6hy3
From Proteopedia
(Difference between revisions)
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<StructureSection load='6hy3' size='340' side='right'caption='[[6hy3]], [[Resolution|resolution]] 1.30Å' scene=''> | <StructureSection load='6hy3' size='340' side='right'caption='[[6hy3]], [[Resolution|resolution]] 1.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6hy3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HY3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HY3 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6hy3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"cytophaga_drobachiensis"_barbeyron_et_al._1998 "cytophaga drobachiensis" barbeyron et al. 1998]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HY3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HY3 FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | ||
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">agaC, zobellia_4267 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=63186 "Cytophaga drobachiensis" Barbeyron et al. 1998])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-agarase Beta-agarase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.81 3.2.1.81] </span></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-agarase Beta-agarase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.81 3.2.1.81] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6hy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hy3 OCA], [http://pdbe.org/6hy3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hy3 RCSB], [http://www.ebi.ac.uk/pdbsum/6hy3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hy3 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6hy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hy3 OCA], [http://pdbe.org/6hy3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hy3 RCSB], [http://www.ebi.ac.uk/pdbsum/6hy3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hy3 ProSAT]</span></td></tr> | ||
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== Function == | == Function == | ||
[[http://www.uniprot.org/uniprot/AGAC_ZOBGA AGAC_ZOBGA]] Cleaves the beta-1,4-linkages between beta-D-galactose and alpha-L-3,6-anhydro-galactose residues in agarose. Cleaves agarose in a random manner with retention of the anomeric-bond configuration, producing beta-anomers that give rise progressively to alpha-anomers when mutarotation takes place (By similarity). | [[http://www.uniprot.org/uniprot/AGAC_ZOBGA AGAC_ZOBGA]] Cleaves the beta-1,4-linkages between beta-D-galactose and alpha-L-3,6-anhydro-galactose residues in agarose. Cleaves agarose in a random manner with retention of the anomeric-bond configuration, producing beta-anomers that give rise progressively to alpha-anomers when mutarotation takes place (By similarity). | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Agars are sulfated galactans from red macroalgae and are composed of D-galactose (G unit) and L-galactose (L unit) alternatively linked by alpha-1,3 and beta-1,4 glycosidic bonds. These polysaccharides display high complexity, with numerous modifications of their backbone (e.g. presence of 3,6-anhydro-bridge (LA unit) and sulfations and methylation). Currently, bacterial polysaccharidases that hydrolyze agars (beta-agarases and beta-porphyranases) have been characterized on simple agarose and more rarely on porphyran, a polymer containing both agarobiose (G-LA) and porphyranobiose (GL6S) motifs. How bacteria can degrade complex agars remains therefore an open question. Here, we studied an enzyme from the marine bacterium Zobellia galactanivorans (ZgAgaC) that is distantly related to the glycoside hydrolase 16 (GH16) family beta-agarases and beta-porphyranases. Using a large red algae collection, we demonstrate that ZgAgaC hydrolyzes not only agarose but also complex agars from Ceramiales species. Using tandem MS analysis, we elucidated the structure of a purified hexasaccharide product, L6S-G-LA2Me-G(2Pentose)-LA2S-G, released by the activity of ZgAgaC on agar extracted from Osmundea pinnatifida By resolving the crystal structure of ZgAgaC at high resolution (1.3 A) and comparison with the structures of ZgAgaB and ZgPorA in complex with their respective substrates, we determined that ZgAgaC recognizes agarose via a mechanism different from that of classical beta-agarases. Moreover, we identified conserved residues involved in the binding of complex oligoagars and demonstrate a probable influence of the acidic polysaccharide's pH microenvironment on hydrolase activity. Finally, a phylogenetic analysis supported the notion that ZgAgaC homologs define a new GH16 subfamily distinct from beta-porphyranases and classical beta-agarases. | ||
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| + | The agar-specific hydrolase ZgAgaC from the marine bacterium Zobellia galactanivorans defines a new GH16 protein subfamily.,Naretto A, Fanuel M, Ropartz D, Rogniaux H, Larocque R, Czjzek M, Tellier C, Michel G J Biol Chem. 2019 Mar 7. pii: RA118.006609. doi: 10.1074/jbc.RA118.006609. PMID:30846563<ref>PMID:30846563</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6hy3" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Cytophaga drobachiensis barbeyron et al. 1998]] | ||
[[Category: Beta-agarase]] | [[Category: Beta-agarase]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
Revision as of 08:24, 20 March 2019
Three-dimensional structure of AgaC from Zobellia galactanivorans
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