Recent advances in enzyme promiscuity
Tóm tắt
Enzyme promiscuity is defined as the capability of an enzyme to catalyze a reaction other than the reaction for which it has been specialized. Although, enzyme is known for its specificity, many enzymes are reported to be promiscuous in nature. However, the promiscuous function may not be relevant in physiological conditions. The reasons could be either very low level of catalytic activity or unavailability of the substrates in the cell. Hitherto, the enzyme promiscuity is of great importance because they are the starting point for the evolution of new functions in the nature. In addition, the promiscuous activities are utilized for the development of new catalytic functions by applying directed laboratory evolution and protein engineering techniques. The aim of this review is to provide recent developments on the understanding of the mechanism of catalytic promiscuity, evolvability of promiscuous functions and the applications of enzyme promiscuity in the designing of enhanced or new functional biocatalysts.
Tài liệu tham khảo
Khersonsky O, Tawfik DS (2010) Enzyme promiscuity: mechanistic and evolutionary perspective. Annu Rev Biochem 79:471–505
Copley SD (2014) An evolutionary perspective on protein moonlighting. Biochem Soc Trans 42(6):1684–1691
Gupta RD, Goldsmith M, Ashani Y, Simo Y, Mullokandov G, Bar H, Ben-David M, Leader H, Margalit R, Silman I, Sussman JL, Tawfik DS (2011) Directed evolution of hydrolases for prevention of G-type nerve agent intoxication. Nat Chem Biol 7(2):120–125
Jackson CJ, Foo JL, Tokuriki N, Afriat L, Carr PD, Kim HK, Schenk G, Tawfik DS, Ollis DL (2009) Conformational sampling, catalysis, and evolution of the bacterial phosphotriesterase. Proc Natl Acad Sci USA 106(51):21631–21636
Bigley AN, Mabanglo MF, Harvey SP, Raushel FM (2015) Variants of phosphotriesterase for the enhanced detoxification of the chemical warfare agent VR. Biochemistry 54(35):5502–5512
Nobeli I, Favia AD, Thornton JM (2009) Protein promiscuity and its implications for biotechnology. Nat Biotechnol 27:157–167
Copley SD (2009) Evolution of efficient pathways for degradation of anthropogenic chemicals. Nat Chem Biol 5(8):559–566
López-Iglesias M, Gotor-Fernández V (2015) Recent advances in biocatalytic promiscuity: hydrolase-catalyzed reactions for nonconventional transformations. Chem Rec 15(4):743–759
Baier F, Tokuriki N (2014) Connectivity between catalytic landscapes of the metallo-β-lactamase superfamily. J Mol Biol 426(13):2442–2456
Parera M, Martinez MA (2014) Strong epistatic interactions within a single protein. Mol Biol Evol 31(6):1546–1553
Copley SD (2015) An evolutionary biochemist’s perspective on promiscuity. Trends Biochem Sci 40(2):72–78
Atkins WM (2015) Biological messiness vs. biological genius: mechanistic aspects and roles of protein promiscuity. J Steroid Biochem Mol Biol 151:3–11
Arora B, Mukherjee J, Gupta MN (2014) Enzyme promiscuity: using the dark side of enzyme specificity in white Biotechnology. Sustainable Chemical Processes 2:25
Penning TM, Chen M, Jin Y (2015) Promiscuity and diversity in 3-ketosteroid reductases. J Steroid Biochem Mol Biol 151:93–101
Miao Y, Rahimi M, Geertsema EM, Poelarends GJ (2015) Recent developments in enzyme promiscuity for carbon-carbon bond-forming reactions. Curr Opin Chem Biol 25:115–123
Matange N, Podobnik M, Visweswariah SS (2015) Metallophosphoesterases: structural fidelity with functional promiscuity. Biochem J 467(2):201–216
Noda-García L, Juárez-Vázquez AL, Ávila-Arcos MC, Verduzco-Castro EA, Montero-Morán G, Gaytán P, Carrillo-Tripp M, Barona-Gómez F (2015) Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα) isomerase evolutionary intermediates from a diverse metagenome. BMC Evol Biol 15:107
Huang H, Pandya C, Liu C, Al-Obaidi NF, Wang M, Zheng L, Toews Keating S, Aono M, Love JD, Evans B, Seidel RD, Hillerich BS, Garforth SJ, Almo SC, Dunaway-Mariano PS, Mariano D, Allen KN, Farelli JD (2015) Panoramic view of a superfamily of phosphatases through substrate profiling. Proc Natl Acad Sci USA 112(16):e1974
Mashiyama ST, Malabanan MM, Akiva E, Bhosle R, Branch MC, Hillerich B, Jagessar K, Kim J, Patskovsky Y, Seidel RD, Stead M, Toro R, Vetting MW, Almo SC, Armstrong RN, Babbitt PC (2014) Large-scale determination of sequence, structure, and function relationships in cytosolic glutathione transferases across the biosphere. PLoS Biol 12(4):e1001843
Pratap S, Katiki M, Gill P, Kumar P, Golemi-Kotra D (2015) Active-site plasticity is essential to carbapenem hydrolysis by OXA-58 Class D β-lactamase of Acinetobacter baumannii. Antimicrob Agents Chemother 60:75–86
Alcolombri U, Elias M, Tawfik DS (2011) Directed evolution of sulfotransferases and paraoxonases by ancestral libraries. J Mol Biol 411(4):837–853
Kraus ML, Grimm C, Seibel J (2015) Redesign of the active site of sucrose phosphorylase by a clash induced cascade of loop shifts. Chem Bio Chem. doi:10.1002/cbic.201500514
Afriat-Jurnou L, Jackson CJ, Tawfik DS (2012) Reconstructing a missing link in the evolution of a recently diverged phosphotriesterase by active-site loop remodeling. Biochemistry 51(31):6047–6055
Yasutake Y, Yao M, Sakai N, Kirita T, Tanaka I (2004) Crystal structure of the Pyrococcus horikoshii isopropylmalate isomerase small subunit provides insight into the dual substrate specificity of the enzyme. J Mol Biol 344:325–333
Sevrioukova IF, Poulos TL (2013) Understanding the mechanism of cytochrome P450 3A4:recent advances and remaining problems. Dalton Trans 42(9):3116–3126
Yao J, Guo H, Chaiprasongsuk M, Zhao N, Chen F, Yang X, Guo H (2015) Substrate-assisted catalysis in the reaction catalyzed by salicylic acid binding protein 2 (SABP2), a potential mechanism of substrate discrimination for some promiscuous enzymes. Biochemistry 54(34):5366–5375
Baier F, Chen J, Solomonson M, Strynadka NC, Tokuriki N (2015) Distinct metal isoforms underlie promiscuous activity profiles of metalloenzymes. ACS Chem Biol 10(7):1684–1693
Marschner A, Klein CD (2015) Metal promiscuity and metal-dependent substrate preferences of Trypanosoma brucei methionine aminopeptidase 1. Biochimie 115:35–43
Pordea A (2015) Metal-binding promiscuity in artificial metalloenzyme design. Curr Opin Chem Biol 25:124–132
Rivera-Perez C, Nyati P, Noriega FG (2015) A corpora allata farnesyl diphosphate synthase in mosquitoes displaying a metal ion dependent substrate specificity. Insect Biochem Mol Biol 64:44–50
Kim Y, Cunningham MA, Mire J, Tesar C, Sacchettini J, Joachimiak A (2013) NDM-1, the ultimate promiscuous enzyme: substrate recognition and catalytic mechanism. FASEB J 27(5):1917–1927
Tokuriki N, Tawfik DS (2009) Protein dynamism and evolvability. Science 324:203–207
Kaltenbach M, Tokuriki N (2014) Dynamics and constraints of enzyme evolution. J Exp Zool B Mol Dev Evol 322(7):468–487
Amitai G, Gupta RD, Tawfik DS (2007) Laten evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J 1(1):67–78
Gupta RD, Tawfik DS (2008) Directed enzyme evolution via small and effective neutral drift libraries. Nat Methods 5(11):939–942
Miles ZD, Roberts SA, McCarty RM, Bandarian V (2014) Biochemical and structural studies of 6-carboxy-5, 6, 7, 8-tetrahydropterin synthase reveal the molecular basis of catalytic promiscuity within the tunnel-fold superfamily. J Biol Chem 289(34):23641–23652
Luo XJ, Kong XD, Zhao J, Chen Q, Zhou J, Xu JH (2014) Switching a newly discovered lactonase into an efficient and thermostable phosphotriesterase by simple double mutations His250Ile/Ile263Trp. Biotechnol Bioeng 111(10):1920–1930
Khanal A, Yu McLoughlin S, Kershner JP, Copley SD (2015) Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution. Mol Biol Evol 32(1):100–108
de Visser JA, Krug J (2014) Empirical fitness landscapes and the predictability of evolution. Nat Rev Genet 15(7):480–490
Harms MJ, Thornton JW (2013) Evolutionary biochemistry: revealing the historical and physical causes of protein properties. Nat Rev Genet 14(8):559–571
Renata H, Wang ZJ, Arnold FH (2015) Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution. Angew Chem Int Ed Engl 54(11):3351–3367
Colin PY, Kintses B, Gielen F, Miton CM, Fischer G, Mohamed MF, Hyvönen M, Morgavi DP, Janssen DB, Hollfelder F (2015) Ultrahigh-throughput discovery of promiscuous enzymes by picodroplet functional metagenomics. Nat Commun 6:10008
Meier MM, Rajendran C, Malisi C, Fox NG, Xu C, Schlee S, Barondeau DP, Höcker B, Sterner R, Raushel FM (2013) Molecular engineering of organophosphate hydrolysis activity from a weak promiscuous lactonase template. J Am Chem Soc 135(31):11670–11677
Bigley AN, Xu C, Henderson TJ, Harvey SP, Raushel FM (2013) Enzymatic neutralization of the chemical warfare agent VX: evolution of phosphotriesterase for phosphorothiolate hydrolysis. J Am Chem Soc 135(28):10426–10432
Naqvi T, Warden AC, French N, Sugrue E, Carr PD, Jackson CJ, Scott C (2014) A 5000-fold increase in the specificity of a bacterial phosphotriesterase for malathion through combinatorial active site mutagenesis. PLoS One. 9(4):e94177
Dorr BM, Ham HO, An C, Chaikof EL, Liu DR (2014) Reprogramming the specificity of sortase enzymes. Proc Natl Acad Sci USA 111(37):13343–13348
Sharma UK, Sharma N, Kumar R, Kumar R, Sinha AK (2009) Biocatalytic promiscuity of lipase in chemoselective oxidation of aryl alcohols/acetates: a unique synergism of CAL-B and [hmim] Br for the metal-free H2O2 activation. Org Lett 11(21):4846–4848
Bordes I, Recatalá J, Świderek K, Moliner V (2015) Is promiscuous CALB a good scaffold for designing new epoxidases? Molecules 20(10):17789–17806
Leščić Ašler I, Ivić N, Kovačić F, Schell S, Knorr J, Krauss U, Wilhelm S, Kojić-Prodić B, Jaeger KE (2010) Probing enzyme promiscuity of SGNH hydrolases. Chem Bio Chem 11(15):2158–2167
Li R, Perez B, Jian H, Jensen MM, Gao R, Dong M, Glasius M, Guo Z (2015) Characterization and mechanism insight of accelerated catalytic promiscuity of Sulfolobus tokodaii (ST0779) peptidase for aldol addition reaction. Appl Microbiol Biotechnol 99:9625–9634
Cai Y, Bhuiya MW, Shanklin J, Liu CJ (2015) Engineering a Monolignol 4-O-methyltransferase with High Selectivity for the Condensed Lignin Precursor Coniferyl Alchohol. J Biol Chem. 290:26715–26724
Koval’ T, Lipovová P, Podzimek T, Matoušek J, Dušková J, Skálová T, Stěpánková A, Hašek J, Dohnálek J (2013) Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis. Acta Crystallogr D Biol Crystallogr 69(Pt 2):213–226
Norrgård MA, Mannervik B (2011) Engineering GST M2-2 for high activity with indene 1,2-oxide and indication of an H-site residue sustaining catalytic promiscuity. J Mol Biol 412(1):111–120