem., 2014, 19(8), 1263-1275.
[http://dx.doi.org/10.1007/s00775-014-1183-9] [PMID: 25104333]
Merone, L.; Mandrich, L.; Rossi, M.; Manco, G. A thermostable phosphotriesterase from the archaeon Sulfolobus solfataricus: Cloning, overexpression and properties. Extremophiles, 2005, 9(4), 297-305.
[http://dx.doi.org/10.1007/s00792-005-0445-4] [PMID: 15909078]
Porzio, E.; Merone, L.; Mandrich, L.; Rossi, M.; Manco, G. A new phosphotriesterase from Sulfolobus acidocaldarius and its comparison with the homologue from Sulfolobus solfataricus. Biochimie, 2007, 89(5), 625-636.
[http://dx.doi.org/10.1016/j.biochi.2007.01.007] [PMID: 17337320]
Elias, M.; Dupuy, J.; Merone, L.; Mandrich, L.; Porzio, E.; Moniot, S.; Rochu, D.; Lecomte, C.; Rossi, M.; Masson, P.; Manco, G.; Chabriere, E. Structural basis for natural lactonase and promiscuous phosphotriesterase activities. J. Mol. Biol., 2008, 379(5), 1017-1028.
[http://dx.doi.org/10.1016/j.jmb.2008.04.022] [PMID: 18486146]
Afriat, L.; Roodveldt, C.; Manco, G.; Tawfik, D.S. The latent promiscuity of newly identified microbial lactonases is linked to a recently diverged phosphotriesterase. Biochemistry, 2006, 45(46), 13677-13686.
[http://dx.doi.org/10.1021/bi061268r] [PMID: 17105187]
Xiang, D.F.; Kolb, P.; Fedorov, A.A.; Meier, M.M.; Fedorov, L.V.; Nguyen, T.T.; Sterner, R.; Almo, S.C.; Shoichet, B.K.; Raushel, F.M. Functional annotation and three-dimensional structure of Dr0930 from Deinococcus radiodurans, a close relative of phosphotriesterase in the amidohydrolase superfamily. Biochemistry, 2009, 48(10), 2237-2247.
[http://dx.doi.org/10.1021/bi802274f] [PMID: 19159332]
Mandrich, L.; Di Gennaro, S.; Palma, A.; Manco, G. A further biochemical characterization of DrPLL the thermophilic lactonase from Deinococcus radiodurans. Protein Pept. Lett., 2013, 20(1), 36-44.
[http://dx.doi.org/10.2174/092986613804096810] [PMID: 22789107]
Zhang, Y.; An, J.; Yang, G-Y.; Bai, A.; Zheng, B.; Lou, Z.; Wu, G.; Ye, W.; Chen, H-F.; Feng, Y.; Manco, G. Active site loop conformation regulates promiscuous activity in a lactonase from Geobacillus kaustophilus HTA426. PLoS One, 2015, 10(2), e0115130
[http://dx.doi.org/10.1371/journal.pone.0115130] [PMID: 25706379]
Mandrich, L.; Manco, G. Evolution in the amidohydrolase superfamily: Substrate-assisted gain of function in the E183K mutant of a phosphotriesterase-like metal-carboxylesterase. Biochemistry, 2009, 48(24), 5602-5612.
[http://dx.doi.org/10.1021/bi801932x] [PMID: 19438255]
Reedy, C.J.; Gibney, B.R. Heme protein assemblies. Chem. Rev., 2004, 104(2), 617-649.
[http://dx.doi.org/10.1021/cr0206115] [PMID: 14871137]
Danielson, P.B. The cytochrome P450 superfamily: Biochemistry, evolution and drug metabolism in humans. Curr. Drug Metab., 2002, 3(6), 561-597.
[http://dx.doi.org/10.2174/1389200023337054] [PMID: 12369887]
Bhattacharya, S.S.; Yadav, J.S. Microbial P450 enzymes in bioremediation and drug discovery: Emerging potentials and challenges. Curr. Protein Pept. Sci., 2018, 19(1), 75-86.
[PMID: 27875967]
Durairaj, P.; Hur, J.S.; Yun, H. Versatile biocatalysis of fungal cytochrome P450 monooxygenases. Microb. Cell Fact., 2016, 15(1), 125.
[http://dx.doi.org/10.1186/s12934-016-0523-6] [PMID: 27431996]
Guo, J.; Ma, X.; Cai, Y.; Ma, Y.; Zhan, Z.; Zhou, Y.J.; Liu, W.; Guan, M.; Yang, J.; Cui, G.; Kang, L.; Yang, L.; Shen, Y.; Tang, J.; Lin, H.; Ma, X.; Jin, B.; Liu, Z.; Peters, R.J.; Zhao, Z.K.; Huang, L. Cytochrome P450 promiscuity leads to a bifurcating biosynthetic pathway for tanshinones. New Phytol., 2016, 210(2), 525-534.
[http://dx.doi.org/10.1111/nph.13790] [PMID: 26682704]
Casida, J.E. Pesticide interactions: Mechanisms, benefits, and risks. J. Agric. Food Chem., 2017, 65(23), 4553-4561.
[http://dx.doi.org/10.1021/acs.jafc.7b01813] [PMID: 28537748]
Hayes, C.; Ansbro, D.; Kontoyianni, M. Elucidating substrate promiscuity in the human cytochrome 3A4. J. Chem. Inf. Model., 2014, 54(3), 857-869.
[http://dx.doi.org/10.1021/ci4006782] [PMID: 24571781]
Foti, R.S.; Honaker, M.; Nath, A.; Pearson, J.T.; Buttrick, B.; Isoherranen, N.; Atkins, W.M. Catalytic versus inhibitory promiscuity in cytochrome P450s: Implications for evolution of new function. Biochemistry, 2011, 50(13), 2387-2393.
[http://dx.doi.org/10.1021/bi1020716] [PMID: 21370922]
Urlacher, V.; Schmid, R.D. Biotransformations using prokaryotic P450 monooxygenases. Curr. Opin. Biotechnol., 2002, 13(6), 557-564.
[http://dx.doi.org/10.1016/S0958-1669(02)00357-9] [PMID: 12482514]
Nishida, C.R.; Ortiz de Montellano, P.R. Thermophilic cytochrome P450 enzymes. Biochem. Biophys. Res. Commun., 2005, 338(1), 437-445.
[http://dx.doi.org/10.1016/j.bbrc.2005.08.093] [PMID: 16139791]
Hofrichter, M.; Kellner, H.; Pecyna, M.J.; Ullrich, R. Fungal unspecific peroxygenases: Heme-thiolate proteins that combine peroxidase and cytochrome P450 properties. Adv. Exp. Med. Biol., 2015, 851, 341-368.
[http://dx.doi.org/10.1007/978-3-319-16009-2_13] [PMID: 26002742]
Renault, H.; Bassard, J-E.; Hamberger, B.; Werck-Reichhart, D. Cytochrome P450-mediated metabolic engineering: Current progress and future challenges. Curr. Opin. Plant Biol., 2014, 19, 27-34.
[http://dx.doi.org/10.1016/j.pbi.2014.03.004] [PMID: 24709279]
Zagrobelny, M.; de Castro, É.C.P.; Møller, B.L.; Bak, S. Cyanogenesis in arthropods: From Chemical warfare to nuptial gifts. Insects, 2018, 9(2), 51.
[http://dx.doi.org/10.3390/insects9020051] [PMID: 29751568]
a)Foti, R.S.; Dalvie, D.K. Cytochrome P450 and non–cytochrome P450 oxidative metabolism: Contributions to the pharmacokinetics, safety, and efficacy of xenobiotics. Drug Metab. Dispos., 2016, 44, 1229-1245.
b)Jensen, R.A. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol., 1976, 30, 409-425.
Copley, S.D. Shining a light on enzyme promiscuity. Curr. Opin. Struct. Biol., 2017, 47, 167-175.
[http://dx.doi.org/10.1016/j.sbi.2017.11.001] [PMID: 29169066]
Pabis, A.; Risso, V.A.; Sanchez-Ruiz, J.M.; Kamerlin, S.C. Cooperativity and flexibility in enzyme evolution. Curr. Opin. Struct. Biol., 2018, 48, 83-92.
[http://dx.doi.org/10.1016/j.sbi.2017.10.020] [PMID: 29141202]
Giuseppe, M.; Luigia, M.; Elena, P.; Yan, F.; Luigi, M. Enzyme promiscuity in the hormone-sensitive lipase family of proteins. Protein Pept. Lett., 2012, 19(2), 144-154.
[http://dx.doi.org/10.2174/092986612799080400] [PMID: 21933124]
Skolnick, J.; Gao, M.; Roy, A.; Srinivasan, B.; Zhou, H. Implications of the small number of distinct ligand binding pockets in proteins for drug discovery, evolution and biochemical function. Bioorg. Med. Chem. Lett., 2015, 25(6), 1163-1170.
[http://dx.doi.org/10.1016/j.bmcl.2015.01.059] [PMID: 25690787]
Ramalho, T.C.; de Castro, A.A.; Silva, D.R.; Silva, M.C.; Franca, T.C.; Bennion, B.J.; Kuca, K. Computational enzymology and organophosphorus degrading enzymes: Promising approaches toward remediation technologies of warfare agents and pesticides. Curr. Med. Chem., 2016, 23(10), 1041-1061.
[http://dx.doi.org/10.2174/0929867323666160222113504] [PMID: 26898655]
Wei, R.; Zimmermann, W. Microbial enzymes for the recycling of recalcitrant petroleum-based plastics: How far are we? Microb. Biotechnol., 2017, 10(6), 1308-1322.
[http://dx.doi.org/10.1111/1751-7915.12710] [PMID: 28371373]
Brandelli, A.; Sala, L.; Kalil, S.J. Microbial enzymes for bioconversion of poultry waste into added-value products. Food Res. Int., 2015, 73, 3-12.

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Year: 2020
Published on: 27 April, 2020
Page: [400 - 410]
Pages: 11
DOI: 10.2174/0929866527666191223141205
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