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The crystal structure of the outer membrane lipoprotein YbhC from Escherichia coli sheds new light on the phylogeny of carbohydrate esterase family 8
KTH, School of Biotechnology (BIO), Glycoscience.
KTH, School of Biotechnology (BIO).
KTH, School of Biotechnology (BIO), Glycoscience.ORCID iD: 0000-0002-5805-2693
KTH, School of Biotechnology (BIO), Glycoscience.
2009 (English)In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 76, no 4, p. 1029-1036Article in journal (Refereed) Published
Place, publisher, year, edition, pages
2009. Vol. 76, no 4, p. 1029-1036
Keywords [en]
carbohydrate-active enzyme (CAZyme), CE8, pectin methylesterase (PME), palmitoyl coenzyme A, murein, Enterobacteriaceae, penicillin-binding protein-5, pectin methylesterase, maximum-likelihood, sequence, identification, specificity, models
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:kth:diva-18676DOI: 10.1002/prot.22453ISI: 000268839400020Scopus ID: 2-s2.0-68149162197OAI: oai:DiVA.org:kth-18676DiVA, id: diva2:336723
Note

QC 20100525

Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2018-01-26Bibliographically approved
In thesis
1. A holistic approach to understanding CAZy families through reductionist methods
Open this publication in new window or tab >>A holistic approach to understanding CAZy families through reductionist methods
2009 (English)Licentiate thesis, comprehensive summary (Other academic)
Abstract [en]

 

In a time when the amount of biological data present in the public domain is becoming increasingly vast, the need for good classification systems has never been greater. In the field of glycoscience the necessity of a good classification for the enzymes involved in the biosynthesis, modification and degradation of polysaccharides is even more pronounced than in other fields. This is due to the complexity of the substrates, the polysaccharides, as the theoretical number of possible hexa-oligosaccharides from only hexoses exceeds 1012 isomers! 

An initiative to classify enzymes acting on carbohydrates began around 1990 by the French scientist Bernard Henrissat. The resulting database, the Carbohydrate Active enzymes database (CAZy), classifies enzymes by sequence similarity into families allowing the inference of structure and catalytic mechanism. What CAZy does not provide however, are means to understand how members of a family are related, and in what way they differ from each other. The top-down approach used in this thesis, combining phylogenetic analysis of whole CAZy families, or sub-families, with structural determinations and detailed kinetic analysis allows for exactly that.  

Finding determinants for transglycosylation versus hydrolysis within the xth gene product family of GH16 as well as restricting the hydrolytic enzymes to a well defined clade are integral parts of paper I. In paper II a new bacterial sub-clade within CE8 was discovered. The structural determination of theEscherichia coli outer membrane lipoprotein YbhC from from the new sub-clade explained the difference in specificity. The information provided in the two papers of this thesis gives a better understanding of the development of different specificities of diverse CAZY families as well as it aids in future gene product annotations. Furthermore this work has begun to fill the white spots uncovered in the phylogenetic trees.

 

 

Place, publisher, year, edition, pages
Stockholm: KTH, 2009. p. viii, 55
Series
Trita-BIO-Report, ISSN 1654-2312 ; 2009:5
Keywords
Carbohydrate esterase family 8, XET, PME, YbhC
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:kth:diva-10183 (URN)978-91-7415-269-2 (ISBN)
Presentation
2009-04-29, FA31, Albanova University Center, Stockholm, 14:00 (English)
Opponent
Supervisors
Available from: 2009-05-13 Created: 2009-03-30 Last updated: 2010-10-27Bibliographically approved

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