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Difference between revisions of "User:Jens Eklof"

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[[Image:Jens.jpg|200px|right]]
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{| {{Prettytable}}
 
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|-
 
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|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family 16'''
 
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|-
 
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|'''Clan''' 
 
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|GH-B
 
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|-
 
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|'''Mechanism'''
 
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|retaining
 
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|-
 
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|'''Active site residues'''
 
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|known
 
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|-
 
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|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''
 
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|-
 
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| colspan="2" |http://www.cazy.org/fam/GH16.html
 
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|}
 
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</div>
 
  
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== Substrate specificities ==
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'''Jens Ekl&ouml;f''' took his M.Sc.Eng. at the Royal Institute of Technology (KTH) and did his Ph.D. with Harry Brumer at the department of [http://www.biotech.kth.se/glycoscience/ Glycoscience, KTH]. His main focus areas are enzymes acting on the plant polysaccharide xyloglucan with special emphasis on the plant ''xth''-gene product family of [[GH16]]. He has also been working with pectin methylesterases from Carbohydrate family 8 (CE8). His Ph. D. thesis entitled, "Plant and microbial xyloglucanses: Function, Structure and Phylogeny" can be accessed by clicking [http://kth.diva-portal.org/smash/record.jsf?searchId=1&pid=diva2:405550/ here].
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Family 16 enzymes cleave &beta;-1,4 or &beta;-1,3 glycosidic bonds in various glucans and galactans. Some members of this family have evolved to loose their hydrolytic activity and become strict transglycosylases.<cite>REF1</cite>
 
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The substrate specificities found in GH16 are: xyloglucan:xyloglucosyltransferases (EC 2.4.1.207),
 
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keratan-sulfate ''endo''-1,4-&beta;-galactosidases (EC 3.2.1.103), ''endo''-1,3-&beta;-glucanases (EC 3.2.1.39), ''endo''-1,3(4)-&beta;-glucanases (EC 3.2.1.6), lichenases (EC 3.2.1.73), &beta;-agarases (EC 3.2.1.81), &kappa;-carrageenases (EC 3.2.1.83) and xyloglucanases (EC 3.2.1.151).
 
  
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== Kinetics and Mechanism ==
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He is currently working as a post doc in Vancouver, Canada in Harry Brumer's group.
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Family 16 enzymes are retaining enzymes, as first shown by NMR <cite>REF3</cite> on an ''endo''-1,3-1,4-&beta;-D-glucan 4-glucanohydrolase from ''Bacillus licheniformis''.  
 
  
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== Catalytic Residues ==
 
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The nucleophile was detected using an epoxyalkyl &beta;-glycoside inhibitor and subsequent peptide identification by ESI-MS and Edman degradation on an ''endo''-1,3-1,4-&beta;-D-glucan 4-glucanohydrolase from ''Bacillus amyloliquefaciens''.<cite>REF4</cite>
 
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The acid/base was found by mutation of all Asp and Glu into Asn and Gln respectively on an ''endo''-1,3-1,4-&beta;-D-glucan 4-glucanohydrolase from ''Bacillus licheniformis''. <cite>7</cite>
 
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== Three-dimensional structures ==
 
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Several family 16 three-dimensional structures have been solved of both archeal, bacterial and eukaryotic origin. The first solved 3-D structure was that of lichenase M from ''Paenibacillus macerans'' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1BYH PDB 1byh]) in 1992. <cite>5</cite>
 
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The first eukaryotic 3-D structure was the xyloglucan ''endo''-transglycosylase ''Ptt''XET16-34 from ''Populus tremula&times;tremuloides'' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1UMZ PDB 1umz]).<cite>REF1</cite> The first archeal 3-D structure was a &beta;-1,3-''endo''glucanase Lam16 from ''Pyrococcus furiosus'' ([http://www.rcsb.org/pdb/explore/explore.do?structureId=2VY0 PDB 2vy0]). <cite>8</cite>
 
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== Evolution of GH16 ==
 
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Family 16 is a member of clan GH-B together with family 7 with whom they share their &beta;-jellyroll fold. The different specificities of family 16 has been proposed to have evoloved from a ancestral &beta;-1,3-glucanase.<cite>10</cite>
 
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== Family firsts ==
 
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; First stereochemistry determination : ''Bacillus licheniformis'' 1,3-1,4-&beta;-D-glucan 4-glucanohydrolase by NMR.<cite>REF3</cite>
 
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; First nucleophile identification : ''Bacillus amyloliquefaciens'' 1,3-1,4-&beta;-D-glucan 4-glucanohydrolase.<cite>REF4</cite>
 
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; First general acid/base residue identification : ''Bacillus licheniformis'' 1,3-1,4-&beta;-D-glucan 4-glucanohydrolase, first by sequence homology and mutational studies.<cite>6</cite> This was later verified by azide rescue of inactivated mutants.<cite>7</cite>
 
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; First 3-D structure : On a hybrid lichenase between ''Bacillus amyloliquefaciens'' and ''Paenibacillus macerans''  by X-ray crystallography ([http://www.rcsb.org/pdb/explore/explore.do?structureId=1BYH PDB 1byh]). <cite>5</cite>
 
 
== Reference list ==
 
== Reference list ==
 
<biblio>
 
<biblio>
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#REF1 pmid=15020748
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#Eklof2010 pmid=20421457
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#REF4 pmid=1360982
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#Eklof2009 pmid=19452549
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#REF3 pmid=8280073
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#Baumann2007 pmid=17557806
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#5 pmid=8099449
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#Ariza2011 pmid=21795708
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#6 pmid=8182059
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#Mark2009 pmid=19004021
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#7 pmid=9698381
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#Nordgren2008 pmid=18260631
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#8 pmid=19154353
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#Gloster2007 pmid=17376777
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#9 pmid=11435116 tree GH16
 
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#10 pmid=9580981 first GH16 paper
 
 
</biblio>
 
</biblio>
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[[Category:Contributors|Ekl&ouml;f, Jens]]
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<!-- DO NOT REMOVE THIS CATEGORY TAG! -->
 
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[[Category:Glycoside Hydrolase Families]]
 

Latest revision as of 13:32, 20 January 2012

Jens.jpg

Jens Eklöf took his M.Sc.Eng. at the Royal Institute of Technology (KTH) and did his Ph.D. with Harry Brumer at the department of Glycoscience, KTH. His main focus areas are enzymes acting on the plant polysaccharide xyloglucan with special emphasis on the plant xth-gene product family of GH16. He has also been working with pectin methylesterases from Carbohydrate family 8 (CE8). His Ph. D. thesis entitled, "Plant and microbial xyloglucanses: Function, Structure and Phylogeny" can be accessed by clicking here.

He is currently working as a post doc in Vancouver, Canada in Harry Brumer's group.

Reference list

Error fetching PMID 20421457:
Error fetching PMID 19452549:
Error fetching PMID 17557806:
Error fetching PMID 21795708:
Error fetching PMID 19004021:
Error fetching PMID 18260631:
Error fetching PMID 17376777:
  1. Error fetching PMID 20421457: [Eklof2010]
  2. Error fetching PMID 19452549: [Eklof2009]
  3. Error fetching PMID 17557806: [Baumann2007]
  4. Error fetching PMID 21795708: [Ariza2011]
  5. Error fetching PMID 19004021: [Mark2009]
  6. Error fetching PMID 18260631: [Nordgren2008]
  7. Error fetching PMID 17376777: [Gloster2007]

All Medline abstracts: PubMed

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