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The 3D structure of the defense-related rice protein Pir7b predicted by homology modeling and ligand binding studies

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Abstract

To better understand the ligand-binding mechanism of protein Pir7b, important part in detoxification of a pathogen-derived compound against Pyricularia oryzae, a 3D structure model of protein Pir7b was constructed based on the structure of the template SABP2. Three substrates were docking to this protein, two of them were proved to be active, and some critical residues are identified, which had not been confirmed by the experiments. His87 and Leu17 considered as ‘oxyanion hole’ contribute to initiating the Ser86 nucleophilic attack. Gln187 and Asp139 can form hydrogen bonds with the anilid group to maintain the active binding orientation with the substrates. The docking model can well interpret the specificity of protein Pir7b towards the anilid moiety of the substrates and provide valuable structure information about the ligand binding to protein Pir7b.

Ligand binding analysis based on the refined Pir7b model. Magenta dash line, hydrogen bond; Red dash line, distance label. (a) Docking of 2-naphthol AS-acetate to Pir7b model. A 3D figure of 2-naphthol AS-acetate-Pir7b complex is also attached (b) Docking of 2-naphthol AS-2-chlor-propionate to Pir7b model. (c) Docking of 2-naphthol-acetate to Pir7b model.

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References

  1. Smith JA, Metraux JP (1991) Physiol Mol Plant Pathol 39:451–461

    Article  Google Scholar 

  2. Reimmann C, Hofmann C, Mauch F, Dudler R (1995) Physiol Mol Plant Pathol 46:71–81

    Article  CAS  Google Scholar 

  3. Zhang LH, Birch RG (1997) Appl Microbiol 82:448–454

    Article  CAS  Google Scholar 

  4. Waspi U, Misteli B, Hasslacher M, Jandrositz A, Kohlwein SD, Schwab H, Dudler R (1998) Eur J Biochem 254:32–37

    Article  CAS  Google Scholar 

  5. Nardini M, Dijkstra BW (1999) Curr Opin Struct Biol 9:732–737

    Article  CAS  Google Scholar 

  6. Fojan P, Jonson PH, Petersen MTN, Petersen SB (2000) Biochimie 82:1033–1041

    Article  CAS  Google Scholar 

  7. Hakulinen N, Tenkanen M, Rouvinen J (2000) J Struct Bio 132:180–190

    Article  CAS  Google Scholar 

  8. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Nucleic Acids Res 25:3389–3402

    Article  CAS  Google Scholar 

  9. Forouhar F, Yang Y, Kumar D, Chen Y, Fridman E, Park SW, Chiang Y, Acton TB, Montelione GT, Pichersky E, Klessig DF, Tong L (2005) Proc Natl Acad Sci USA 102:1773–1778

    Article  CAS  Google Scholar 

  10. Zuegg J, Gruber K, Gugganig M, Wagner UG, Kratky C (1999) Protein Sci 8:1990–2000

    Article  CAS  Google Scholar 

  11. Kumar D, Klessig DF (2003) Proc Natl Acad Sci USA 100:16101–16106

    Article  CAS  Google Scholar 

  12. Klessig DF, Durner J, Noad R, Navarre DA, Wendehenne D, Kumar D, Zhou JM, Shah J, Zhang S, Kachroo P, Trifa Y, Pontier D, Lam E, Silva H (2000) Proc Natl Acad Sci USA 97:8849–8855

    Article  CAS  Google Scholar 

  13. Gruber K, Gartler G, Krammer B, Schwab H, Kratky C (2004) J Biol Chem 279:20501–20510

    Article  CAS  Google Scholar 

  14. Raghava GPS (2000) CASP 4:75–76

    Google Scholar 

  15. Garnier J, Osguthorpe DJ, Robson B (1978) J Mol Biol 120:97–120

    Article  CAS  Google Scholar 

  16. Zhang CT, Zhang R (2000) J Biomol Struct Dyn 17:829–842

    CAS  Google Scholar 

  17. Geourjon C, Deleage G (1995) Comput Appl Biosci 11:681–684

    CAS  Google Scholar 

  18. Han CL, Zhang W, Dong HT, Han X, Wang MJ (2006) Interferon Cytokine Res 26:441–448

    Article  CAS  Google Scholar 

  19. Higgins DG, Bleasby AJ, Fuchs R (1992) Comput Appl Biosci 8:189–191

    CAS  Google Scholar 

  20. InsightII, Homology User Guide, SanDiego:Biosym/MSI (2000)

  21. Hakulinen N, Tenkanen M, Rouvinen J (2000) J Struct Biol 132:180–190

    Article  CAS  Google Scholar 

  22. Ke YY, Chen YC, Lin TH (2006) J Comput Chem 27:1556–1570

    Article  CAS  Google Scholar 

  23. Yang H, Ahn JH, Ibrahim RK, Lee S, Lim Y (2004) J Mol Graph Model 23:77–87

    Article  CAS  Google Scholar 

  24. Laskowski RA, Moss DS, Thornton JM (1993) J Mol Biol 231:1049–1067

    Article  CAS  Google Scholar 

  25. Insight II Profiles-3D, MolecularSimulations Inc, San Diego (2000)

  26. Luthy R, Bowie JU, Eisenberg D (1992) Nature 356:83–85

    Article  CAS  Google Scholar 

  27. Sippl MJ (1993) J Comput Aided Mol Des 7:473–501

    Article  CAS  Google Scholar 

  28. Frisch MJ, Trucks GW, Schlegel HB Gaussian 03 (Revision A.1) Gaussian Pittsburgh (2003)

  29. Affinity San Diego Molecular Simulations Inc (2000)

  30. Bartlett P A, Shea G.T, Telfer SJ, Waterman S (1989) R Soc Chem 182–196

  31. Shoichet BK, Kuntz ID, Bodian DL (1992) J Comput. Chem 13:380–397

    Article  CAS  Google Scholar 

  32. Harvey SC, McCammon JA (1987) Cambridge University Press

  33. Simmerling C, Strockbine B, Roitberg AE (2002) J Am Chem Soc 124:11258–11259

    Article  CAS  Google Scholar 

  34. Hornak V, Okur A, Rizzo R, Simmerling C (2006) Proc Nat Acad Sci USA 103:915–920

    Article  CAS  Google Scholar 

  35. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) J Comput Chem 26:1668–1688

    Article  CAS  Google Scholar 

  36. Ponder JW, Case DA (2003) Adv Prot Chem 66:27–85

    CAS  Google Scholar 

  37. Pratt LR, Hummer G., Melville Ed (1999) American Institute of Physics, Melville, New York pp. 104–113

  38. Kabsch W, Sander C (1983) Biopolymers 22:2577–2637

    Article  CAS  Google Scholar 

  39. Baudouin E, Charpenteau M, Roby D, Marco Y, Ranjeva R, Ranty B (1997) Eur J Biochem 248:700–706

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Science Foundation of China (20333050, 20673044), Doctor Foundation by the Ministry of Education, Foundation for University Key Teacher by the Ministry of Education, Key subject of Science and Technology by the Ministry of Education of China, and Key subject of Science and Technology by Jilin Province.

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  1. State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, 130023, People’s Republic of China

    Quan Luo, Wei-Wei Han, Yi-Han Zhou, Yuan Yao & Ze-Sheng Li

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  1. Quan Luo
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  2. Wei-Wei Han
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  3. Yi-Han Zhou
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  4. Yuan Yao
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Correspondence to Ze-Sheng Li.

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Luo, Q., Han, WW., Zhou, YH. et al. The 3D structure of the defense-related rice protein Pir7b predicted by homology modeling and ligand binding studies. J Mol Model 14, 559–569 (2008). https://doi.org/10.1007/s00894-008-0310-3

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  • DOI: https://doi.org/10.1007/s00894-008-0310-3

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