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Difference between revisions of "User:Jens Eklof"

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{| {{Prettytable}}
 
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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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|'''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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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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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 first suggested 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>. This was subsequently verified by azide resque of the E134A mutant of a ''Bacillus licheniformis''  1,3-1,4-&beta;-D-glucan 4-glucanohydrolase resulting in an &alpha;-glycosyl product from the &beta-glycosyl substrate <cite>7</cite>.
 
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The acid-base was found by making the E138A mutant from the ''Bacillus licheniformis''  1,3-1,4-&beta;-D-glucan 4-glucanohydrolase and subsequent azide rescue resulting in a &beta;-glycosyl azide product <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>. The first branching in family 16 lead to the evolution of the &kappa;-carrageenases and the &beta;-agarases and a later branching event lead to the arisal of the lichenases and the XETs<cite>10</cite> (see figure).
 
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[[Image:TreeclanB.png|thumb]]
 
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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 : Suggested in  ''Bacillus amyloliquefaciens'' 1,3-1,4-&beta;-D-glucan 4-glucanohydrolase <cite>REF4</cite>. Later verified in by azide rescue of inactivated mutants <cite>7</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>.
 
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== Reference list ==
 
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<biblio>
 
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#REF1 pmid=15020748
 
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#REF4 pmid=1360982
 
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#REF3 pmid=8280073
 
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#5 pmid=8099449
 
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#6 pmid=8182059
 
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#7 pmid=9698381
 
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#8 pmid=19154353
 
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#9 pmid=11435116 tree GH16
 
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#10 pmid=9580981 first GH16 paper
 
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</biblio>
 
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<!-- DO NOT REMOVE THIS CATEGORY TAG! -->
 
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[[Category:Glycoside Hydrolase Families]]
 

Revision as of 03:59, 29 May 2009

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