Skip to main content

Advertisement

SpringerLink
Log in

Electronic and geometric structures of the organophosphate-degrading enzyme from Agrobacterium radiobacter (OpdA)

  • Original Paper
  • Published:
JBIC Journal of Biological Inorganic Chemistry Aims and scope Submit manuscript

Abstract

The organophosphate-degrading enzyme from Agrobacterium radiobacter (OpdA) is a highly efficient catalyst for the degradation of pesticides and some nerve agents such as sarin. OpdA requires two metal ions for catalytic activity, and hydrolysis is initiated by a nucleophilic hydroxide that is bound to one of these metal ions. The precise location of this nucleophile has been contentious, with both a terminal and a metal-ion-bridging hydroxide as likely candidates. Here, we employed magnetic circular dichroism to probe the electronic and geometric structures of the Co(II)-reconstituted dinuclear metal center in OpdA. In the resting state the metal ion in the more secluded α site is five-coordinate, whereas the Co(II) in the solvent-exposed β site is predominantly six-coordinate with two terminal water ligands. Addition of the slow substrate diethyl 4-methoxyphenyl phosphate does not affect the α site greatly but lowers the coordination number of the β site to five. A reduction in the exchange coupling constant indicates that substrate binding also triggers a shift of the μ-hydroxide into a pseudoterminal position in the coordination sphere of either the α or the β metal ion. Mechanistic implications of these observations are discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

Abbreviations

AOM:

Angular overlap model

EPO:

Diethyl 4-methoxyphenyl phosphate

GpdQ:

Glycerophosphodiesterase from Enterobacter aerogenes

HEPES:

N-(2-Hydroxyethyl)piperazine-N′-ethanesulfonic acid

MCD:

Magnetic circular dichroism

OP:

Organophosphate

OpdA:

Organophosphate-degrading enzyme from Agrobacterium radiobacter

OPH:

Organophosphate hydrolase from Pseudomonas diminuta

PAP:

Purple acid phosphatase

VTVH:

Variable temperature, variable field

ZFS:

Zero-field splitting

References

  1. Aubert SD, Li Y, Raushel FM (2004) Biochemistry 43:5707–5715

    Article  PubMed  CAS  Google Scholar 

  2. Ely F, Foo J-L, Jackson CJ, Gahan LR, Ollis DL, Schenk G (2007) Curr Top Biochem Res 9:63–78

    CAS  Google Scholar 

  3. Jackson CJ, Foo J-L, Kim H-K, Carr PD, Liu J-W, Salem G, Ollis DL (2008) J Mol Biol 375:1189–1196

    Article  PubMed  CAS  Google Scholar 

  4. Yang H, Carr PD, McLoughlin SY, Liu JW, Horne I, Qiu X, Jeffries CMJ, Russell RJ, Oakeshott JG, Ollis DL (2003) Protein Eng 16:135–145

    Article  PubMed  CAS  Google Scholar 

  5. Benning MM, Kuo JM, Raushel FM, Holden HM (1994) Biochemistry 33:15001–15007

    Article  PubMed  CAS  Google Scholar 

  6. Benning MM, Shim H, Raushel FM, Holden HM (2001) Biochemistry 40:2712–2722

    Article  PubMed  CAS  Google Scholar 

  7. Jackson C, Kim H-K, Carr PD, Liu J-W, Ollis DL (2005) Biochim Biophys Acta 1752:56–64

    PubMed  CAS  Google Scholar 

  8. Benning MM, Kuo JM, Raushel FM, Holden HM (1995) Biochemistry 34:7973–7978

    Article  PubMed  CAS  Google Scholar 

  9. Wong K-Y, Gao J (2007) Biochemistry 46:13352–13369

    Article  PubMed  CAS  Google Scholar 

  10. Ely F, Hadler KS, Gahan LR, Guddat LW, Ollis DL, Schenk G (2010) Biochem J 432:565–573

    Article  PubMed  CAS  Google Scholar 

  11. Hadler KS, Mitić N, Ely F, Hanson GR, Gahan LR, Larrabee JA, Ollis DL, Schenk G (2009) J Am Chem Soc 131:11900–11908

    Article  PubMed  CAS  Google Scholar 

  12. Hadler KS, Mitić N, Yip SH-C, Gahan LR, Ollis DL, Schenk G, Larrabee JA (2010) Inorg Chem 49:2727–2734

    Article  PubMed  CAS  Google Scholar 

  13. Hadler KS, Gahan LR, Ollis DL, Schenk G (2010) J Inorg Biochem 104:211–213

    Article  PubMed  CAS  Google Scholar 

  14. Hadler KS, Tanifum EA, Yip SH-C, Mitić N, Guddat LW, Jackson CJ, Gahan LR, Nguyen K, Carr PD, Ollis DL, Hengge AC, Larrabee JA, Schenk G (2008) J Am Chem Soc 130:14129–14138

    Article  PubMed  CAS  Google Scholar 

  15. Ghanem E, Li Y, Xu C, Raushel FM (2007) Biochemistry 46:9032–9040

    Article  PubMed  CAS  Google Scholar 

  16. McLoughlin SY, Jackson C, Liu J-W, Ollis DL (2004) Appl Environ Microbiol 70:404–412

    Article  PubMed  CAS  Google Scholar 

  17. Neylon C, Brown SE, Kralicek AV, Miles CS, Love CA, Dixon NE (2000) Biochemistry 39:11989–11999

    Article  PubMed  CAS  Google Scholar 

  18. Ely F, Nunes J, Schroeder E, Frazzon J, Palma M, Santos D, Basso L (2008) BMC Biochem 9:13–28

    Article  PubMed  Google Scholar 

  19. Grossman TH, Kawasaki ES, Punreddy SR, Osbourne MS (1998) Gene 209:95–103

    Article  PubMed  CAS  Google Scholar 

  20. Neese F, Solomon EI (1999) Inorg Chem 38:1847–1865

    Article  PubMed  CAS  Google Scholar 

  21. Reem RC, Solomon EI (1987) J Am Chem Soc 109:1216–1226

    Article  CAS  Google Scholar 

  22. Solomon EI, Pavel EG, Loeb KE, Campochiaro C (1995) Coord Chem Rev 144:369–460

    Article  CAS  Google Scholar 

  23. Strand KR, Yang Y-S, Andersson KK, Solomon EI (2003) Biochemistry 42:12223–12234

    Article  PubMed  CAS  Google Scholar 

  24. Wei P-P, Skulan AJ, Mitić N, Yang Y-S, Saleh L, Bollinger JM, Solomon EI (2004) J Am Chem Soc 126:3777–3788

    Article  PubMed  CAS  Google Scholar 

  25. Wei P-P, Tomter AB, Rohr AK, Andersson KK, Solomon EI (2006) Biochemistry 45:14043–14051

    Article  PubMed  CAS  Google Scholar 

  26. Mitić N, Clay MD, Saleh L, Bollinger JM, Solomon EI (2007) J Am Chem Soc 129:9049–9065

    Article  PubMed  Google Scholar 

  27. Mitić N, Saleh L, Schenk G, Bollinger JM, Solomon EI (2003) J Am Chem Soc 125:11200–11201

    Article  PubMed  Google Scholar 

  28. Adamsky H, Schonherr T, Atanasov M (2004) AOMX: angular overlap model computation. In: McCleverty JA, Meyer TJ (eds) Comprehensive coordination chemistry II, vol 2. Elsevier, Oxford, pp 661–664

  29. Schonherr T, Atanasov M, Adamsky H (2004) AOMX: angular overlap model computation. In: McCleverty JA, Meyer TJ (eds) Comprehensive coordination chemistry II, vol 2. Elsevier, Oxford, pp 443–455

  30. Harding MJ, Briat B (1973) Mol Phys 25:745–776

    Article  CAS  Google Scholar 

  31. Larrabee JA, Alessi CM, Asiedu ET, Cook JO, Hoerning KR, Klingler LJ, Okin GS, Santee SG, Volkert TL (1997) J Am Chem Soc 119:4182–4196

    Article  CAS  Google Scholar 

  32. Jackson CJ, Foo J-L, Tokuriki N, Afriat L, Carr PD, Kim H-K, Schenk G, Tawfik DS, Ollis DL (2009) Proc Natl Acad Sci USA 106:21631–21636

    Article  PubMed  CAS  Google Scholar 

  33. Larrabee JA, Leung CH, Moore RL, Thamrong-nawasawat T, Wessler BSH (2004) J Am Chem Soc 126:12316–12324

    Article  PubMed  CAS  Google Scholar 

  34. Larrabee JA, Chyun S-A, Volwiler AS (2008) Inorg Chem 47:10499–10508

    Article  PubMed  CAS  Google Scholar 

  35. Larrabee JA, Johnson WR, Volwiler AS (2009) Inorg Chem 48:8822–8829

    Article  PubMed  CAS  Google Scholar 

  36. Johansson FB, Bond AD, Nielsen UG, Moubaraki B, Murray KS, Berry KJ, Larrabee JA, McKenzie CJ (2008) Inorg Chem 47:5079–5092

    Article  PubMed  CAS  Google Scholar 

  37. Xavier FR, Neves A, Casellato A, Peralta RA, Bortoluzzi AJ, Szpoganicz B, Severino PC, Terenzi H, Tomkowicz Z, Ostrovsky S, Haase W, Ozarowski A, Krzystek J, Telser J, Schenk G, Gahan LR (2009) Inorg Chem 48:7905–7921

    Article  PubMed  CAS  Google Scholar 

  38. Schultz BE, Ye B-H, Li X-y, Chan SI (1997) Inorg Chem 36:2617–2622

    Article  CAS  Google Scholar 

  39. Yang Y-S, McCormick JM, Solomon EI (1997) J Am Chem Soc 119:11832–11842

    Article  CAS  Google Scholar 

  40. Wang X, Ho RYN, Whiting AK, Que L (1999) J Am Chem Soc 121:9235–9236

    Article  CAS  Google Scholar 

  41. Schenk G, Elliott T, Leung E, Carrington L, Mitić N, Gahan L, Guddat L (2008) BMC Struct Biol 8(18):6

    Google Scholar 

  42. Mitić N, Hadler KS, Gahan L, Hengge AC, Schenk G (2010) J Am Chem Soc 132:7049–7054

    Article  PubMed  Google Scholar 

  43. Cox RS, Schenk G, Mitić N, Gahan LR, Hengge AC (2007) J Am Chem Soc 129:9550–9551

    Article  PubMed  CAS  Google Scholar 

  44. Foo J-L, Jackson CJ, Carr PD, Kim H-K, Schenk G, Gahan L, Ollis DL (2010) Biochem J 429:313–321

    Article  PubMed  CAS  Google Scholar 

  45. Kim J, Tsai P-C, Chen S-L, Himo F, Almo SC, Raushel FM (2008) Biochemistry 47:9497–9504

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

J.A.L. wishes to acknowledge the National Science Foundation (USA) for financial support from grant CHE0848433 and grant CHE0820965 (MCD instrument). G.S., D.L.O., and L.R.G. acknowledge funding from the Australian Research Council. F.E. is supported by an International Postgraduate Research Scholarship and a University of Queensland International Living Allowance Scholarship.

Author information

Authors and Affiliations

  1. School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD, 4072, Australia

    Fernanda Ely, Kieran S. Hadler, Nataša Mitić, Lawrence R. Gahan & Gerhard Schenk

  2. Research School of Chemistry, Australian National University, Canberra, ACT, 0200, Australia

    David L. Ollis

  3. Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, 05753, USA

    Nicholas M. Plugis, Marie T. Russo & James A. Larrabee

  4. Department of Chemistry, National University of Ireland, Maynooth, Kildare, Ireland

    Nataša Mitić & Gerhard Schenk

Authors
  1. Fernanda Ely
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kieran S. Hadler
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nataša Mitić
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Lawrence R. Gahan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. David L. Ollis
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Nicholas M. Plugis
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Marie T. Russo
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. James A. Larrabee
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Gerhard Schenk
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to James A. Larrabee or Gerhard Schenk.

Additional information

F. Ely and K.S. Hadler contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 130 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ely, F., Hadler, K.S., Mitić, N. et al. Electronic and geometric structures of the organophosphate-degrading enzyme from Agrobacterium radiobacter (OpdA). J Biol Inorg Chem 16, 777–787 (2011). https://doi.org/10.1007/s00775-011-0779-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00775-011-0779-6

Keywords

Search

Navigation