Skip to main content
SpringerLink
Log in

Unraveling the Helicobacter pylori UreG zinc binding site using X-ray absorption spectroscopy (XAS) and structural modeling

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

Abstract

The pathogenicity of Helicobacter pylori depends on the activity of urease for pH modification. Urease activity requires assembly of a dinickel active site that is facilitated in part by GTP hydrolysis by UreG. The proper functioning of Helicobacter pylori UreG (HpUreG) is dependent on Zn(II) binding and dimerization. X-ray absorption spectroscopy and structural modeling were used to elucidate the structure of the Zn(II) site in HpUreG. These studies independently indicated a site at the dimer interface that has trigonal bipyramidal geometry and is composed of two axial cysteines at 2.29(2) Å, two equatorial histidines at 1.99(1) Å, and a solvent-accessible coordination site. The final model for the Zn(II) site structure was determined by refining multiple-scattering extended X-ray absorption fine structure fits using the geometry predicted by homology modeling and ab initio calculations.

Graphical abstract

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

Similar content being viewed by others

Abbreviations

DTT:

Dithiothreitol

EDTA:

Ethylenediaminetetraacetic acid

EXAFS:

Extended X-ray absorption fine structure

GTP:

Guanosine triphosphate

HpUreE:

Helicobacter pylori UreE

HpUreG:

Helicobacter pylori UreG

MjHypB:

Methanocaldococcus jannaschii HypB

Tris:

Tris(hydroxymethyl)aminomethane

XANES:

X-ray absorption near edge structure

XAS:

X-ray absorption spectroscopy

References

  1. Bruce MG, Maaroos HI (2008) Helicobacter 13:1–6

    Article  PubMed  Google Scholar 

  2. Ferreira AC, Isomoto H, Moriyama M, Fujioka T, Machado JC, Yamaoka Y (2008) Helicobacter 13:28–34

    Article  PubMed  CAS  Google Scholar 

  3. Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D (2011) CA Cancer J Clin 61:69–90. doi:10.3322/caac.20107

    Article  PubMed  Google Scholar 

  4. Sachs G, Weeks DL, Melchers K, Scott DR (2003) Annu Rev Physiol 65:349–369. doi:10.1146/annurev.physiol.65.092101.142156

    Article  PubMed  CAS  Google Scholar 

  5. Zambelli B, Musiani F, Benini S, Ciurli S (2011) Acc Chem Res 44(7):520–530. doi:10.1021/ar200041k

    Article  PubMed  CAS  Google Scholar 

  6. Ha NC, Oh ST, Sung JY, Cha KA, Lee MH, Oh BH (2001) Nat Struct Biol 8:505–509

    Article  PubMed  CAS  Google Scholar 

  7. Lam R, Romanov V, Johns K, Battaile KP, Wu-Brown J, Guthrie JL, Hausinger RP, Pai EF, Chirgadze NY (2010) Proteins Struct Funct Bioinform 78:2839–2848. doi:10.1002/prot.22802

    Article  CAS  Google Scholar 

  8. Moncrief MBC, Hausinger RP (1996) J Bacteriol 178:5417–5421

    PubMed  CAS  Google Scholar 

  9. Benoit S, Maier RJ (2003) J Bacteriol 185:4787–4795. doi:10.1128/jb.185.16.4787-4795.2003

    Article  PubMed  CAS  Google Scholar 

  10. Bellucci M, Zambelli B, Musiani F, Turano P, Ciurli S (2009) Biochem J 422:91–100. doi:10.1042/bj20090434

    Article  PubMed  CAS  Google Scholar 

  11. Zambelli B, Musiani F, Savini M, Tucker P, Ciurli S (2007) Biochemistry 46:3171–3182. doi:10.1021/bi6024676

    Article  PubMed  CAS  Google Scholar 

  12. Ciurli S, Benini S, Rypniewski WR, Wilson KS, Miletti S, Mangani S (1999) Coord Chem Rev 192:331–355

    Article  Google Scholar 

  13. Moncrief MBC, Hausinger RP (1997) J Bacteriol 179:4081–4086

    PubMed  CAS  Google Scholar 

  14. Soriano A, Hausinger RP (1999) Proc Natl Acad Sci USA 96:11140–11144

    Article  PubMed  CAS  Google Scholar 

  15. Zambelli B, Turano P, Musiani F, Neyroz P, Ciurli S (2009) Proteins Struct Funct Bioinform 74:222–239. doi:10.1002/prot.22205

    Article  CAS  Google Scholar 

  16. Zambelli B, Stola M, Musiani F, De Vriendt K, Samyn B, Devreese B, Van Beeumen J, Turano P, Dikiy A, Bryant DA, Ciurli S (2005) J Biol Chem 280:4684–4695. doi:10.1074/jbc.M408483200

    Article  PubMed  CAS  Google Scholar 

  17. Dyson HJ, Wright PE (2005) Nat Rev Mol Cell Biol 6:197–208. doi:10.1038/nrm1589

    Article  PubMed  CAS  Google Scholar 

  18. Boer JL, Quiroz-Valenzuela S, Anderson KL, Hausinger RP (2010) Biochemistry 49:5859–5869. doi:10.1021/bi1004987

    Article  PubMed  CAS  Google Scholar 

  19. Stola M, Musiani F, Mangani S, Turano P, Safarov N, Zambelli B, Ciurli S (2006) Biochemistry 45:6495–6509. doi:10.1021/bi0601003

    Article  PubMed  CAS  Google Scholar 

  20. Webb SM (2005) Phys Scr T115:1011–1014

    Article  CAS  Google Scholar 

  21. Ravel B, Newville M (2005) J Synchrotron Radiat 12:537–541. doi:10.1107/s0909049505012719

    Article  PubMed  CAS  Google Scholar 

  22. Newville M (2001) J Synchrotron Radiat 8:96–100

    Article  PubMed  CAS  Google Scholar 

  23. Zabinsky SI, Rehr JJ, Ankudinov A, Albers RC, Eller MJ (1995) Phys Rev B 52:2995–3009

    Article  CAS  Google Scholar 

  24. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A (2000) Annu Rev Biophys Biomol Struct 29:291–325

    Article  PubMed  CAS  Google Scholar 

  25. Harding MM (1999) Acta Crystallogr 55:1432–1443

    CAS  Google Scholar 

  26. Harding MM (2006) Acta Crystallogr 62:678–682. doi:10.1107/s0907444906014594

    Google Scholar 

  27. Shen MY, Sali A (2006) Protein Sci 15:2507–2524. doi:10.1110/ps.062416606

    Article  PubMed  CAS  Google Scholar 

  28. Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) J Appl Crystallogr 26:283–291

    Article  CAS  Google Scholar 

  29. Neese F (2010) ORCAv2.8.0, an ab initio, density functional and semiempirical program package. Institute for Physical and Theoretical Chemistry, Universitat Bonn, Bonn. http://www.thch.uni-bonn.de/tc/orca/

  30. Jacquamet L, Aberdam D, Adrait A, Hazemann JL, Latour JM, Michaud-Soret I (1998) Biochemistry 37:2564–2571

    Article  PubMed  CAS  Google Scholar 

  31. Diakun GP, Fairall L, Klug A (1986) Nature 324:698–699

    Article  PubMed  CAS  Google Scholar 

  32. Strange RW, Blackburn NJ, Knowles PF, Hasnain SS (1987) J Am Chem Soc 109:7157–7162. doi:10.1021/ja00257a042

    Article  CAS  Google Scholar 

  33. Engh RA, Huber R (1991) Acta Crystallogr 47:392–400

    Article  Google Scholar 

  34. Ferreira GC, Franco R, Mangravita A, George GN (2002) Biochemistry 41:4809–4818. doi:10.1021/bi015814m

    Article  PubMed  CAS  Google Scholar 

  35. Blackburn NJ, Hasnain SS, Pettingill TM, Strange RW (1991) J Biol Chem 266:23120–23127

    PubMed  CAS  Google Scholar 

  36. Soriano A, Colpas GJ, Hausinger RP (2000) Biochemistry 39:12435–12440

    Article  PubMed  CAS  Google Scholar 

  37. Voland P, Weeks DL, Marcus EA, Prinz C, Sachs G, Scott D (2003) Am J Physiol Gastrointest Liver Physiol 284:G96–G106. doi:10.1152/ajpgi.00160.2002

    PubMed  CAS  Google Scholar 

  38. Levina A, Armstrong RS, Lay PA (2005) Coord Chem Rev 249:141–160. doi:10.1016/j.ccr.2004.10.008

    Article  CAS  Google Scholar 

  39. Robert AS (1985) In: Hirs CHW, Timasheff SN (eds) Methods in Enzymology. Academic Press, New York, pp 414–459

  40. Teo BK (1986) EXAFS: basic principles and data analysis. Springer, Berlin

    Google Scholar 

  41. Bunker G (2010) Introduction to XAFS: a practical guide to X-ray absorption fine structure spectroscopy. Cambridge University Press, London

    Book  Google Scholar 

  42. Clark-Baldwin K, Tierney DL, Govindaswamy N, Gruff ES, Kim C, Berg J, Koch SA, Penner-Hahn JE (1998) J Am Chem Soc 120:8401–8409. doi:10.1021/ja980580o

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by NIH grant R01-GM-69696 (M.J.M.), by Italian PRIN2007, and by the Center for Magnetic Resonance (CERM), University of Florence (Italy). Portions of this research were performed at the Stanford Synchrotron Radiation Lightsource, a national user facility operated by Stanford University on behalf of the US Department of Energy, Office of Basic Energy Sciences. The Stanford Synchrotron Radiation Lightsource Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and Environmental Research, and by the National Institutes of Health, National Center for Research Resources, Biomedical Technology Program. F.M. was a recipient of a joint postdoctoral grant from the University of Bologna and CERM.

Author information

Authors and Affiliations

  1. Department of Chemistry, University of Massachusetts, Amherst, 01003, MA, USA

    Vlad Martin-Diaconescu & Michael J. Maroney

  2. Laboratory of Bioinorganic Chemistry, Department of Agro-Environmental Science and Technology, University of Bologna, Bologna, Italy

    Matteo Bellucci, Francesco Musiani & Stefano Ciurli

  3. Center for Magnetic Resonance (CERM), University of Florence, Florence, Italy

    Stefano Ciurli

Authors
  1. Vlad Martin-Diaconescu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Matteo Bellucci
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Francesco Musiani
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Stefano Ciurli
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Michael J. Maroney
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Stefano Ciurli or Michael J. Maroney.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary information (PDF 384 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Martin-Diaconescu, V., Bellucci, M., Musiani, F. et al. Unraveling the Helicobacter pylori UreG zinc binding site using X-ray absorption spectroscopy (XAS) and structural modeling. J Biol Inorg Chem 17, 353–361 (2012). https://doi.org/10.1007/s00775-011-0857-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00775-011-0857-9

Keywords

Search

Navigation