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Exploring glycoside hydrolase family 5 (GH5) enzymes
KTH, School of Biotechnology (BIO), Glycoscience.
2013 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

In 1990, the classification of carbohydrate-active enzymes (CAZymes) was introduced by the scientist Bernard Henrissat. According to sequence similarity, these enzymes were separated into families with conserved structures and reaction mechanisms. One interesting class of CAZymes is the group of glycoside hydrolases (GHs) containing more than 138000 modules divided into 131 families as of February 2013. One of the most versatile and the largest of these GH families, containing enzymes with numerous biomass-deconstructing activities, is glycoside hydrolase family 5 (GH5). However, for large and diverse families like the GH5 family, another layer of classification is required to get a better understanding of the evolution of diverse enzyme activities. In Paper I, a new subfamily classification of GH5 is presented in order to sort the family members into distinct groups with predictive power. In total, 51 subfamilies were defined. Despite the fact that several hundred GH5 enzymes have been characterized, 20 subfamilies lacking biochemically characterized enzymes and 38 subfamilies without structural data were identified. These highlighted subfamilies contain interesting targets for future investigation.

The GH5 family includes endo-β-mannanases catalyzing the hydrolysis of the β-1,4-linked backbone of mannan polysaccharides, which are common hemicelluloses found as storage and structural polymers in plant cell walls. Mannans are commonly utilized as raw biomaterials in food, feed, paper, textile and cosmetic industries, and mannanases are often applied for modifying and controlling the property of mannan polysaccharides in such applications. The overwhelming majority of characterized mannanases are from microbial origin. The situation for plant mannanases is quite different, as the catalytic properties for only a handful have been determined. Paper II describes the first characterization of a heterologously expressed Arabidopsis β-mannanase.

Abstract [sv]

År 1990 introducerade forskaren Bernard Henrissat en klassificering av kolhydrataktiva enzymer (CAZymer), enligt vilken enzymerna - baserat på sekvenslikhet - delades in i familjer med konserverade strukturer och reaktionsmekanismer. En intressant CAZym-klass är glykosidhydrolaserna (GH), en klass som i februari 2013 innehöll fler än 138000 katalytiska moduler indelade i 131 olika familjer. En av de största och mest varierade av GH-familjerna är glykosidhydrolasfamilj 5 (GH5), vilken innehåller en mångfald av identifierade enzymaktiviteter relevanta för nedbrytning av biomassa. För stora och diversifierade familjer som GH5 krävs det dock ytterligare en klassificeringsnivå för att bättre förstå evolutionen och uppkomsten av de många förekommande enzymaktiviteterna. I manuskript I presenteras en ny uppdelning av GH5 enzymer i subfamiljer med syfte att dela upp familjemedlemmarna i distinkta grupper som representerar olika funktioner. Utifrån denna klassificering kan sedan ett enzyms funktion förutsägas baserat på vilken subfamilj det tillhör. Totalt definierades 51 subfamiljer. Trots att hundratals GH5 enzymer har karaktäristerats så visade det sig att 20 av subfamiljerna helt saknar biokemiskt karaktäriserade enzymer och 38 av dem saknar publicerade proteinstrukturer. Dessa subfamiljer är särskilt intressanta för framtida studier.

GH5-familjen inkluderar endo-β-mannanaser som katalyserar hydrolysen av den β-1,4-länkade huvudkedjan i mannanpolysackarider. Dessa växtpolymerer som ingår i hemicellulosagruppen är vanligt förekommande i cellväggarna, där de fungerar som energilagringsmolekyler eller har en strukturell funktion. Mannaner används ofta som råmaterial för industriell livs- och djurfodersproduktion, papper, textilier och kosmetika. I dessa processer behövs ofta mannanaser för modifiering och kontroll av egenskaperna hos dessa polysackarider. Den överväldigande majoriteten av alla karaktäriserade mannanaser kommer från mikroorganismer. Endast för ett fåtal växtmannanaser har de katalytiska egenskaperna analyserats. Manuskript II beskriver den första karaktäriseringen av ett heterologt uttryckt β-mannanas från Arabidopsis.

Place, publisher, year, edition, pages
Stockholm: KTH Royal Institute of Technology, 2013. , 41 p.
Trita-BIO-Report, ISSN 1654-2312 ; 2013:8
Keyword [en]
GH5, glycoside hydrolase, subfamily classification, mannans, polysaccharides, mannanases, cell wall
Keyword [sv]
GH5, glykosidhydrolas, subfamiljklassificering, mannaner, polysackarider, mannanaser, cellvägg
National Category
Engineering and Technology Natural Sciences
Research subject
SRA - Molecular Bioscience
URN: urn:nbn:se:kth:diva-121537ISBN: 978-91-7501-719-8OAI: diva2:619225
2013-05-28, FP41, AlbaNova Universitetscentrum, Roslagstullsbacken 33, Stockholm, 10:30 (English)
Swedish Foundation for Strategic Research

QC 20130506

Available from: 2013-05-06 Created: 2013-04-30 Last updated: 2013-05-06Bibliographically approved
List of papers
1. Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)
Open this publication in new window or tab >>Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5)
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2012 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, Vol. 12, no 1, 186- p.Article in journal (Refereed) Published
Abstract [en]

Background: The large Glycoside Hydrolase family 5 (GH5) groups together a wide range of enzymes acting on beta-linked oligo- and polysaccharides, and glycoconjugates from a large spectrum of organisms. The long and complex evolution of this family of enzymes and its broad sequence diversity limits functional prediction. With the objective of improving the differentiation of enzyme specificities in a knowledge-based context, and to obtain new evolutionary insights, we present here a new, robust subfamily classification of family GH5. Results: About 80% of the current sequences were assigned into 51 subfamilies in a global analysis of all publicly available GH5 sequences and associated biochemical data. Examination of subfamilies with catalytically-active members revealed that one third are monospecific (containing a single enzyme activity), although new functions may be discovered with biochemical characterization in the future. Furthermore, twenty subfamilies presently have no characterization whatsoever and many others have only limited structural and biochemical data. Mapping of functional knowledge onto the GH5 phylogenetic tree revealed that the sequence space of this historical and industrially important family is far from well dispersed, highlighting targets in need of further study. The analysis also uncovered a number of GH5 proteins which have lost their catalytic machinery, indicating evolution towards novel functions. Conclusion: Overall, the subfamily division of GH5 provides an actively curated resource for large-scale protein sequence annotation for glycogenomics; the subfamily assignments are openly accessible via the Carbohydrate-Active Enzyme database at

Protein evolution, Enzyme evolution, Functional prediction, Glycogenomics, Glycoside hydrolase family 5, Phylogenetic analysis, Subfamily classification
National Category
Bioinformatics and Systems Biology
urn:nbn:se:kth:diva-109742 (URN)10.1186/1471-2148-12-186 (DOI)000312732100001 ()22992189 (PubMedID)2-s2.0-84866500048 (ScopusID)
Swedish Research Council FormasSwedish Foundation for Strategic Research

QC 20130201

Available from: 2013-01-08 Created: 2013-01-08 Last updated: 2015-02-24Bibliographically approved
2. Enzymatic characterization of a GH5_7 mannanase from Arabidopsis thaliana
Open this publication in new window or tab >>Enzymatic characterization of a GH5_7 mannanase from Arabidopsis thaliana
(English)Manuscript (preprint) (Other academic)
National Category
Bioinformatics and Systems Biology
urn:nbn:se:kth:diva-121886 (URN)

QS 2013

Available from: 2013-05-06 Created: 2013-05-06 Last updated: 2013-05-06Bibliographically approved

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