Abstract
Homology modeling is a very powerful tool in the absence of atomic structures for understanding the general fold of the enzyme, conserved residues, catalytic tunnel/pocket as well as substrate and product binding sites. This information is useful for structure-assisted enzyme design approach for the development of robust enzymes especially for industrial applications.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Muñoz IG, Ubhayasekera W, Henriksson H et al (2001) Family 7 cellobiohydrolases from Phanerochaete chrysosporium: crystal structure of the catalytic module of Cel7D (CBH58) at 1.32 angstrom resolution and homology models of the isozymes. J Mol Biol 314(5):1097–1111
Steenbakkers PJM, Ubhayasekera W, Goossen JAM et al (2002) An intron-containing glycoside hydrolase family 9 cellulase gene encodes the dominant 90 kDa component of the cellulosome of the anaerobic fungus Piromyces sp strain E2. Biochem J 365:193–204
Harhangi HR, Freelove AC, Ubhayasekera W et al (2003) Cel6A, a major exoglucanase from the cellulosome of the anaerobic fungi Piromyces sp E2 and Piromyces equi. Biochim Biophys Acta 1628(1):30–39
Sorensen A, Ahring BK, Lübeck M et al (2012) Identifying and characterizing the most significant beta-glucosidase of the novel species Aspergillus saccharolyticus. Can J Microbiol 58(9):1035–1046
Benson DA, Karsch-Mizrachi I, Lipman DJ et al (2004) GenBank: update. Nucleic Acids Res 32:D23–D26
Ubhayasekera W, Muñoz IG, Vassella A et al (2005) Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors. FEBS J 272(8):1952–1964
von Ossowski I, Ståhlberg J, Koivula A et al (2003) Engineering the exo-loop of Trichoderma reesei cellobiohydrolase, Cel7A. A comparison with Phanerochaete chrysosporium Cel7D. J Mol Biol 333(4):817–829
Becker D, Braet C, Brunner H et al (2001) Engineering of a glycosidase Family 7 cellobiohydrolase to more alkaline pH optimum: the pH behaviour of Trichoderma reesei Cel7A and its E223S/A224H/L225V/T226A/D262G mutant. Biochem J 356(Pt 1):19–30
Goedegebuur F, Dankmeyer L, Gualfetti P et al (2017) Improving the thermal stability of cellobiohydrolase Cel7A from Hypocrea jecorina by directed evolution. J Biol Chem 292(42):17418–17430
Momeni MH, Goedegebuur F, Hansson H et al (2014) Expression, crystal structure and cellulase activity of the thermostable cellobiohydrolase Cel7A from the fungus Humicola grisea var. thermoidea. Acta Crystallogr D Biol Crystallogr 70(Pt 9):2356–2366
Divne C, Ståhlberg J, Teeri TT, Jones TA (1998) High-resolution crystal structures reveal how a cellulose chain is bound in the 50 angstrom long tunnel of cellobiohydrolase I from Trichoderma reesei. J Mol Biol 275(2):309–325
Ubhayasekera W (2005) Structural studies of cellulose and chitin active enzymes, Dissertation, Swedish University of Agricultural Sciences, Uppsala, Sweden. https://pub.epsilon.slu.se/772/
Momeni MH, Ubhayasekera W, Sandgreen M et al (2015) Structural insights into the inhibition of cellobiohydrolase Cel7A by xylo-oligosaccharides. FEBS J 282(11):2167–2177
Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5(4):823–826
Jones TA, Zou JY, Cowan-Jacob SW, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47:110–119
Kleywegt GJ, Zou JY, Kejldgaard M, Jones TA (2001) Around O. In: Rossmann MG, Arnold E (eds) International tables for crystallography, Vol. F. Crystallography of Biological Macromolecules. Kluwer Academic, Dordrecht, pp 353–356
Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340(4):783–795
Altschul SF, Madden TL, Schäffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402
Berman HM, Westbrook J, Reng Z et al (2000) The protein data bank. Nucleic Acids Res 28(1):235–242
Henrissat B (1991) A classification of glycosyl hydrolases based on amino-acid-sequence similarities. Biochem J 280:309–316
Kraulis PJ (1991) Molscript - a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24:946–950
Harris M, Jones TA (2001) Molray-a web interface between O and the POV-ray ray tracer. Acta Crystallogr D Biol Crystallogr 57(Pt 8):1201–1203
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Ubhayasekera, W. (2018). Homology Modeling for Enzyme Design. In: Lübeck, M. (eds) Cellulases. Methods in Molecular Biology, vol 1796. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7877-9_21
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7877-9_21
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7876-2
Online ISBN: 978-1-4939-7877-9
eBook Packages: Springer Protocols