Skip to main content
Log in

Structural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca

  • Biotechnologically relevant enzymes and proteins
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Bacterial cutinases are promising catalysts for the modification and degradation of the widely used plastic polyethylene terephthalate (PET). The improvement of the enzyme for industrial purposes is limited due to the lack of structural information for cutinases of bacterial origin. We have crystallized and structurally characterized a cutinase from Thermobifida fusca KW3 (TfCut2) in free as well as in inhibitor-bound form. Together with our analysis of the thermal stability and modelling studies, we suggest possible reasons for the outstanding thermostability in comparison to the less thermostable homolog from Thermobifida alba AHK119 and propose a model for the binding of the enzyme towards its polymeric substrate. The TfCut2 structure is the basis for the rational design of catalytically more efficient enzyme variants for the hydrolysis of PET and other synthetic polyesters.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy A, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) PHENIX: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66(Pt 2):213–221. doi:10.1107/S0907444909052925

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Araùjo R, Silva C, O’Neill A, Micaelo N, Guebitz G, Soares CM, Casal M, Cavaco-Paulo A (2007) Tailoring cutinase activity towards polyethylene terephthalate and polyamide 6,6 fibers. J Biotechnol 128(4):849–857. doi:10.1016/j.jbiotec.2006.12.028

    Article  PubMed  Google Scholar 

  • Baker PJ, Poultney C, Liu Z, Gross R, Montclare JK (2012) Identification and comparison of cutinases for synthetic polyester degradation. Appl Microbiol Biotechnol 93(1):229–240. doi:10.1007/s00253-011-3402-4

    Article  PubMed  Google Scholar 

  • Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81(8):3684–3690, http://link.aip.org/link/?JCP/81/3684/1

    Article  CAS  Google Scholar 

  • Bozonnet S, Jensen M, Nielsen M, Aghajari N, Jensen M, Kramhoft B, Willemoes M, Tranier S, Haser R, Svensson B (2007) The ‘pair of sugar tongs’ site on the non-catalytic domain c of barley-amylase participates in substrate binding and activity. FEBS J 274(19):5055–5067, PM:17803687

    Article  CAS  PubMed  Google Scholar 

  • Brueckner T, Eberl A, Heumann S, Rabe M, Guebitz GM (2008) Enzymatic and chemical hydrolysis of poly(ethylene terephthalate) fabrics. J Polym Sci A Polym Chem 46(19):6435–6443. doi:10.1002/pola.22952

    Article  CAS  Google Scholar 

  • Burnley BT, Afonine PV, Adams PD, Gros P (2012) Modelling dynamics in protein crystal structures by ensemble refinement. Elife 1:e00311. doi:10.7554/eLife.00311

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Chakravarty S, Varadarajan R (2002) Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 41(25):8152–8161

    Article  CAS  PubMed  Google Scholar 

  • Chen W, McCarthy TJ (1998) Chemical surface modification of poly(ethylene terephthalate). Macromolecules 31(11):3648–3655. doi:10.1021/ma9710601

    Article  CAS  Google Scholar 

  • Chen S, Tong X, Woodard RW, Du G, Wu J, Chen J (2008) Identification and characterization of bacterial cutinase. J Biol Chem 283(38):25854–25862

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Chen S, Su L, Billig S, Zimmermann W, Chen J, Wu J (2010a) Biochemical characterization of the cutinases from Thermobifida fusca. J Mol Catal B Enzym 63:121–127, http://www.sciencedirect.com/science/article

    Article  CAS  Google Scholar 

  • Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010b) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66(Pt 1):12–21. doi:10.1107/S0907444909042073

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66(Pt 4):486–501. doi:10.1107/S0907444910007493

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Evans P (2006) Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 62(Pt 1):72–82

    Article  PubMed  Google Scholar 

  • Greenfield NJ (2004) Analysis of circular dichroismdata. Methods Enzymol 383:282–317. doi:10.1016/S0076-6879(04)83012-X

    Article  CAS  PubMed  Google Scholar 

  • Guebitz GM, Cavaco-Paulo A (2008) Enzymes go big: surface hydrolysis and functionalization of synthetic polymers. Trends Biotechnol 26(1):32–38. doi:10.1016/j.tibtech.2007.10.003

    Article  CAS  PubMed  Google Scholar 

  • Haack M, Enck S, Seger H, Geyer A, Beck-Sickinger AG (2008) Pyridone dipeptide backbone scan to elucidate structural properties of a flexible peptide segment. J Am Chem Soc 130(26):8326–8336. doi:10.1021/ja8004495

    Article  CAS  PubMed  Google Scholar 

  • Han Z-l, Han S-Y, Zheng S-Y, Lin Y (2009) Enhancing thermostability of a Rhizomucor miehei lipase by engineering a disulfide bond and displaying on the yeast cell surface. Appl Microbiol Biotechnol 85(1):117–126. doi:10.1007/s00253-009-2067-8

    Article  CAS  PubMed  Google Scholar 

  • Herrero Acero E, Ribitsch D, Steinkellner G, Gruber K, Greimel K, Eiteljoerg I, Trotscha E, Wei R, Zimmermann W, Zinn M, Cavaco-Paulo A, Freddi G, Schwab H, Guebitz G (2011) Enzymatic surface hydrolysis of PET: effect of structural diversity on kinetic properties of cutinases from Thermobifida. Macromolecules 44(12):4632–4640. doi:10.1021/ma200949p

    Article  CAS  Google Scholar 

  • Herrero Acero E, Ribitsch D, Dellacher A, Zitzenbacher S, Marold A, Steinkellner G, Gruber K, Schwab H, Guebitz GM (2013) Surface engineering of a cutinase from Thermobifida cellulosilytica for improved polyester hydrolysis. Biotechnol Bioeng. doi:10.1002/bit.24930

    PubMed  Google Scholar 

  • Holm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38(Web Server issue):W545–W549. doi:10.1093/nar/gkq366

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hooft RW, Vriend G, Sander C, Abola EE (1996) Errors in protein structures. Nature 381(6580):272. doi:10.1038/381272a0

    Article  CAS  PubMed  Google Scholar 

  • Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 65(3):712–725. doi:10.1002/prot.21123

    Article  CAS  PubMed  Google Scholar 

  • Ikai A (1980) Thermostability and aliphatic index of globular proteins. J Biochem 88(6):1895–1898

    CAS  PubMed  Google Scholar 

  • Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267(3):727–748. doi:10.1006/jmbi.1996.0897

    Article  CAS  PubMed  Google Scholar 

  • Kabsch W (2010) XDS. Acta Crystallogr D Biol Crystallogr 66(Pt 2):125–132, PM:20124692

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kim H-W, Ishikawa K (2013) The role of disulfide bond in hyperthermophilic endocellulase. Extremophiles 17(4):593–599. doi:10.1007/s00792-013-0542-8

    Google Scholar 

  • Kitadokoro K, Thumarat U, Nakamura R, Nishimura K, Karatani H, Suzuki H, Kawai F (2012) Crystal structure of cutinase Est119 from Thermobifida alba AHK119 that can degrade modified polyethylene terephthalate at 1.76 Å resolution. Polym Degrad Stab 97(5):771–775, http://www.sciencedirect.com/science/article

    Google Scholar 

  • Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK—a program to check the stereochemical quality of protein structures. J Appl Cryst 26:283–291

    Article  CAS  Google Scholar 

  • Leslie AGW (1992) Recent changes to the MOSFLM package for processing film and image plate data, Joint CCP4 + ESF-EAMCB Newsletter on Proteincrystallography 26

  • Liu Z, Gosser Y, Baker PJ, Ravee Y, Lu Z, Alemu G, Li H, Butterfoss GL, Kong X-P, Gross R, Montclare JK (2009) Structural and functional studies of Aspergillus oryzae cutinase: enhanced thermostability and hydrolytic activity of synthetic ester and polyester degradation. J Am Chem Soc 131(43):15711–15716. doi:10.1021/ja9046697

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Longhi S, Cambillau C (1999) Structure-activity of cutinase, a small lipolyticenzyme. Biochim Biophys Acta 1441(2–3):185–196

    Article  CAS  PubMed  Google Scholar 

  • Longhi S, Czjzek M, Lamzin V, Nicolas A, Cambillau C (1997) Atomic resolution (1.0 Å) crystal structure of Fusarium solani cutinase: stereochemical analysis. J Mol Biol 268(4):779–799. doi:10.1006/jmbi.1997.1000

  • Murshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 67(Pt 4):355–367. doi:10.1107/S0907444911001314

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Oeser T, Wei R, Baumgarten T, Billig S, Föllner C, Zimmermann W (2010) High level expression of a hydrophobic poly(ethylene terephthalate)-hydrolyzing carboxylesterase from Thermobifida fusca KW3 in Escherichia coli BL21(DE3). J Biotechnol 146(3):100–104. doi:10.1016/j.jbiotec.2010.02.006

    Google Scholar 

  • Porcelli M, De Leo E, Del Vecchio P, Fuccio F, Cacciapuoti G (2012) Thermal unfolding of nucleoside hydrolases from the hyperthermophilic archaeon Sulfolobus solfataricus: role of disulfidebonds. Protein Pept Lett 19(3):369–374

    Article  CAS  PubMed  Google Scholar 

  • Riccardi C, Barni R, Selli E, Mazzone G, Massafra MR, Marcandalli B, Poletti G (2003) Surface modification of poly(ethylene terephthalate) fibers induced by radio frequency air plasma treatment. Appl Surf Sci 211:386–397, http://www.sciencedirect.com/science/article

    Article  CAS  Google Scholar 

  • Ronkvist M, Xie W, Lu W, Gross RA (2009) Cutinase-catalyzed hydrolysis of poly(ethylene terephthalate). Macromolecules 42(14):5128–5138. doi:10.1021/ma9005318

    Article  CAS  Google Scholar 

  • Thumarat U, Nakamura R, Kawabata T, Suzuki H, Kawai F (2012) Biochemical and genetic analysis of a cutinase-type polyesterase from a thermophilic Thermobifida alba AHK119. Appl Microbiol Biotechnol 95(2):419–430. doi:10.1007/s00253-011-3781-6

    Article  CAS  PubMed  Google Scholar 

  • Vagin A, Teplyakov A (2010) Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr 66(Pt 1):22–25

    Article  CAS  PubMed  Google Scholar 

  • Wallace AC, Laskowski RA, Thornton JM (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 8(2):127–134

    Article  CAS  PubMed  Google Scholar 

  • Wei Y, Swenson L, Castro C, Derewenda U, Minor W, Arai H, Aoki J, Inoue K, Servin-Gonzalez L, Derewenda ZS (1998) Structure of a microbial homologue of mammalian platelet-activating factor acetylhydrolases: Streptomyces exfoliatus lipase at 1.9Å resolution. Structure 6(4):511–519

    Article  CAS  PubMed  Google Scholar 

  • Zimmermann W, Billig S (2011) Enzymes for the biofunctionalization of poly(ethylene terephthalate). Adv Biochem Eng Biotechnol 125:97–120. doi:10.1007/10_2010_87

    CAS  PubMed  Google Scholar 

Download references

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Christian Roth, Wolfgang Zimmermann or Norbert Sträter.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 517 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Roth, C., Wei, R., Oeser, T. et al. Structural and functional studies on a thermostable polyethylene terephthalate degrading hydrolase from Thermobifida fusca . Appl Microbiol Biotechnol 98, 7815–7823 (2014). https://doi.org/10.1007/s00253-014-5672-0

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-014-5672-0

Keywords

Navigation