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Shelley D. Copley - Publications

Affiliations: 
University of Colorado, Boulder, Boulder, CO, United States 
Area:
Biochemistry
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2025 Widney KA, Phillips LC, Rusch LM, Copley SD. A cheater founds the winning lineages during evolution of a novel metabolic pathway. Biorxiv : the Preprint Server For Biology. PMID 39990456 DOI: 10.1101/2025.01.26.634942  0.33
2022 Copley SD, Newton MS, Widney KA. How to Recruit a Promiscuous Enzyme to Serve a New Function. Biochemistry. PMID 35729117 DOI: 10.1021/acs.biochem.2c00249  0.443
2020 Copley SD. Evolution of new enzymes by gene duplication and divergence. The Febs Journal. 287: 1262-1283. PMID 32250558 DOI: 10.1111/Febs.15299  0.459
2019 Morgenthaler AB, Kinney WR, Ebmeier CC, Walsh CM, Snyder DJ, Cooper VS, Old WM, Copley SD. Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome. Elife. 8. PMID 31815667 DOI: 10.7554/Elife.53535  0.433
2019 Kim J, Flood JJ, Kristofich MR, Gidfar C, Morgenthaler AB, Fuhrer T, Sauer U, Snyder D, Cooper VS, Ebmeier CC, Old WM, Copley SD. Hidden resources in the genome restore PLP synthesis and robust growth after deletion of the essential gene . Proceedings of the National Academy of Sciences of the United States of America. PMID 31712440 DOI: 10.1073/Pnas.1915569116  0.473
2019 Morgenthaler AB, Kinney WR, Ebmeier CC, Walsh CM, Snyder DJ, Cooper VS, Old WM, Copley SD. Author response: Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome Elife. DOI: 10.7554/Elife.53535.Sa2  0.312
2018 Flood JJ, Copley SD. Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum. Msystems. 3. PMID 30505947 DOI: 10.1128/mSystems.00275-18  0.334
2018 Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ, Old WM, Cooper VS, Copley SD. Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. Plos Genetics. 14: e1007615. PMID 30148850 DOI: 10.1371/Journal.Pgen.1007615  0.403
2018 Mikkonen A, Yläranta K, Tiirola M, Dutra LAL, Salmi P, Romantschuk M, Copley S, Ikäheimo J, Sinkkonen A. Successful aerobic bioremediation of groundwater contaminated with higher chlorinated phenols by indigenous degrader bacteria. Water Research. 138: 118-128. PMID 29574199 DOI: 10.1016/J.Watres.2018.03.033  0.343
2017 Copley SD. Shining a light on enzyme promiscuity. Current Opinion in Structural Biology. 47: 167-175. PMID 29169066 DOI: 10.1016/J.Sbi.2017.11.001  0.506
2016 Kershner JP, Yu McLoughlin S, Kim J, Morgenthaler A, Ebmeier CC, Old WM, Copley SD. A Synonymous Mutation Upstream of the Gene Encoding a Weak-link Enzyme Causes an Ultrasensitive Response in Growth Rate. Journal of Bacteriology. PMID 27501982 DOI: 10.1128/Jb.00262-16  0.423
2016 Thiaville JJ, Flood J, Yurgel S, Prunetti L, Elbadawi-Sidhu M, Hutinet G, Forouhar F, Zhang X, Ganesan V, Reddy P, Fiehn O, Gerlt JA, Hunt JF, Copley SD, De Crecy-Lagard V. Members of a novel kinase family (DUF1537) can recycle toxic intermediates into an essential metabolite. Acs Chemical Biology. PMID 27294475 DOI: 10.1021/Acschembio.6B00279  0.367
2015 Copley SD. An evolutionary biochemist's perspective on promiscuity. Trends in Biochemical Sciences. 40: 72-8. PMID 25573004 DOI: 10.1016/J.Tibs.2014.12.004  0.461
2015 Khanal A, Yu McLoughlin S, Kershner JP, Copley SD. Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution. Molecular Biology and Evolution. 32: 100-8. PMID 25246702 DOI: 10.1093/Molbev/Msu271  0.451
2014 Rudolph J, Erbse AH, Behlen LS, Copley SD. A radical intermediate in the conversion of pentachlorophenol to tetrachlorohydroquinone by Sphingobium chlorophenolicum. Biochemistry. 53: 6539-49. PMID 25238136 DOI: 10.1021/Bi5010427  0.49
2013 Novikov Y, Copley SD. Reactivity landscape of pyruvate under simulated hydrothermal vent conditions. Proceedings of the National Academy of Sciences of the United States of America. 110: 13283-8. PMID 23872841 DOI: 10.1073/Pnas.1304923110  0.357
2013 Yadid I, Rudolph J, Hlouchova K, Copley SD. Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol. Proceedings of the National Academy of Sciences of the United States of America. 110: E2182-90. PMID 23676275 DOI: 10.1073/Pnas.1214052110  0.712
2013 Kim J, Copley SD. The orphan protein bis-γ-glutamylcystine reductase joins the pyridine nucleotide disulfide reductase family. Biochemistry. 52: 2905-13. PMID 23560638 DOI: 10.1021/Bi4003343  0.416
2012 Kim J, Copley SD. Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network. Proceedings of the National Academy of Sciences of the United States of America. 109: E2856-64. PMID 22984162 DOI: 10.1073/Pnas.1208509109  0.382
2012 Hlouchova K, Rudolph J, Pietari JM, Behlen LS, Copley SD. Pentachlorophenol hydroxylase, a poorly functioning enzyme required for degradation of pentachlorophenol by Sphingobium chlorophenolicum. Biochemistry. 51: 3848-60. PMID 22482720 DOI: 10.1021/Bi300261P  0.742
2012 Copley SD, Rokicki J, Turner P, Daligault H, Nolan M, Land M. The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway. Genome Biology and Evolution. 4: 184-98. PMID 22179583 DOI: 10.1093/Gbe/Evr137  0.362
2012 Copley SD. Toward a systems biology perspective on enzyme evolution. The Journal of Biological Chemistry. 287: 3-10. PMID 22069330 DOI: 10.1074/Jbc.R111.254714  0.478
2010 Kim J, Kershner JP, Novikov Y, Shoemaker RK, Copley SD. Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis. Molecular Systems Biology. 6: 436. PMID 21119630 DOI: 10.1038/Msb.2010.88  0.524
2010 Rudolph J, Kim J, Copley SD. Multiple turnovers of the nicotino-enzyme PdxB require α-keto acids as cosubstrates. Biochemistry. 49: 9249-55. PMID 20831184 DOI: 10.1021/Bi101291D  0.452
2010 Copley SD, Crooks GP. Enzymic Dehalogenation of 4-Chlorobenzoyl Coenzyme A in Acinetobacter sp. Strain 4-CB1. Applied and Environmental Microbiology. 58: 1385-7. PMID 16348702 DOI: 10.1128/Aem.58.4.1385-1387.1992  0.437
2009 Copley SD. Prediction of function in protein superfamilies. F1000 Biology Reports. 1: 91. PMID 20948600 DOI: 10.3410/B1-91  0.393
2009 Copley SD. Evolution of efficient pathways for degradation of anthropogenic chemicals. Nature Chemical Biology. 5: 559-66. PMID 19620997 DOI: 10.1038/Nchembio.197  0.403
2008 McLoughlin SY, Copley SD. A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities. Proceedings of the National Academy of Sciences of the United States of America. 105: 13497-502. PMID 18757760 DOI: 10.1073/Pnas.0804804105  0.419
2008 Warner JR, Behlen LS, Copley SD. A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase. Biochemistry. 47: 3258-65. PMID 18275157 DOI: 10.1021/Bi702431N  0.659
2007 Warner JR, Copley SD. Pre-steady-state kinetic studies of the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry. 46: 13211-22. PMID 17956123 DOI: 10.1021/Bi701069N  0.658
2007 Kim J, Copley SD. Why metabolic enzymes are essential or nonessential for growth of Escherichia coli K12 on glucose. Biochemistry. 46: 12501-11. PMID 17935357 DOI: 10.1021/Bi7014629  0.45
2007 Warner JR, Copley SD. Mechanism of the severe inhibition of tetrachlorohydroquinone dehalogenase by its aromatic substrates. Biochemistry. 46: 4438-47. PMID 17355122 DOI: 10.1021/Bi0620104  0.67
2005 Warner JR, Lawson SL, Copley SD. A mechanistic investigation of the thiol-disulfide exchange step in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry. 44: 10360-8. PMID 16042413 DOI: 10.1021/Bi050666B  0.654
2005 Morowitz HJ, Srinivasan V, Copley S, Smith E. The simplest enzyme revisited: The chicken and egg argument solved Complexity. 10: 12-13. DOI: 10.1002/Cplx.20087  0.387
2004 Copley SD, Novak WR, Babbitt PC. Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry. 43: 13981-95. PMID 15518547 DOI: 10.1021/Bi048947R  0.314
2004 Dai M, Copley SD. Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723. Applied and Environmental Microbiology. 70: 2391-7. PMID 15066836 DOI: 10.1128/Aem.70.4.2391-2397.2004  0.338
2003 Copley SD. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Current Opinion in Chemical Biology. 7: 265-72. PMID 12714060 DOI: 10.1016/S1367-5931(03)00032-2  0.377
2003 Dai M, Rogers JB, Warner JR, Copley SD. A previously unrecognized step in pentachlorophenol degradation in Sphingobium chlorophenolicum is catalyzed by tetrachlorobenzoquinone reductase (PcpD). Journal of Bacteriology. 185: 302-10. PMID 12486067 DOI: 10.1128/Jb.185.1.302-310.2003  0.615
2002 Copley SD, Dhillon JK. Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes. Genome Biology. 3: research0025. PMID 12049666 DOI: 10.1186/Gb-2002-3-5-Research0025  0.365
2002 Kiefer PM, Copley SD. Characterization of the initial steps in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry. 41: 1315-22. PMID 11802732 DOI: 10.1021/Bi0117504  0.484
2002 Kiefer PM, McCarthy DL, Copley SD. The reaction catalyzed by tetrachlorohydroquinone dehalogenase does not involve nucleophilic aromatic substitution. Biochemistry. 41: 1308-14. PMID 11802731 DOI: 10.1021/Bi0117495  0.484
2000 Copley SD. Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends in Biochemical Sciences. 25: 261-5. PMID 10838562 DOI: 10.1016/S0968-0004(00)01562-0  0.508
2000 Anandarajah K, Kiefer PM, Donohoe BS, Copley SD. Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol Biochemistry. 39: 5303-5311. PMID 10820000 DOI: 10.1021/Bi9923813  0.483
1999 Xu L, Resing K, Lawson SL, Babbitt PC, Copley SD. Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723. Biochemistry. 38: 7659-69. PMID 10387005 DOI: 10.1021/Bi990103Y  0.445
1999 Copley SD. Microbial dehalogenases: enzymes recruited to convert xenobiotic substrates. Current Opinion in Chemical Biology. 2: 613-7. PMID 9818187 DOI: 10.1016/S1367-5931(98)80092-6  0.457
1997 McCarthy DL, Claude AA, Copley SD. In vivo levels of chlorinated hydroquinones in a pentachlorophenol-degrading bacterium. Applied and Environmental Microbiology. 63: 1883-8. PMID 9143119 DOI: 10.1128/Aem.63.5.1883-1888.1997  0.31
1997 Willett WS, Copley SD. Identification and localization of a stable sulfenic acid in peroxide-treated tetrachlorohydroquinone dehalogenase using electrospray mass spectrometry. Chemistry & Biology. 3: 851-7. PMID 8939704 DOI: 10.1016/S1074-5521(96)90071-X  0.336
1997 McCarthy DL, Louie DF, Copley SD. Identification of a Covalent Intermediate between Glutathione and Cysteine13 Formed during Catalysis by Tetrachlorohydroquinone Dehalogenase Journal of the American Chemical Society. 119: 11337-11338. DOI: 10.1021/Ja9726365  0.395
1996 McCarthy DL, Navarrete S, Willett WS, Babbitt PC, Copley SD. Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily. Biochemistry. 35: 14634-42. PMID 8931562 DOI: 10.1021/bi961730f  0.362
1995 Crooks GP, Xu L, Barkley RM, Copley SD. Exploration of possible mechanisms for 4-chlorobenzoyl CoA dehalogenase: Evidence for an aryl-enzyme intermediate Journal of the American Chemical Society. 117: 10791-10798. DOI: 10.1021/Ja00149A001  0.519
1994 Crooks GP, Copley SD. Purification and characterization of 4-chlorobenzoyl CoA dehalogenase from Arthrobacter sp. strain 4-CB1. Biochemistry. 33: 11645-9. PMID 7918379 DOI: 10.1021/Bi00204A028  0.364
1993 Crooks GP, Copley SD. A surprising effect of leaving group on the nucleophilic aromatic substitution reaction catalyzed by 4-chlorobenzoyl CoA dehalogenase Journal of the American Chemical Society. 115: 6422-6423. DOI: 10.1021/Ja00067A072  0.396
1987 Guilford WJ, Copley SD, Knowles JR. The mechanism of the chorismate mutase reaction Journal of the American Chemical Society. 109: 5013-5019. DOI: 10.1021/Ja00250A041  0.342
1987 Copley SD, Knowles JR. The conformational equilibrium of chorismate in solution: Implications for the mechanism of the non-enzymic and the enzyme-catalyzed rearrangement of chorismate to prephenate Journal of the American Chemical Society. 109: 5008-5013. DOI: 10.1021/Ja00250A040  0.429
1987 Copley SD, Knowles JR. The conformational equilibrium of chorismate in solution: implications for the mechanism of the non-enzymic and the enzyme-catalyzed rearrangement of chorismate to prephenate Journal of the American Chemical Society. 109: 5008-5013. DOI: 10.1021/ja00250a040  0.325
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