Skip to main content
SpringerLink
Log in

Spectroscopic signature of a ubiquitous metal binding site in the metallo-β-lactamase superfamily

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

Abstract

The metallo-β-lactamase (MβL) superfamily is a functionally diverse group of metalloproteins sharing a distinctive αβ/αβ fold and a characteristic metal binding motif. A large number of open reading frames identified in genomic sequencing efforts have been annotated as members of this superfamily through sequence comparisons. However, structural and functional studies performed on purified proteins are normally needed to unequivocally include a newly discovered protein in the MβL superfamily. Here we report the spectroscopic characterization of recombinant YcbL, a gene product annotated as a member of the MβL superfamily whose function in vivo remains unknown. By taking advantage of the structural features characterizing the MβL superfamily metal binding motif, we performed spectroscopic studies on Zn(II)- and Co(II)-substituted YcbL to structurally interrogate the metal binding site. The dinuclear center in Co(II)-YcbL was shown to display characteristic electronic absorption features in the visible region, which were also observed in an engineered MβL aimed at mimicking this metal site. Thus, the spectroscopic features reported herein can be employed as a signature to readily identify and characterize the presence of these ubiquitous metal binding sites.

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

Similar content being viewed by others

References

  1. Daiyasu H, Osaka K, Ishino Y, Toh H (2001) FEBS Lett 503:1–6

    Article  CAS  PubMed  Google Scholar 

  2. Gomes CM, Frazao C, Xavier AV, LeGall J, Teixeira M (2002) Protein Sci 11:707–712

    Article  CAS  PubMed  Google Scholar 

  3. Carfi A, Pares S, Duee E, Galleni M, Duez C, Frère JM, Dideberg O (1995) EMBO J 14:4914–4921

    CAS  PubMed  Google Scholar 

  4. Campos-Bermudez VA, Leite NR, Krog R, Costa-Filho AJ, Soncini FC, Oliva G, Vila AJ (2007) Biochemistry 46:11069–11079

    Article  CAS  PubMed  Google Scholar 

  5. Andreini C, Banci L, Bertini I, Rosato A (2006) J Proteome Res 5:3173–3178

    Article  CAS  PubMed  Google Scholar 

  6. Alfredson DA, Korolik V (2007) FEMS Immunol Med Microbiol 49:159–164

    Article  CAS  PubMed  Google Scholar 

  7. Bebrone C (2007) Biochem Pharmacol 74:1686–1701

    Article  CAS  PubMed  Google Scholar 

  8. Periyannan GR, Costello AL, Tierney DL, Yang KW, Bennett B, Crowder MW (2006) Biochemistry 45:1313–1320

    Article  CAS  PubMed  Google Scholar 

  9. Llarrull LI, Tioni MF, Kowalski J, Bennett B, Vila AJ (2007) J Biol Chem 282:30586–30595

    Article  CAS  PubMed  Google Scholar 

  10. McClelland M, Sanderson KE, Spieth J, Clifton SW, Latreille P, Courtney L, Porwollik S, Ali J, Dante M, Du F, Hou S, Layman D, Leonard S, Nguyen C, Scott K, Holmes A, Grewal N, Mulvaney E, Ryan E, Sun H, Florea L, Miller W, Stoneking T, Nhan M, Waterston R, Wilson RK (2001) Nature 413:852–856

    Article  CAS  PubMed  Google Scholar 

  11. Checa SK, Espariz M, Audero ME, Botta PE, Spinelli SV, Soncini FC (2007) Mol Microbiol 63:1307–1318

    Article  CAS  PubMed  Google Scholar 

  12. Sharrocks AD (1994) Gene 138:105–108

    Article  CAS  PubMed  Google Scholar 

  13. Gonzalez JM, Medrano Martin FJ, Costello AL, Tierney DL, Vila AJ (2007) J Mol Biol 373:1141–1156

    Article  CAS  PubMed  Google Scholar 

  14. Gill SC, von Hippel PH (1989) Anal Biochem 182:319–326

    Article  CAS  PubMed  Google Scholar 

  15. Paul-Soto R, Bauer R, Frere JM, Galleni M, Meyer-Klaucke W, Nolting H, Rossolini GM, de Seny D, Hernandez-Valladares M, Zeppezauer M, Adolph HW (1999) J Biol Chem 274:13242–13249

    Article  CAS  PubMed  Google Scholar 

  16. Hunt JB, Neece SH, Ginsburg A (1985) Anal Biochem 146:150–157

    Article  CAS  PubMed  Google Scholar 

  17. Thomas PW, Stone EM, Costello AL, Tierney DL, Fast W (2005) Biochemistry 44:7559–7569

    Article  CAS  PubMed  Google Scholar 

  18. Ankudinov AL, Ravel B, Rehr JJ, Conradson SD (1998) Phys Rev B 58:7565–7576

    Article  CAS  Google Scholar 

  19. McClure CP, Rusche KM, Peariso K, Jackman JE, Fierke CA, Penner-Hahn JE (2003) J Inorg Biochem 94:78–85

    Article  CAS  PubMed  Google Scholar 

  20. Costello A, Periyannan G, Yang KW, Crowder MW, Tierney DL (2006) J Biol Inorg Chem 11:351–358

    Article  CAS  PubMed  Google Scholar 

  21. Siemann S, Brewer D, Clarke AJ, Dmitrienko GI, Lajoie G, Viswanatha T (2002) Biochim Biophys Acta 1571:190–200

    CAS  PubMed  Google Scholar 

  22. Kuzmic P (1996) Anal Biochem 237:260–273

    Article  CAS  PubMed  Google Scholar 

  23. Inubushi T, Becker ED (1983) J Magn Reson 51:128–133

    CAS  Google Scholar 

  24. Bertini I, Turano P, Vila AJ (1993) Chem Rev 93:2833–2932

    Article  CAS  Google Scholar 

  25. Marasinghe GP, Sander IM, Bennett B, Periyannan G, Yang KW, Makaroff CA, Crowder MW (2005) J Biol Chem 280:40668–40675

    Article  CAS  PubMed  Google Scholar 

  26. Garcia-Saez I, Mercuri PS, Papamicael C, Kahn R, Frere JM, Galleni M, Rossolini GM, Dideberg O (2003) J Mol Biol 325:651–660

    Article  CAS  PubMed  Google Scholar 

  27. Sali A, Blundell TL (1993) J Mol Biol 234:779–815

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  29. Schilling O, Wenzel N, Naylor M, Vogel A, Crowder M, Makaroff C, Meyer-Klaucke W (2003) Biochemistry 42:11777–11786

    Article  CAS  PubMed  Google Scholar 

  30. Vogel A, Schilling O, Meyer-Klaucke W (2004) Biochemistry 43:10379–10386

    Article  CAS  PubMed  Google Scholar 

  31. Dong YJ, Bartlam M, Sun L, Zhou YF, Zhang ZP, Zhang CG, Rao Z, Zhang XE (2005) J Mol Biol 353:655–663

    Article  CAS  PubMed  Google Scholar 

  32. Cameron AD, Ridderstrom M, Olin B, Mannervik B (1999) Structure 7:1067–1078

    Article  CAS  PubMed  Google Scholar 

  33. Bertini I, Luchinat C, Viezzoli MS (1986) In: Bertini I, Luchinat C, Maret W, Zeppezauer M (eds) Zinc enzymes. Birkhauser, Boston

    Google Scholar 

  34. Bertini I, Luchinat C (1985) Adv Inorg Biochem 6:71–111

    Google Scholar 

  35. de Seny D, Heinz U, Wommer S, Kiefer M, Meyer-Klaucke W, Galleni M, Frere JM, Bauer R, Adolph HW (2001) J Biol Chem 276:45065–45078

    Article  PubMed  Google Scholar 

  36. Liu D, Thomas PW, Momb J, Hoang QQ, Petsko GA, Ringe D, Fast W (2007) Biochemistry 46:11789–11799

    Article  CAS  PubMed  Google Scholar 

  37. Kostelecky B, Pohl E, Vogel A, Schilling O, Meyer-Klaucke W (2006) J Bacteriol 188:1607–1614

    Article  CAS  PubMed  Google Scholar 

  38. Ishii R, Minagawa A, Takaku H, Takagi M, Nashimoto M, Yokoyama S (2005) J Biol Chem 280:14138–14144

    Article  CAS  PubMed  Google Scholar 

  39. Vila AJ, Fernandez CO (1996) J Am Chem Soc 118:7291–7298

    Article  CAS  Google Scholar 

  40. Orellano EG, Girardini JE, Cricco JA, Ceccarelli EA, Vila AJ (1998) Biochemistry 37:10173–10180

    Article  CAS  PubMed  Google Scholar 

  41. McGuffin LJ, Jones DT (2003) Bioinformatics 19:874–881

    Article  CAS  PubMed  Google Scholar 

  42. DeLano WL (2002) The PyMOL molecular graphics system. DeLano Scientific, San Carlos

    Google Scholar 

Download references

Acknowledgments

This work was supported by grants from ANPCyT and HHMI to A.J.V. V.C.B is a recipient of a fellowship from CONICET. A.J.V. is a staff member from CONICET and an International Research Scholar of the Howard Hughes Medical Institute. The 600 MHz NMR spectrometer was purchased with funds from ANPCyT (PME2003-0026) and CONICET.

Author information

Author notes

  1. Valeria A. Campos-Bermudez

    Present address: Centro de Estudios Fotosintéticos y Bioquímicos, CEFOBI, Rosario, Argentina

  2. Javier M. González

    Present address: UMXSS Crystallography Service, Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Baltimore, MD, 21201, USA

Authors and Affiliations

  1. Instituto de Biología Molecular y Celular de Rosario, IBR-CONICET, Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario Suipacha 531, S2002LRK, Rosario, Argentina

    Valeria A. Campos-Bermudez, Javier M. González & Alejandro J. Vila

  2. Department of Chemistry and Biochemistry, Miami University, Oxford, OH, 45056, USA

    David L. Tierney

Authors
  1. Valeria A. Campos-Bermudez
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Javier M. González
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. David L. Tierney
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Alejandro J. Vila
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Alejandro J. Vila.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 29 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Campos-Bermudez, V.A., González, J.M., Tierney, D.L. et al. Spectroscopic signature of a ubiquitous metal binding site in the metallo-β-lactamase superfamily. J Biol Inorg Chem 15, 1209–1218 (2010). https://doi.org/10.1007/s00775-010-0678-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00775-010-0678-2

Keywords

Search

Navigation