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Volume 8   Issue 2   Year 2013
Method of Search for Substrate Specificity Regions in Cellulase Class Enzymes Based on their Primary and Tertiary Structures

Igolkina A.A., Andronov E.E., Porozov Yu.B.

St. Petersburg State Polytechnic University, St. Petersburg, 195251, Russia
All-Russia Research Institute for Agricultural Microbiology, Pushkin, St. Petersburg, 196608, Russia
St. Petersburg National Research University of Information Technologies, Mechanics and Optics, St. Petersburg, 197101, Russia
Abstract. In nature, the degradation of plant biomass, which mostly consists of plant cell walls, is implemented by microorganisms synthesizing cellulase class enzymes (CCEs). Cell walls fibers are composed of complex of polysaccharides, which is split by complicated CCEs. CCEs contain two types of domains. The first type is the catalytic domains that decompose polysaccharides. The second type is the binding domains with substrates (carbohydrate binding module, CBM). The ability of enzymes to decompose polysaccharides is due to the configuration of the catalytic site in the catalytic domain; in particular, the catalytic site should contain the complimentary binding site to the substrate. In this work, we have developed and tested a combined approach to identify CCEs’ binding sites which could make the contact zone with plant polysaccharide substrates. This approach was applied to the 90 proteins identified with cellulase activity based on data from M. Hess et al.. As a result, we have found two consensus sequences of CCEs’ binding sites which are complimentary with polysaccharide substrates, Carboxymethyl Cellulose (CMC) and Xylan. On the basis of the approach, we have developed a software that implements the basic stages of search and detection of binding sites. The developed method and the software can be used in the analysis of large groups of proteins with diverse substrate specificity to detect functional areas.
Key words: cellulase, graph, site searching algorithm, structure of the protein, binding site, biofuels.


Table of Contents Original Article
Math. Biol. Bioinf.
doi: 10.17537/2013.8.407
published in Russian

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References Translation into English
Math. Biol. Bioinf.
doi: 10.17537/2013.8.t1

Full text (eng., pdf)


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