Aaron J Oakley

Summary

Affiliation: Australian National University
Country: Australia

Publications

  1. ncbi request reprint Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III
    Aaron J Oakley
    Crystallography Centre, University of Western Australia, Nedlands, WA 6907, Australia
    Acta Crystallogr D Biol Crystallogr 59:1192-9. 2003
  2. ncbi request reprint Glutathione transferases: new functions
    Aaron J Oakley
    Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
    Curr Opin Struct Biol 15:716-23. 2005
  3. doi request reprint Structural insights into the dehydroascorbate reductase activity of human omega-class glutathione transferases
    Huina Zhou
    John Curtin School of Medical Research, Australian National University, Canberra, ACT 0200, Australia
    J Mol Biol 420:190-203. 2012
  4. pmc Structural insights into omega-class glutathione transferases: a snapshot of enzyme reduction and identification of a non-catalytic ligandin site
    Joseph Brock
    Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
    PLoS ONE 8:e60324. 2013
  5. ncbi request reprint S-(4-Nitrophenacyl)glutathione is a specific substrate for glutathione transferase omega 1-1
    Philip G Board
    Molecular Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
    Anal Biochem 374:25-30. 2008
  6. ncbi request reprint Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations
    Conrad J Burden
    Centre for Bioinformation Science, Mathematical Sciences Institute, Australian National University, Canberra, ACT, Australia
    Phys Biol 4:79-90. 2007
  7. pmc Crystallization and diffraction data of 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase: a cofactor-free oxygenase of the alpha/beta-hydrolase family
    Ruhu Qi
    Research School of Chemistry, Australian National University, Acton, ACT 0200, Australia
    Acta Crystallogr Sect F Struct Biol Cryst Commun 63:378-81. 2007
  8. ncbi request reprint Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy
    Dmitry Shishmarev
    Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia, Centre for Medical and Molecular Bioscience and School of Chemistry, University of Wollongong, New South Wales 2522, Australia and Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Parkville Victoria 3052, Australia
    Nucleic Acids Res 42:2750-7. 2014
  9. pmc Novel folding and stability defects cause a deficiency of human glutathione transferase omega 1
    Huina Zhou
    John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
    J Biol Chem 286:4271-9. 2011
  10. ncbi request reprint Crystal and solution structures of the helicase-binding domain of Escherichia coli primase
    Aaron J Oakley
    Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
    J Biol Chem 280:11495-504. 2005

Collaborators

  • Gottfried Otting
  • Thomas Huber
  • Gerhard Schenk
  • Conrad J Burden
  • Philip Board
  • Jan Petersen
  • Gene Wijffels
  • Michael W Parker
  • J Damborsky
  • Michal Otyepka
  • Mark Prescott
  • Joseph Brock
  • Huina Zhou
  • Matthew C J Wilce
  • Nicholas E Dixon
  • Dmitry Shishmarev
  • Leiliane Paiva
  • Lorien J Parker
  • Colin J Jackson
  • Ruhu Qi
  • Mark D Mulcair
  • Mario Lo Bello
  • Jason W Schmidberger
  • Richard Bourgault
  • Rungrutai Udomsinprasert
  • Patrick M Schaeffer
  • Karin Loscha
  • Emilia Ortiz-Salmerón
  • Bim Graham
  • Claire E Mason
  • Xun Cheng Su
  • Yao Wang
  • Dan Liu
  • Marco G Casarotto
  • Sarah Ciccone
  • Ricard Marcos
  • Marjorie Coggan
  • Alessandra Primavera
  • Craig J Morton
  • David L Ollis
  • Nancy C Hancock
  • Sylvia Yip
  • Kieran S Hadler
  • Paul D Carr
  • Louis C Italiano
  • Amadeu Creus
  • Susanne Fetzner
  • Thomas M Hill
  • Cameron Neylon
  • Hannah F Cross
  • Jimmy S H Tsang
  • La aied Prapanthadara
  • Saengtong Pongjaroenkit
  • Jantana Wongsantichon
  • Albert J Ketterman
  • J Derek Bewley
  • Bogdan Bancia
  • Pavel Prosselkov
  • Marzia Nuccetelli
  • Luis García-Fuentes

Detail Information

Publications24

  1. ncbi request reprint Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III
    Aaron J Oakley
    Crystallography Centre, University of Western Australia, Nedlands, WA 6907, Australia
    Acta Crystallogr D Biol Crystallogr 59:1192-9. 2003
    ..This suggests that these residues are likely to be relatively mobile in solution. Some implications of this flexibility for the function of beta are discussed...
  2. ncbi request reprint Glutathione transferases: new functions
    Aaron J Oakley
    Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
    Curr Opin Struct Biol 15:716-23. 2005
    ..Recent structural studies of integral membrane glutathione S-transferases from microsomes have revealed common patterns of tertiary and quaternary structure...
  3. doi request reprint Structural insights into the dehydroascorbate reductase activity of human omega-class glutathione transferases
    Huina Zhou
    John Curtin School of Medical Research, Australian National University, Canberra, ACT 0200, Australia
    J Mol Biol 420:190-203. 2012
    ..Mutation of Y34 to alanine in GSTO2-2 eliminates DHAR activity. From these structures and other biochemical data, we propose a mechanism of substrate binding and catalysis of DHAR activity...
  4. pmc Structural insights into omega-class glutathione transferases: a snapshot of enzyme reduction and identification of a non-catalytic ligandin site
    Joseph Brock
    Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia
    PLoS ONE 8:e60324. 2013
    ..The ligandin site, conserved in Omega class GSTs from a range of species, is hydrophobic in nature and may represent the binding location for tocopherol esters that are uncompetitive hGSTO1-1 inhibitors...
  5. ncbi request reprint S-(4-Nitrophenacyl)glutathione is a specific substrate for glutathione transferase omega 1-1
    Philip G Board
    Molecular Genetics Group, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
    Anal Biochem 374:25-30. 2008
    ..A spectrophotometric assay with 4NPG as a substrate has been used to determine GSTO1-1 activity in several human breast cancer cell lines and in mouse liver and brain tissues...
  6. ncbi request reprint Anisotropic atomic motions in high-resolution protein crystallography molecular dynamics simulations
    Conrad J Burden
    Centre for Bioinformation Science, Mathematical Sciences Institute, Australian National University, Canberra, ACT, Australia
    Phys Biol 4:79-90. 2007
    ..In order to make our comparisons, we have developed a compact graphical technique for assessing agreement between spatial atomic distributions determined by MD simulations and observed anisotropic temperature factors...
  7. pmc Crystallization and diffraction data of 1H-3-hydroxy-4-oxoquinoline 2,4-dioxygenase: a cofactor-free oxygenase of the alpha/beta-hydrolase family
    Ruhu Qi
    Research School of Chemistry, Australian National University, Acton, ACT 0200, Australia
    Acta Crystallogr Sect F Struct Biol Cryst Commun 63:378-81. 2007
    ..The unit-cell parameters were a = b = 90.1, c = 168.6 A, alpha = beta = 90, gamma = 120 degrees. Using synchrotron radiation, these crystals diffract to 2.5 A. The expression, purification and crystallization of QDO are reported here...
  8. ncbi request reprint Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy
    Dmitry Shishmarev
    Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia, Centre for Medical and Molecular Bioscience and School of Chemistry, University of Wollongong, New South Wales 2522, Australia and Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Parkville Victoria 3052, Australia
    Nucleic Acids Res 42:2750-7. 2014
    ....
  9. pmc Novel folding and stability defects cause a deficiency of human glutathione transferase omega 1
    Huina Zhou
    John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
    J Biol Chem 286:4271-9. 2011
    ....
  10. ncbi request reprint Crystal and solution structures of the helicase-binding domain of Escherichia coli primase
    Aaron J Oakley
    Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
    J Biol Chem 280:11495-504. 2005
    ..It is proposed that the connecting helix contributes necessary structural flexibility in the primase-helicase complex at replication forks...
  11. ncbi request reprint Expression, purification, crystallization, and NMR studies of the helicase interaction domain of Escherichia coli DnaG primase
    Karin Loscha
    Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
    Protein Expr Purif 33:304-10. 2004
    ..2A, c=192.1A, and diffracted beyond 2.7A resolution with synchrotron radiation...
  12. pmc Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference
    Colin J Jackson
    Research School of Chemistry, Australian National University, Australia
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:681-5. 2008
    ..Catalytic implications of the structure and its Fe2+ metal-ion preference are discussed...
  13. ncbi request reprint A molecular mousetrap determines polarity of termination of DNA replication in E. coli
    Mark D Mulcair
    Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
    Cell 125:1309-19. 2006
    ..Lock formation specifically requires the cytosine residue, C(6). The crystal structure of the locked complex showed that C(6) moves 14 A from its normal position to bind in a cytosine-specific pocket on the surface of Tus...
  14. ncbi request reprint The 2.0-A crystal structure of eqFP611, a far red fluorescent protein from the sea anemone Entacmaea quadricolor
    Jan Petersen
    The Protein Crystallography Unit, School of Biomedical Sciences, Monash University, Victoria, Australia
    J Biol Chem 278:44626-31. 2003
    ..The eqFP611 structure extends our knowledge on the range of conformations a chromophore can adopt within closely related members of the green fluorescent protein family...
  15. ncbi request reprint The anti-cancer drug chlorambucil as a substrate for the human polymorphic enzyme glutathione transferase P1-1: kinetic properties and crystallographic characterisation of allelic variants
    Lorien J Parker
    Biota Structural Biology Laboratory, St Vincent s Institute of Medical Research, Fitzroy, Victoria 3065, Australia
    J Mol Biol 380:131-44. 2008
    ..Finally, we show that chlorambucil is a very poor inhibitor of the enzyme in contrast to ethacrynic acid, which binds to the enzyme in a similar fashion but can act as both substrate and inhibitor...
  16. pmc Three-dimensional structure of (1,4)-beta-D-mannan mannanohydrolase from tomato fruit
    Richard Bourgault
    Department of Botany, University of Guelph, Ontario, Canada
    Protein Sci 14:1233-41. 2005
    ..reesei isozyme. A model of substrate binding in LeMAN4a is proposed in which the mannosyl residue occupying the -1 subsite of the enzyme adopts the (1)S(5) skew-boat conformation...
  17. pmc Identification, characterization and structure of a new Delta class glutathione transferase isoenzyme
    Rungrutai Udomsinprasert
    Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, 25 25 Putthamonthol Road 4, Salaya, Nakon Pathom 73170, Thailand
    Biochem J 388:763-71. 2005
    ..We obtained a crystal structure for adGSTD5-5 and compared it with other Delta GSTs, which showed that adGSTD5-5 possesses an elongated and more polar active-site topology...
  18. ncbi request reprint Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues
    Aaron J Oakley
    Crystallography Centre, School of Biomedical and Chemical Sciences, University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia, Australia
    Biochemistry 43:870-8. 2004
    ..The results presented here indicate that the positions of the catalytic residues and charge state of the catalytic base are important for determining reaction energetics in LinB...
  19. doi request reprint Polymorphism of glutathione transferase Omega 1 in a population exposed to a high environmental arsenic burden
    Leiliane Paiva
    Group of Mutagenesis, Department of Genetics and Microbiology, Universitat Autonoma de Barcelona, Spain
    Pharmacogenet Genomics 18:1-10. 2008
    ..Urinary arsenic profiles were determined by inductive coupled plasma/mass spectrometry...
  20. pmc Purification, crystallization and preliminary crystallographic analysis of DehIVa, a dehalogenase from Burkholderia cepacia MBA4
    Jason W Schmidberger
    Structural Biology and Bioinformatics Group, School of Pharmacology and Medicine, University of Western Australia, Crawley, Western Australia, Australia
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:271-3. 2005
    ..2, c = 135.8 A, alpha = beta = 90, gamma = 120 degrees. Determining this structure will provide valuable insights into the characterization of the catalytic mechanisms of this group of enzymes...
  21. ncbi request reprint Thermodynamic description of the effect of the mutation Y49F on human glutathione transferase P1-1 in binding with glutathione and the inhibitor S-hexylglutathione
    Emilia Ortiz-Salmerón
    Physical Chemistry, Faculty of Experimental Sciences, University of Almeria, La Canada de San Urbano, Almeria 04120, Spain
    J Biol Chem 278:46938-48. 2003
    ..9 cal K-1 mol-1 for GSH binding and -333.6 +/- 28.8 cal K-1 mol-1 for S-hexylglutathione binding. The thermodynamic parameters are consistent with the mutation Tyr49 --> Phe, producing a slight conformational change in the active site...
  22. ncbi request reprint Characterization of a family 11 xylanase from Bacillus subtillis B230 used for paper bleaching
    Aaron J Oakley
    School of Biomedical and Chemical Sciences, School of Medicine and Pharmacology, University of Western Australia, Nedlands, Australia
    Acta Crystallogr D Biol Crystallogr 59:627-36. 2003
    ..It has a greater abundance of side chain to side chain hydrogen bonds compared with all other family 11 xylanase crystal structures. Means by which the thermostability of Xyn11X might be improved are suggested...
  23. ncbi request reprint The 2.2 A crystal structure of a pocilloporin pigment reveals a nonplanar chromophore conformation
    Mark Prescott
    Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, 3800, Victoria, Australia
    Structure 11:275-84. 2003
    ..Furthermore, the fluorescent variant adopted a noncoplanar chromophore conformation. The data presented here demonstrates that the conformation of the chromophore is highly dependent on its immediate environment...
  24. ncbi request reprint Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition
    Aaron J Oakley
    Department of Pharmacology Crystallography Centre, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
    Biochemistry 41:4847-55. 2002
    ..These data provide an explanation for the low activity of LinB with small, chlorinated alkanes and show the importance of active site water molecules and reaction products in molecular docking...