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JBIC Journal of Biological Inorganic Chemistry

, Volume 19, Issue 6, pp 937–945 | Cite as

MetalS3, a database-mining tool for the identification of structurally similar metal sites

  • Yana Valasatava
  • Antonio Rosato
  • Gabriele Cavallaro
  • Claudia Andreini
Original Paper

Abstract

We have developed a database search tool to identify metal sites having structural similarity to a query metal site structure within the MetalPDB database of minimal functional sites (MFSs) contained in metal-binding biological macromolecules. MFSs describe the local environment around the metal(s) independently of the larger context of the macromolecular structure. Such a local environment has a determinant role in tuning the chemical reactivity of the metal, ultimately contributing to the functional properties of the whole system. The database search tool, which we called MetalS3 (Metal Sites Similarity Search), can be accessed through a Web interface at http://metalweb.cerm.unifi.it/tools/metals3/. MetalS3 uses a suitably adapted version of an algorithm that we previously developed to systematically compare the structure of the query metal site with each MFS in MetalPDB. For each MFS, the best superposition is kept. All these superpositions are then ranked according to the MetalS3 scoring function and are presented to the user in tabular form. The user can interact with the output Web page to visualize the structural alignment or the sequence alignment derived from it. Options to filter the results are available. Test calculations show that the MetalS3 output correlates well with expectations from protein homology considerations. Furthermore, we describe some usage scenarios that highlight the usefulness of MetalS3 to obtain mechanistic and functional hints regardless of homology.

Keywords

Metalloprotein Metalloenzyme Bioinorganic chemistry Structural biology Zinc Iron 

Notes

Acknowledgments

This work was supported by the Ministero Italiano dell’Università e della Ricerca through the FIRB project RBFR08WGXT and by the European Commission through the BioMedBridges project (grant no. 284209). We gratefully acknowledge the technical help of Enrico Morelli.

Supplementary material

775_2014_1128_MOESM1_ESM.pdf (1.1 mb)
Supplementary material 1 (PDF 1088 kb)

References

  1. 1.
    Frausto da Silva JJR, Williams RJP (2001) The biological chemistry of the elements: the inorganic chemistry of life. Oxford University Press, New YorkGoogle Scholar
  2. 2.
    Bertini I, Sigel A, Sigel H (2001) Handbook on metalloproteins. Dekker, New YorkGoogle Scholar
  3. 3.
    Bertini I, Gray HB, Stiefel EI, Valentine JS (2006) Biological inorganic chemistry. University Science Books, SausalitoGoogle Scholar
  4. 4.
    Bertini I, Rosato A (2003) Proc Natl Acad Sci USA 100:3601–3604PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Hsin K, Sheng Y, Harding MM, Taylor P, Walkinshaw MD (2008) J Appl Crystallogr 41:963–968CrossRefGoogle Scholar
  6. 6.
    Schnabl J, Suter P, Sigel RKO (2012) Nucleic Acids Res 40:D434–D438PubMedCentralPubMedCrossRefGoogle Scholar
  7. 7.
    Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne PE (2011) Nucleic Acids Res 39:D392–D401PubMedCentralPubMedCrossRefGoogle Scholar
  8. 8.
    Andreini C, Bertini I, Rosato A (2009) Acc Chem Res 42:1471–1479PubMedCrossRefGoogle Scholar
  9. 9.
    Andreini C, Bertini I, Rosato A (2004) Bioinformatics 20:1373–1380PubMedCrossRefGoogle Scholar
  10. 10.
    Shu N, Zhou T, Hovmoller S (2008) Bioinformatics 24:775–782PubMedCrossRefGoogle Scholar
  11. 11.
    Andreini C, Bertini I, Cavallaro G (2011) PLoS ONE 10:e26325CrossRefGoogle Scholar
  12. 12.
    Andreini C, Cavallaro G, Rosato A, Valasatava Y (2013) J Chem Inf Model 53:3064–3075PubMedCrossRefGoogle Scholar
  13. 13.
    Andreini C, Bertini I, Cavallaro G, Najmanovich RJ, Thornton JM (2009) J Mol Biol 388:356–380PubMedCrossRefGoogle Scholar
  14. 14.
    Maret W, Li Y (2009) Chem Rev 109:4682–4707PubMedCrossRefGoogle Scholar
  15. 15.
    Choi M, Davidson VL (2011) Metallomics 3:140–151PubMedCrossRefGoogle Scholar
  16. 16.
    Banci L, Bertini I, Calderone V, Della Malva N, Felli IC, Neri S, Pavelkova A, Rosato A (2009) Biochem J 422:37–42PubMedCrossRefGoogle Scholar
  17. 17.
    Bertini I, Fragai M, Luchinat C, Melikian M, Venturi C (2009) Chem Eur J 15:7842–7845PubMedCrossRefGoogle Scholar
  18. 18.
    Andreini C, Cavallaro G, Lorenzini S, Rosato A (2013) Nucleic Acids Res 41:D312–D319PubMedCentralPubMedCrossRefGoogle Scholar
  19. 19.
    Fufezan C, Specht M (2009) BMC Bioinform 10:258CrossRefGoogle Scholar
  20. 20.
    Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (2012) Nucleic Acids Res 40:D290–D301PubMedCentralPubMedCrossRefGoogle Scholar
  21. 21.
    Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006) Nucleic Acids Res 34:D247–D251PubMedCentralPubMedCrossRefGoogle Scholar
  22. 22.
    Lancaster CR, Kroger A, Auer M, Michel H (1999) Nature 402:377–385PubMedCrossRefGoogle Scholar
  23. 23.
    Hirata A, Klein BJ, Murakami KS (2008) Nature 451:851–854PubMedCentralPubMedCrossRefGoogle Scholar
  24. 24.
    Hirata A, Murakami KS (2009) Curr Opin Struct Biol 19:724–731PubMedCentralPubMedCrossRefGoogle Scholar
  25. 25.
    Groll M, Bajorek M, Kohler A, Moroder L, Rubin DM, Huber R, Glickman MH, Finley D (2000) Nat Struct Biol 7:1062–1067PubMedCrossRefGoogle Scholar
  26. 26.
    Blamey CJ, Ceccarelli C, Naik UP, Bahnson BJ (2005) Protein Sci 14:1214–1221PubMedCentralPubMedCrossRefGoogle Scholar
  27. 27.
    Malmendal A, Linse S, Evenas J, Forsen S, Drakenberg T (1999) Biochemistry 38:11844–11850PubMedCrossRefGoogle Scholar
  28. 28.
    Hastie KM, Kimberlin CR, Zandonatti MA, MacRae IJ, Saphire EO (2011) Proc Natl Acad Sci USA 108:2396–2401PubMedCentralPubMedCrossRefGoogle Scholar
  29. 29.
    Riboldi-Tunnicliffe A, Isaacs NW, Mitchell TJ (2005) FEBS Lett 579:5353–5360PubMedCrossRefGoogle Scholar
  30. 30.
    Thoden JB, Ruzicka FJ, Frey PA, Rayment I, Holden HM (1997) Biochemistry 36:1212–1222PubMedCrossRefGoogle Scholar
  31. 31.
    Geeganage S, Frey PA (1999) Biochemistry 38:13398–13406PubMedCrossRefGoogle Scholar
  32. 32.
    Noble CG, Lim SP, Chen YL, Liew CW, Yap L, Lescar J, Shi PY (2013) J Virol 87:5291–5295PubMedCentralPubMedCrossRefGoogle Scholar
  33. 33.
    Yap TL, Xu T, Chen YL, Malet H, Egloff MP, Canard B, Vasudevan SG, Lescar J (2007) J Virol 81:4753–4765PubMedCentralPubMedCrossRefGoogle Scholar
  34. 34.
    Yasui N, Nogi T, Kitao T, Nakano Y, Hattori M, Takagi J (2007) Proc Natl Acad Sci USA 104:9988–9993PubMedCentralPubMedCrossRefGoogle Scholar
  35. 35.
    Yasui N, Nogi T, Takagi J (2010) Structure 18:320–331PubMedCrossRefGoogle Scholar
  36. 36.
    Petrarca P, Ammendola S, Pasquali P, Battistoni A (2010) J Bacteriol 192:1553–1564PubMedCentralPubMedCrossRefGoogle Scholar
  37. 37.
    Ilari A, Alaleona F, Tria G, Petrarca P, Battistoni A, Zamparelli C, Verzili D, Falconi M, Chiancone E (2014) Biochim Biophys Acta 1840:535–544PubMedCrossRefGoogle Scholar
  38. 38.
    David G, Blondeau K, Schiltz M, Penel S, Lewit-Bentley A (2003) J Biol Chem 278:43728–43735PubMedCrossRefGoogle Scholar
  39. 39.
    Havemann J, Vogel D, Loll B, Keller U (2014) Chem Biol 21:146–155PubMedCrossRefGoogle Scholar
  40. 40.
    Elkins JM, Rutledge PJ, Burzlaff NI, Clifton IJ, Adlington RM, Roach PL, Baldwin JE (2003) Org Biomol Chem 1:1455–1460PubMedCrossRefGoogle Scholar
  41. 41.
    Roach PL, Clifton IJ, Fulop V, Harlos K, Barton GJ, Hajdu J, Andersson I, Schofield CJ, Baldwin JE (1995) Nature 375:700–704PubMedCrossRefGoogle Scholar
  42. 42.
    Holm L, Sander C (1995) Trends Biochem Sci 20:478–480PubMedCrossRefGoogle Scholar
  43. 43.
    Hopkinson RJ, Tumber A, Yapp C, Chowdhury R, Aik W, Che KH, Li XS, Kristensen JBL, King ONF, Chan MC, Yeoh KK, Choi H, Walport LJ, Thinnes CC, Bush JT, Lejeune C, Rydzik AM, Rose NR, Bagg EA, McDonough MA, Krojer TJ, Yue WW, Ng SS, Olsen L, Brennan PE, Oppermann U, Muller S, Klose RJ, Ratcliffe PJ, Schofield CJ, Kawamura A (2013) Chem Sci 4:3110–3117CrossRefGoogle Scholar
  44. 44.
    Yu B, Edstrom WC, Benach J, Hamuro Y, Weber PC, Gibney BR, Hunt JF (2006) Nature 439:879–884PubMedCrossRefGoogle Scholar
  45. 45.
    Yi C, Jia G, Hou G, Dai Q, Zhang W, Zheng G, Jian X, Yang CG, Cui Q, He C (2010) Nature 468:330–333PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© SBIC 2014

Authors and Affiliations

  • Yana Valasatava
    • 1
  • Antonio Rosato
    • 1
    • 2
  • Gabriele Cavallaro
    • 1
  • Claudia Andreini
    • 1
    • 2
  1. 1.Magnetic Resonance Center (CERM)University of FlorenceSesto FiorentinoItaly
  2. 2.Department of ChemistryUniversity of FlorenceSesto FiorentinoItaly

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