JBIC Journal of Biological Inorganic Chemistry

, Volume 22, Issue 8, pp 1197–1209 | Cite as

Catalytic diversity and homotropic allostery of two Cytochrome P450 monooxygenase like proteins from Trichoderma brevicompactum

  • Razak Hussain
  • Indu Kumari
  • Shikha Sharma
  • Mushtaq Ahmed
  • Tabreiz Ahmad Khan
  • Yusuf Akhter
Original Paper


Trichothecenes are the secondary metabolites produced by Trichoderma spp. Some of these molecules have been reported for their ability to stimulate plant growth by suppressing plant diseases and hence enabling Trichoderma spp. to be efficiently used as biocontrol agents in modern agriculture. Many of the proteins involved in the trichothecenes biosynthetic pathway in Trichoderma spp. are encoded by the genes present in the tri cluster. Tri4 protein catalyzes three consecutive oxygenation reaction steps during biosynthesis of isotrichodiol in the trichothecenes biosynthetic pathway, while tri11 protein catalyzes the C4 hydroxylation of 12, 13-epoxytrichothec-9-ene to produce trichodermol. In the present study, we have homology modelled the three-dimensional structures of tri4 and tri11 proteins. Furthermore, molecular dynamics simulations were carried out to elucidate the mechanism of their action. Both tri4 and tri11 encode for cytochrome P450 monooxygenase like proteins. These data also revealed effector-induced allosteric changes on substrate binding at an alternative binding site and showed potential homotropic negative cooperativity. These analyses also showed that their catalytic mechanism relies on protein–ligand and protein–heme interactions controlled by hydrophobic and hydrogen-bonding interactions which orient the complex in optimal conformation within the active sites.


Trichoderma brevicompactum Cytochrome P450 monooxygenase Trichodiene 12, 13-epoxytrichothec-9-ene Homotropic cooperativity 



Molecular dynamics




12, 13-epoxytrichothec-9-ene


Secondary metabolites


Substrate recognition sites


Cytochrome P450 monooxygenases



We acknowledge Central University of Himachal Pradesh and Bioinformatics Resources and Applications Facility, Centre for Development in Advanced Computing, Pune for providing the computational infrastructure. RH acknowledges National Fellowship for Higher Education from University Grants Commission, Govt. of India (UGC). SS receives research stipend from UGC. Research in YA lab is supported by extramural research funds from UGC, Science and Engineering Research Board (DST, Govt. of India), and Indian Council of Medical Research. We thank Dr. P. Aparoy for his generous help during the revision. Prof. Claudio Luchinat (editor-in-chief) and two anonymous referees are also sincerely acknowledged, whose insightful comments and advice during the editorial review helped us to improve our work enormously.

Supplementary material

775_2017_1496_MOESM1_ESM.pdf (1.8 mb)
Supplementary material 1 (PDF 1874 kb)


  1. 1.
    Reino JL, Guerrer ORF, Hrnndez-Galn RIG, Collado IG (2008) Phytochem Rev 7:89–123CrossRefGoogle Scholar
  2. 2.
    Hermosa R, Viterbo A, Chet I, Monte E (2012) Microbiology 158:17–25CrossRefPubMedGoogle Scholar
  3. 3.
    Vinale F, Sivasithamparam K, Ghisalberti EL, Marra R, Barbetti MJ, Li H, Woo SL, Lorito M (2008) Physiol Mol Plant Pathol 72:80–86CrossRefGoogle Scholar
  4. 4.
    Vinale F, Sivasithamparam K, Ghisalberti EL, Marra R, Woo SL, Lorito M (2008) Soil Biol Biochem 40:1–10CrossRefGoogle Scholar
  5. 5.
    Chen W, Lee MKC, Jefcoate CS-C, Kim SC, Chen FYuJH (2014) Genome Biol Evol 6:1620–1634CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Bowen GD, Rovira AD (1999) Adv Agron 66:1–102CrossRefGoogle Scholar
  7. 7.
    Jain A, Singh A, Singh S, Singh HB (2013) J Plant Growth Regul 32:388–398CrossRefGoogle Scholar
  8. 8.
    Malmierca MG, Cardoza RE, Alexander NJ, Mccormick SP, Hermosa RE, Monte E, Gutiérrez S (2012) Appl. Environ Microbiol 78:4856–4868CrossRefGoogle Scholar
  9. 9.
    Cundliffe E, Cannon M, Davies J (1974) Proc Natl Acad Sci USA 71:30–34CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Cardoza RE, Malmierca MG, Hermosa MR, Alexander NJ, Mccormick SP, Proctor RH, Tijerino AM, Rumbero A, Monte E, Gutie S (2011) Appl. Environ Microbiol 77:4867–4877CrossRefGoogle Scholar
  11. 11.
    Degenkolb T, Dieckmann R, Nielsen KF, Gräfenhan T, Theis C, Zafari D, Chaverri P, Ismaiel A, Brückner H, Döhren HV (2008) Mycol Prog 7:177–219CrossRefGoogle Scholar
  12. 12.
    Tijerino A, Cardoza RE, Moraga J, Malmierca Vicente F, Aleu J, Collado IG, Gutiérrez S, Monte S, Hermosa R (2011) Fungal Genet. Biol 48:285–296Google Scholar
  13. 13.
    Shentu XP, Yuan XF, Liu WP, Xu JF, Yu XP (2015) Am J Biochem Biotechnol 11:169CrossRefGoogle Scholar
  14. 14.
    Hermosa R, Rubio MB, Cardoza RE, Nicolas C, Monte E, Gutiérrez S (2013) Int Microbiol 16:69–80PubMedGoogle Scholar
  15. 15.
    Malmierca MG, Izquierdo I, Bueno McCormick SP, Cardoza RE, Alexander NJ, Barua J, Lindo L, Casquero PA, Collado IG, Monte E (2016) Environ. Microbiol 18:3991–4004Google Scholar
  16. 16.
    Pusztahelyi T, Holb IJ, Pocsi I (2015) Front Plant Sci 6:573CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Kumari I, Ahmed M, Akhter Y (2016) Int J Biochem Cell Biol 78:370–376CrossRefPubMedGoogle Scholar
  18. 18.
    Hlavica P (2017) J Inorg Biochem 167:100–115CrossRefPubMedGoogle Scholar
  19. 19.
    Cresnar B, Petric S (2011) Biochim Biophys Acta (BBA)-Proteins Proteom 1814:29–35CrossRefGoogle Scholar
  20. 20.
    Gotoh O (1992) J Biol Chem 267:83–90PubMedGoogle Scholar
  21. 21.
    Seifert A, Pleiss J (2009) Proteins Struct Funct Bioinform 74:1028–1035CrossRefGoogle Scholar
  22. 22.
    McGuffin LJ, Bryson K, Jones DT (2000) Bioinformatics 16:404–405CrossRefPubMedGoogle Scholar
  23. 23.
    Corpet F (1988) Nucleic Acids Res 16:10881–10890CrossRefPubMedPubMedCentralGoogle Scholar
  24. 24.
    Kim S, Thiessen PA, Bolton EE, Bryant SH (2015) Nucleic Acids Res 43(W1):W605–W611CrossRefPubMedPubMedCentralGoogle Scholar
  25. 25.
    Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE (2015) Nat Protoc 10:845–858CrossRefPubMedPubMedCentralGoogle Scholar
  26. 26.
    Eswar N, Webb B, Marti-Renom MA, Madhusudhan MS, Eramian D, Shen MY, Pieper U, Sali A (2006) Curr Protoc Bioinformatics. doi: 10.1002/0471250953.bi0506s15 PubMedPubMedCentralGoogle Scholar
  27. 27.
    Krieger E, Nabuurs SB, Vriend G (2003) Methods Biochem Anal 44:509–524PubMedGoogle Scholar
  28. 28.
    Berendsen HJC, Spoel Van Der D, Drunen Van R (1995) Comput Phys Commun 91:43–56CrossRefGoogle Scholar
  29. 29.
    Sandhu P, Akhter Y (2016) Arch Biochem Biophys 592:38–49CrossRefPubMedGoogle Scholar
  30. 30.
    Guengerich FP (2001) Chem Res Toxicol 14:611–650CrossRefPubMedGoogle Scholar
  31. 31.
    Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009) J Comput Chem 30:2785–2791CrossRefPubMedPubMedCentralGoogle Scholar
  32. 32.
    SchuÈttelkopf AW, Aalten Van DMF (2004) Acta Crystallogr Sect D Biol Crystallogr 60:1355–1363CrossRefGoogle Scholar
  33. 33.
    Vohra S, Musgaard M, Bell SG, Wong L, Zhou W, Biggin PC (2013) Protein Sci 22:1218–1229CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF (2004) J Comput Chem 25:1656–1676CrossRefPubMedGoogle Scholar
  35. 35.
    Micaelo NM, Macedo AL, Goodfellow BJ, Felix V (2010) J Mol Graph Model 29:396–405CrossRefPubMedGoogle Scholar
  36. 36.
    Cojocaru XYUV, Mustafa G, Salo Ahen OMH, Lepesheva GI, Wade RC (2015) J Mol Recognit 28:59–73CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Graaf CDE, Oostenbrink C, Keizers PHJ, Tvander WIJST, Jongejan A, Vermeulen NPE (2006) J Med Chem 49:2417–2430CrossRefPubMedGoogle Scholar
  38. 38.
    Podust LM, Ouellet H, Kries von JP, Montellano de PRO (2009) J Biol Chem 284:25211–25219CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Zhang H, Gay SC, Shah M, Foroozesh M, Osawa J, Liu Y, Zhang Q, Stout CD, Halpert JR, Hollenberg PF (2013) Biochemistry 52:355CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Guengerich FP, Munro AW (2013) J Biol Chem 288:17065–17073CrossRefPubMedPubMedCentralGoogle Scholar
  41. 41.
    Bischoff R, Schlüter H (2012) J Proteom 75:2275–2296CrossRefGoogle Scholar
  42. 42.
    Hasemann CA, Kurumbail RG, Boddupalli SS, Peterson JA, Deisenhofer J (1995) Structure 3:41–62CrossRefPubMedGoogle Scholar
  43. 43.
    Guallar V, Baik MH, Lippard SJ, Friesner RA (2003) Proc Natl Acad Sci 100:6998–7002CrossRefPubMedPubMedCentralGoogle Scholar
  44. 44.
    Podust LM, Sherman DH (2012) Nat Prod Rep 29:1251–1266CrossRefPubMedPubMedCentralGoogle Scholar
  45. 45.
    Zanger UM, Schwab M (2013) Pharmacol Ther 138:103–141CrossRefPubMedGoogle Scholar
  46. 46.
    Kimura M, Tokai T, Takahashi N, Ohsato S (2007) Biosci Biotechnol Biochem 71:2105–2123CrossRefPubMedGoogle Scholar

Copyright information

© SBIC 2017

Authors and Affiliations

  1. 1.Department of BotanyAligarh Muslim UniversityAligarhIndia
  2. 2.Department of Environmental Science, School of Earth and Environmental SciencesCentral University of Himachal PradeshKangraIndia
  3. 3.Centre for Computational Biology and Bioinformatics, School of Life SciencesCentral University of Himachal PradeshKangraIndia

Personalised recommendations