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

Applied Microbiology and Biotechnology

Volumn 98, Issue 18, 2014, Pages 7815-7823

  Roth, Christian ^a,b   Wei, Ren ^a   Oeser, Thorsten ^a   Then, Johannes ^a   Föllner, Christina ^a   Zimmermann, Wolfgang ^a   Sträter, Norbert ^a  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Crystal structure; Cutinase; PET degradation; PET modification; Thermostability

Indexed keywords

ALIPHATIC COMPOUNDS; CRYSTAL STRUCTURE; ENZYMES; POLYETHYLENE TEREPHTHALATES; STABILITY;

CUTINASE; MODELLING STUDIES; POLYETHYLENE TEREPHTHALATES (PET); POLYMERIC SUBSTRATE; RATIONAL DESIGN; STRUCTURAL INFORMATION; THERMOBIFIDA FUSCA; THERMOSTABILITY;

PLASTIC BOTTLES;

ENZYME VARIANT; HYDROLASE; NITROGEN; OXYGEN; POLYESTER; POLYETHYLENE TEREPHTHALATE; CARBOXYLESTERASE; CUTINASE;

BACTERIUM; BIODEGRADATION; CATALYST; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME ACTIVITY; ETHYLENE; HOMOLOGY; INHIBITOR; POLYMER; TEMPERATURE EFFECT;

ARTICLE; COVALENT BOND; CRYSTAL STRUCTURE; ENZYME DEGRADATION; ENZYME SUBSTRATE COMPLEX; HYDROLYSIS; MOLECULAR DYNAMICS; NONHUMAN; POLYMERIZATION; THERMOBIFIDA ALBA; THERMOBIFIDA FUSCA; THERMOSTABILITY; ACTINOMYCETALES; ENZYMOLOGY; METABOLISM;

BACTERIA (MICROORGANISMS); THERMOBIFIDA ALBA; THERMOBIFIDA FUSCA;

ACTINOMYCETALES; CARBOXYLIC ESTER HYDROLASES; HYDROLASES; POLYETHYLENE TEREPHTHALATES;

EID: 84906944065     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-014-5672-0     Document Type: Article

References (43)

1. 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
2. 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 (Pubitemid 46341488)
3. 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
4. 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
5. 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
6. 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
7. 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
8. 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 (Pubitemid 34655184)
9. Chen W, McCarthy TJ (1998) Chemical surface modification of poly(-ethylene terephthalate).Macromolecules 31(11):3648-3655. doi:10.1021/ma9710601 (Pubitemid 128567772)
10. 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
11. 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
12. Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010b) Mol Probity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66(Pt 1):12-21. doi:10.1107/S0907444909042073
13. 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
14. Evans P (2006) Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 62(Pt 1):72-82
15. Greenfield NJ (2004) Analysis of circular dichroismdata. Methods Enzymol 383:282-317. doi:10.1016/S0076-6879(04)83012-X
16. 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 (Pubitemid 350298596)
17. 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 (Pubitemid 351898552)
18. 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
19. 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
20. 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
21. 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
22. Hooft RW, Vriend G, Sander C, Abola EE (1996) Errors in protein structures. Nature 381(6580):272. doi:10.1038/381272a0
23. 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 (Pubitemid 44583220)
24. Ikai A (1980) Thermostability and aliphatic index of globular proteins. J Biochem 88(6):1895-1898
25. 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 (Pubitemid 27170693)
26. Kabsch W (2010) XDS. Acta Crystallogr D Biol Crystallogr 66(Pt 2):125-132, PM:20124692
27. 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
28. 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
29. 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
30. Leslie AGW (1992) Recent changes to the MOSFLM package for processing film and image plate data, Joint CCP4 + ESF-EAMCB Newsletter on Proteincrystallography 26
31. 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
32. Longhi S, Cambillau C (1999) Structure-activity of cutinase, a small lipolyticenzyme. Biochim Biophys Acta 1441(2-3):185-196
33. 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 (Pubitemid 27214437)
34. 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
35. Oeser T, Wei R, Baumgarten T, Billig S, Föllner C, Zimmermann W (2010) High level expression of a hydrophobic poly(ethylene tere-phthalate)- 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
36. 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
37. 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
38. 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
39. 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
40. Vagin A, Teplyakov A (2010) Molecular replacement with MOLREP. Acta Crystallogr D Biol Crystallogr 66(Pt 1):22-25
41. Wallace AC, Laskowski RA, Thornton JM (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 8(2):127-134
42. 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 1.9 Å resolution. Structure 6(4):511-519 (Pubitemid 28205522)
43. 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