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Crystallographic evidence for substrate ring distortion and protein conformational changes during catalysis in cellobiohydrolase Ce16A from trichoderma reesei.

Zou Jy, Kleywegt GJ, Ståhlberg J, Driguez H, Nerinckx W, Claeyssens M, Koivula A, Teeri TT, Jones TA
Structure 7 1035-45 (1999)
Related entries: 1qjw, 1qk0, 3cbh

Cited: 88 times
EuropePMC logo PMID: 10508787

Abstract

Background

Cel6A is one of the two cellobiohydrolases produced by Trichoderma reesei. The catalytic core has a structure that is a variation of the classic TIM barrel. The active site is located inside a tunnel, the roof of which is formed mainly by a pair of loops.

Results

We describe three new ligand complexes. One is the structure of the wild-type enzyme in complex with a nonhydrolysable cello-oligosaccharide, methyl 4-S-beta-cellobiosyl-4-thio-beta-cellobioside (Glc)(2)-S-(Glc)(2), which differs from a cellotetraose in the nature of the central glycosidic linkage where a sulphur atom replaces an oxygen atom. The second structure is a mutant, Y169F, in complex with the same ligand, and the third is the wild-type enzyme in complex with m-iodobenzyl beta-D-glucopyranosyl-beta(1,4)-D-xylopyranoside (IBXG).

Conclusion

The (Glc)(2)-S-(Glc)(2) ligand binds in the -2 to +2 sites in both the wild-type and mutant enzymes. The glucosyl unit in the -1 site is distorted from the usual chair conformation in both structures. The IBXG ligand binds in the -2 to +1 sites, with the xylosyl unit in the -1 site where it adopts the energetically favourable chair conformation. The -1 site glucosyl of the (Glc)(2)-S-(Glc)(2) ligand is unable to take on this conformation because of steric clashes with the protein. The crystallographic results show that one of the tunnel-forming loops in Cel6A is sensitive to modifications at the active site, and is able to take on a number of different conformations. One of the conformational changes disrupts a set of interactions at the active site that we propose is an integral part of the reaction mechanism.

Reviews - 1qk2 mentioned but not cited (2)

  1. Genomics review of holocellulose deconstruction by aspergilli. Segato F, Damásio AR, de Lucas RC, Squina FM, Prade RA. Microbiol. Mol. Biol. Rev. 78 588-613 (2014)
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Articles - 1qk2 mentioned but not cited (12)

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  6. Single-molecule Imaging Analysis of Binding, Processive Movement, and Dissociation of Cellobiohydrolase Trichoderma reesei Cel6A and Its Domains on Crystalline Cellulose. Nakamura A, Tasaki T, Ishiwata D, Yamamoto M, Okuni Y, Visootsat A, Maximilien M, Noji H, Uchiyama T, Samejima M, Igarashi K, Iino R. J. Biol. Chem. 291 22404-22413 (2016)
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Reviews citing this publication (8)

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  4. Towards a molecular-level theory of carbohydrate processivity in glycoside hydrolases. Beckham GT, Ståhlberg J, Knott BC, Himmel ME, Crowley MF, Sandgren M, Sørlie M, Payne CM. Curr. Opin. Biotechnol. 27 96-106 (2014)
  5. A hydrophobic platform as a mechanistically relevant transition state stabilising factor appears to be present in the active centre of all glycoside hydrolases. Nerinckx W, Desmet T, Claeyssens M. FEBS Lett. 538 1-7 (2003)
  6. Dissecting the catalytic mechanism of a plant beta-D-glucan glucohydrolase through structural biology using inhibitors and substrate analogues. Hrmova M, Fincher GB. Carbohydr. Res. 342 1613-1623 (2007)
  7. Sub-Angstrom resolution enzyme X-ray structures: is seeing believing? Vrielink A, Sampson N. Curr. Opin. Struct. Biol. 13 709-715 (2003)
  8. Fungal cellulases: protein engineering and post-translational modifications. Zhang R, Cao C, Bi J, Li Y. Appl Microbiol Biotechnol 106 1-24 (2022)

Articles citing this publication (66)

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  3. Imaging the enzymatic digestion of bacterial cellulose ribbons reveals the endo character of the cellobiohydrolase Cel6A from Humicola insolens and its mode of synergy with cellobiohydrolase Cel7A. Boisset C, Fraschini C, Schülein M, Henrissat B, Chanzy H. Appl. Environ. Microbiol. 66 1444-1452 (2000)
  4. The kappa-carrageenase of P. carrageenovora features a tunnel-shaped active site: a novel insight in the evolution of Clan-B glycoside hydrolases. Michel G, Chantalat L, Duee E, Barbeyron T, Henrissat B, Kloareg B, Dideberg O. Structure 9 513-525 (2001)
  5. Engineering the exo-loop of Trichoderma reesei cellobiohydrolase, Cel7A. A comparison with Phanerochaete chrysosporium Cel7D. von Ossowski I, Ståhlberg J, Koivula A, Piens K, Becker D, Boer H, Harle R, Harris M, Divne C, Mahdi S, Zhao Y, Driguez H, Claeyssens M, Sinnott ML, Teeri TT. J. Mol. Biol. 333 817-829 (2003)
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  10. Crystal structures of Paenibacillus polymyxa beta-glucosidase B complexes reveal the molecular basis of substrate specificity and give new insights into the catalytic machinery of family I glycosidases. Isorna P, Polaina J, Latorre-García L, Cañada FJ, González B, Sanz-Aparicio J. J. Mol. Biol. 371 1204-1218 (2007)
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  12. The crystal structure and catalytic mechanism of cellobiohydrolase CelS, the major enzymatic component of the Clostridium thermocellum Cellulosome. Guimarães BG, Souchon H, Lytle BL, David Wu JH, Alzari PM. J. Mol. Biol. 320 587-596 (2002)
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  16. Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger. van Pouderoyen G, Snijder HJ, Benen JA, Dijkstra BW. FEBS Lett. 554 462-466 (2003)
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  18. Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase. Hrmova M, Varghese JN, De Gori R, Smith BJ, Driguez H, Fincher GB. Structure 9 1005-1016 (2001)
  19. Crystal structure of the polyextremophilic alpha-amylase AmyB from Halothermothrix orenii: details of a productive enzyme-substrate complex and an N domain with a role in binding raw starch. Tan TC, Mijts BN, Swaminathan K, Patel BK, Divne C. J. Mol. Biol. 378 852-870 (2008)
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  21. Dextranase from Penicillium minioluteum: reaction course, crystal structure, and product complex. Larsson AM, Andersson R, Ståhlberg J, Kenne L, Jones TA. Structure 11 1111-1121 (2003)
  22. Molecular cloning, transcriptional, and expression analysis of the first cellulase gene (cbh2), encoding cellobiohydrolase II, from the moderately thermophilic fungus Talaromyces emersonii and structure prediction of the gene product. Murray PG, Collins CM, Grassick A, Tuohy MG. Biochem. Biophys. Res. Commun. 301 280-286 (2003)
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  26. Insights into exo- and endoglucanase activities of family 6 glycoside hydrolases from Podospora anserina. Poidevin L, Feliu J, Doan A, Berrin JG, Bey M, Coutinho PM, Henrissat B, Record E, Heiss-Blanquet S. Appl. Environ. Microbiol. 79 4220-4229 (2013)
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  31. Design of cellulose dissolving ionic liquids inspired by nature. Ohira K, Abe Y, Kawatsura M, Suzuki K, Mizuno M, Amano Y, Itoh T. ChemSusChem 5 388-391 (2012)
  32. Computational and experimental studies of the catalytic mechanism of Thermobifida fusca cellulase Cel6A (E2). André G, Kanchanawong P, Palma R, Cho H, Deng X, Irwin D, Himmel ME, Wilson DB, Brady JW. Protein Eng. 16 125-134 (2003)
  33. The structure of a bacterial cellobiohydrolase: the catalytic core of the Thermobifida fusca family GH6 cellobiohydrolase Cel6B. Sandgren M, Wu M, Karkehabadi S, Mitchinson C, Kelemen BR, Larenas EA, Ståhlberg J, Hansson H. J. Mol. Biol. 425 622-635 (2013)
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  35. Crystal structure of a glycoside hydrolase family 6 enzyme, CcCel6C, a cellulase constitutively produced by Coprinopsis cinerea. Liu Y, Yoshida M, Kurakata Y, Miyazaki T, Igarashi K, Samejima M, Fukuda K, Nishikawa A, Tonozuka T. FEBS J. 277 1532-1542 (2010)
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  37. Determination of thioxylo-oligosaccharide binding to family 11 xylanases using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry and X-ray crystallography. Jänis J, Hakanpää J, Hakulinen N, Ibatullin FM, Hoxha A, Derrick PJ, Rouvinen J, Vainiotalo P. FEBS J. 272 2317-2333 (2005)
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Related citations provided by authors (1)

  1. Three-dimensional structure of cellobiohydrolase II from Trichoderma reesei.. Rouvinen J, Bergfors T, Teeri T, Knowles JK, Jones TA Science 249 380-6 (1990)

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