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Structural studies of cellulose and chitin active enzymes

Ubhayasekera, Wimal (2005). Structural studies of cellulose and chitin active enzymes. Diss. (sammanfattning/summary) Uppsala : Sveriges lantbruksuniv., Acta Universitatis agriculturae Sueciae, 1652-6880 ; 2005:18
ISBN 91-576-7017-X
[Doctoral thesis]

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Abstract

Cellulose and chitin, the main ways of storing biological energy in nature, also play a vital role in the structures of many organisms. Cellulose is the main structural component in plants whereas chitin is found in invertebrates and fungi. Gaining a better understanding of the degradation of these polymers can have direct or indirect economic impact. This thesis summarizes the structural perspectives of the cellulose and chitin degradation machinery. The white-rot fungus Phanerochaete chrysosporium has six cellobiohydrolases, which are expressed differentially with varying stimuli and time intervals. X-ray crystal structures of one of the six isozymes (Pc_Cel7D) suggested that it uses a retention mechanism and acts from the reducing end of cellulose chain. Homology modeling of the other enzymes supported the same sort of mechanism for all except one (Pc_Cel7B) and considerably different dynamic properties for two isozymes (Pc_Cel7A and Pc_Cel7B). Piromyces sp. strain E2 Cel9A and Cel6A as well as Piromyces equi Cel6A are modular structures, which function as parts of the fungal cellulosome of the respective organisms. Homology modeling supported the conclusion that Cel9A is an endoglucanase having a wide active site cleft and a conserved calcium-binding site with an inverting catalytic mechanism, whereas the Cel6As are processive cellobiohydrolases that act via an inverting mechanism that releases cellobiose from the non-reducing end of the cellulose chain. Brassica juncea endo acting chitinase is a pathogenesis-related protein that acts in defense of the plant. A homology model of the catalytic module was useful in designing mutants that helped us to understand the substrate binding and catalytic processes. X-ray crystal structures of the catalytic module and a mutant extended the knowledge of how the enzyme acts during the catalysis, with conformational changes opening and closing the enzyme. The homology model of yam, Dioscorea opposita, class IV endochitinase suggests that this enzyme catalyzes chitin cleavage via an inverting mechanism. Deletions in class IV chitinases compared to class I/II cluster at the ends of the substrate-binding cleft, shortening it by one glycosyl unit at each end. The shorter cleft might be expected to recognize and grasp a small section of exposed chitin on a fungal hyphal wall, more effectively attacking it.

Authors/Creators:Ubhayasekera, Wimal
Title:Structural studies of cellulose and chitin active enzymes
Year of publishing :2005
Volume:2005:18
Number of Pages:53
Papers/manuscripts:
NumberReferences
ALLI. Wimal Ubhayasekera, Muñoz, I.G., Vasella, A., Ståhlberg, J. And Mowbray, S.L. (2004). Structures of Phanerochaete chrysosporium Cel7D in complex with product and inhibitors. Accepted for publication in FEBS Journal. II. Inés G. Muñoz, Wimal Ubhayasekera, Hongbin Henriksson, Istvan Szabó, Göran Pettersson, Gunnar Johansson, Sherry L. Mowbray and Jerry Ståhlberg (2001). Family 7 Cellobiohydrolases from Phanerochaete chrysosporium: Crystal structure of the catalytic module of Cel7D (CBH58) at 1.32 Å resolution and homology models of the isozymes. J. Mol. Biol. 314, 1097-1111. III. Steenbakkers, P. J. M., Ubhayasekera, W., Goossen, H. J. A. M., van Lierop, E. M. H. M., van der Drift, C., Vogels, G. D., Mowbray, S. L. & Op den Camp , H. J. M. (2002). An intron-containing 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. IV. Harry R. Harhangi, Alexander C. J. Freelove, Wimal Ubhayasekera, Maarten van Dinther, Peter J. M. Steenbakkers, Anna Akhmanova, Chris van der Drift, Mike S.M. Jetten, Sherry L. Mowbray, Harry J. Gilbert and Huub J. M. Op den Camp (2003). Cel6A, a major exoglucanase from the cellulosome of the anaerobic fungi Piromyces sp. E2 and Piromyces equi Biochem Biophys Acta, 1628, 30-39. V. Ce Mun Tang, Mee-Len Chye, Sathishkumar Ramalingam, Ouyang Shi-Wen, Kai-Jun Zhao, Wimal Ubhayasekera and Sherry Mowbray (2004). Functional analysis of the chitin-binding domains and the catalytic domain of Brassica juncea chitinase BjCHI1. Plant Mol Biol, 56, 285-298. VI. Wimal Ubhayasekera, Ce Mun Tang, Terese Bergfors, Gunnar Berglund, Mee-Len Chye and Sherry L. Mowbray (2005). Crystal structure of a family 19 chitinase from Brassica juncea shows flexibility of binding cleft loops. manuscript. VII. Takuji Mitsunaga, Minoru Iwase, Wimal Ubhayasekera, Sherry Lynn Mowbray and Daizo Koga (2004). Molecular cloning of a genomic DNA encoding yam class IV chitinase and homology modeling. J. Bioscience, Biotechnology and Biochemistry, 68(7), 1508-17.
Place of Publication:Uppsala
ISBN for printed version:91-576-7017-X
ISSN:1652-6880
Language:English
Publication Type:Doctoral thesis
Full Text Status:Public
Agris subject categories.:X Agricola extesions > X30 Life sciences
Subjects:Not in use, please see Agris categories
Agrovoc terms:cellulose, chitin, chitinase, cellulase, degradation, molecular biology
Keywords:cellobiohydrolase, cellulase, cellulose, chitin, chitinase, endoglucanase, homology modeling, pathogenesis-related protein, structural studies, X-ray crystallography
URN:NBN:urn:nbn:se:slu:epsilon-554
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-554
ID Code:772
Department:(NL, NJ) > Dept. of Molecular Biology (until 131231)
Deposited By: Wimal Ubhayasekera
Deposited On:25 Feb 2005 00:00
Metadata Last Modified:02 Dec 2014 10:07

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