Shelley D Copley

Summary

Affiliation: University of Colorado
Country: USA

Publications

  1. doi request reprint A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase
    Joseph R Warner
    Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Biochemistry 47:3258-65. 2008
  2. pmc Evolution of efficient pathways for degradation of anthropogenic chemicals
    Shelley D Copley
    Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado, USA
    Nat Chem Biol 5:559-66. 2009
  3. doi request reprint Moonlighting is mainstream: paradigm adjustment required
    Shelley D Copley
    Department of Molecular, Cellular and Developmental Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
    Bioessays 34:578-88. 2012
  4. pmc Toward a systems biology perspective on enzyme evolution
    Shelley D Copley
    Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    J Biol Chem 287:3-10. 2012
  5. ncbi request reprint Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor
    Shelley D Copley
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
    Biochemistry 43:13981-95. 2004
  6. ncbi request reprint The origin of the RNA world: co-evolution of genes and metabolism
    Shelley D Copley
    University of Colorado at Boulder, CIRES, Campus Box 216, Boulder, CO 80309, USA
    Bioorg Chem 35:430-43. 2007
  7. pmc Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol
    Itamar Yadid
    Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 110:E2182-90. 2013
  8. ncbi request reprint Mechanism of the severe inhibition of tetrachlorohydroquinone dehalogenase by its aromatic substrates
    Joseph R Warner
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Biochemistry 46:4438-47. 2007
  9. pmc Multiple turnovers of the nicotino-enzyme PdxB require α-keto acids as cosubstrates
    Johannes Rudolph
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
    Biochemistry 49:9249-55. 2010
  10. pmc Pentachlorophenol hydroxylase, a poorly functioning enzyme required for degradation of pentachlorophenol by Sphingobium chlorophenolicum
    Klara Hlouchova
    Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, USA
    Biochemistry 51:3848-60. 2012

Research Grants

Collaborators

Detail Information

Publications33

  1. doi request reprint A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase
    Joseph R Warner
    Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Biochemistry 47:3258-65. 2008
    ....
  2. pmc Evolution of efficient pathways for degradation of anthropogenic chemicals
    Shelley D Copley
    Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado, USA
    Nat Chem Biol 5:559-66. 2009
    ....
  3. doi request reprint Moonlighting is mainstream: paradigm adjustment required
    Shelley D Copley
    Department of Molecular, Cellular and Developmental Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
    Bioessays 34:578-88. 2012
    ....
  4. pmc Toward a systems biology perspective on enzyme evolution
    Shelley D Copley
    Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    J Biol Chem 287:3-10. 2012
    ....
  5. ncbi request reprint Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor
    Shelley D Copley
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
    Biochemistry 43:13981-95. 2004
    ....
  6. ncbi request reprint The origin of the RNA world: co-evolution of genes and metabolism
    Shelley D Copley
    University of Colorado at Boulder, CIRES, Campus Box 216, Boulder, CO 80309, USA
    Bioorg Chem 35:430-43. 2007
    ....
  7. pmc Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol
    Itamar Yadid
    Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 110:E2182-90. 2013
    ..The toxicity of TCBQ may have exerted selective pressure to maintain slow turnover of PcpB (0.02 s(-1)) so that a transient interaction between PcpB and PcpD can occur before TCBQ is released from the active site of PcpB...
  8. ncbi request reprint Mechanism of the severe inhibition of tetrachlorohydroquinone dehalogenase by its aromatic substrates
    Joseph R Warner
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Biochemistry 46:4438-47. 2007
    ..In addition, dissociation of the GSSG product is inhibited by TriCHQ. The thiol-disulfide exchange reaction is the rate-limiting step in the reductive dehalogenation reaction under physiological conditions...
  9. pmc Multiple turnovers of the nicotino-enzyme PdxB require α-keto acids as cosubstrates
    Johannes Rudolph
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309, USA
    Biochemistry 49:9249-55. 2010
    ..7 × 10(6) M⁻¹s⁻¹. Additionally, we have characterized the stereochemistry of α-ketoglutarate reduction by showing that d-2-HGA, but not l-2-HGA, is a competitive inhibitor vs 4PE and a noncompetitive inhibitor vs α-ketoglutarate...
  10. pmc Pentachlorophenol hydroxylase, a poorly functioning enzyme required for degradation of pentachlorophenol by Sphingobium chlorophenolicum
    Klara Hlouchova
    Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, Colorado 80309, USA
    Biochemistry 51:3848-60. 2012
    ..The conversion of TCHQ to TCBQ reverses flux through the pathway. Substantial uncoupling also occurs during the reaction with TCHQ...
  11. pmc A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities
    Sean Yu McLoughlin
    Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute of Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 105:13497-502. 2008
    ..Notably, overexpression does not require a mutation in the regulatory region of the protein; amino acid limitation attributable to the poor catalytic abilities of E383A ProA causes a physiological response that results in overexpression...
  12. pmc Reactivity landscape of pyruvate under simulated hydrothermal vent conditions
    Yehor Novikov
    Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 110:13283-8. 2013
    ..Amino acids and fatty acids formed by analogous processes may have been important components of a protometabolic network that allowed the emergence of life. ..
  13. pmc Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network
    Juhan Kim
    Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 109:E2856-64. 2012
    ..These findings have important implications for evolutionary studies of the emergence of novel pathways in nature as well as genetic engineering of microbes for "green" manufacturing processes...
  14. ncbi request reprint Pre-steady-state kinetic studies of the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase
    Joseph R Warner
    University of Colorado at Boulder, Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Biochemistry 46:13211-22. 2007
    ....
  15. pmc Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis
    Juhan Kim
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO, USA
    Mol Syst Biol 6:436. 2010
    ..One step in the pathway may be non-enzymatic...
  16. pmc The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway
    Shelley D Copley
    Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, CO, USA
    Genome Biol Evol 4:184-98. 2012
    ....
  17. doi request reprint A dimethyl ketal-protected benzoin-based linker suitable for photolytic release of unprotected peptides
    Nataliya Chumachenko
    Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    J Org Chem 76:9409-16. 2011
    ..Additionally, we developed a route to a dithiane-protected linker that requires only two steps and proceeds in 65% yield, a significant improvement over previous synthetic routes...
  18. pmc A mechanism for the association of amino acids with their codons and the origin of the genetic code
    Shelley D Copley
    Cooperative Institute for Research in Environmental Sciences, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 102:4442-7. 2005
    ....
  19. ncbi request reprint Enzymes with extra talents: moonlighting functions and catalytic promiscuity
    Shelley D Copley
    Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder Campus, Box 216, Boulder, CO 80309 0216, USA
    Curr Opin Chem Biol 7:265-72. 2003
    ..New insights into catalytic promiscuity are provided by studies of aminoglycoside kinase (3') type IIIa, tetrachlorohydroquinone dehalogenase, and aldolase antibody 38C2...
  20. pmc A radical intermediate in the conversion of pentachlorophenol to tetrachlorohydroquinone by Sphingobium chlorophenolicum
    Johannes Rudolph
    Department of Molecular, Cellular and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, and Department of Chemistry and Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
    Biochemistry 53:6539-49. 2014
    ..These studies demonstrate how adoption of an ancestral catalytic strategy for conversion of a substrate with different steric and electronic properties can lead to subtle yet (literally) radical changes in enzymatic reaction mechanisms...
  21. pmc A versatile and highly efficient method for scarless genome editing in Escherichia coli and Salmonella enterica
    Juhan Kim
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
    BMC Biotechnol 14:84. 2014
    ..This elegantly designed method did not work well in our hands for most genes...
  22. ncbi request reprint Why metabolic enzymes are essential or nonessential for growth of Escherichia coli K12 on glucose
    Juhan Kim
    Cooperative Institute for Research in Environmental Sciences and Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
    Biochemistry 46:12501-11. 2007
    ..coli to survive in a variety of habitats and therefore to have a metabolism that allows optimal exploitation of varying environmental resources and synthesis of small molecules when they cannot be obtained from the environment...
  23. ncbi request reprint A mechanistic investigation of the thiol-disulfide exchange step in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase
    Joseph R Warner
    Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, Colorado 80309 0216, USA
    Biochemistry 44:10360-8. 2005
    ..Remarkably, single-turnover kinetic studies show that the enzyme catalyzes this step by approximately 10000-fold. This high reactivity requires an as yet unidentified protonated group in the active site...
  24. ncbi request reprint Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli
    MingHua Dai
    Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, CO 80309, USA
    Metab Eng 7:45-52. 2005
    ..This frequency is three-four orders of magnitude better than those previously reported for recombination in fused protoplasts of Gram-negative bacteria such as E. coli and Providencia alcalifaciens...
  25. pmc Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723
    MingHua Dai
    Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Appl Environ Microbiol 70:2391-7. 2004
    ....
  26. pmc The orphan protein bis-γ-glutamylcystine reductase joins the pyridine nucleotide disulfide reductase family
    Juhan Kim
    Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO 80309, USA
    Biochemistry 52:2905-13. 2013
    ..The genomes of most, but not all, halobacteria for which whole genome sequences are available have close homologues of GCR, suggesting that there is more to be learned about the low-molecular weight thiols used in halobacteria...
  27. pmc Lateral gene transfer and parallel evolution in the history of glutathione biosynthesis genes
    Shelley D Copley
    Department of Molecular, Cellular, and Developmental Biology and the Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Campus Box 216, Boulder, CO 80309, USA
    Genome Biol 3:research0025. 2002
    ..To evaluate this, we have used bioinformatics to analyze sequences of the biosynthetic enzymes gamma-glutamylcysteine ligase and glutathione synthetase...
  28. pmc Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution
    Akhil Khanal
    Department of Molecular, Cellular and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder
    Mol Biol Evol 32:100-8. 2015
    ..Further, these results underscore the importance of using multiple orthologs as starting points for directed evolution of novel enzyme activities. ..
  29. pmc A previously unrecognized step in pentachlorophenol degradation in Sphingobium chlorophenolicum is catalyzed by tetrachlorobenzoquinone reductase (PcpD)
    MingHua Dai
    Department of Molecular, Cellular, and Developmental Biology, and Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, CO 80309, USA
    J Bacteriol 185:302-10. 2003
    ..Thus, we proposed and verified experimentally that PcpD is a tetrachlorobenzoquinone reductase that catalyzes the NADPH-dependent reduction of tetrachlorobenzoquinone to tetrachlorohydroquinone...
  30. pmc MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs
    Micah Hamady
    Department of Computer Science, University of Colorado, Boulder, CO 80309, USA
    Genome Biol 9:R128. 2008
    ..We demonstrate MotifCluster's accuracy using gold-standard protein superfamilies; using recommended settings, families were assigned to the correct superfamilies with 0.17% false positive and no false negative assignments...
  31. ncbi request reprint Characterization of the initial steps in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase
    Philip M Kiefer
    Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, Campus Box 216, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Biochemistry 41:1315-22. 2002
    ..Possible similarities between this mechanism and the mechanism for isomerization of maleylacetoacetate and maleylpyruvate are discussed...
  32. ncbi request reprint The reaction catalyzed by tetrachlorohydroquinone dehalogenase does not involve nucleophilic aromatic substitution
    Philip M Kiefer
    Department of Molecular, Cellular, and Developmental Biology and Cooperative Institute for Research in Environmental Sciences, Campus Box 216, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Biochemistry 41:1308-14. 2002
    ..Third, substantial normal solvent kinetic isotope effects on k(cat) and k(cat)/K(M,TriCHQ) are observed. Nonenzymatic and enzymatic nucleophilic S(N)Ar reactions typically show inverse solvent kinetic isotope effects...

Research Grants2

  1. Recruitment of Enzymes to Serve New Functions
    SHELLEY COPLEY; Fiscal Year: 2006
    ....
  2. Mechanisms and Evolutionary Potential of Promiscuous Enzyme Activities
    SHELLEY COPLEY; Fiscal Year: 2007
    ..Thus, the processes by which new enzyme activities evolve are of great interest for both theoretical and practical reasons. ..