7bm6
From Proteopedia
(Difference between revisions)
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==Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium Zobellia galactanivorans DsijT== | ==Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium Zobellia galactanivorans DsijT== | ||
| - | <StructureSection load='7bm6' size='340' side='right'caption='[[7bm6]]' scene=''> | + | <StructureSection load='7bm6' size='340' side='right'caption='[[7bm6]], [[Resolution|resolution]] 2.16Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BM6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7bm6]] is a 2 chain structure with sequence from [https://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=7BM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BM6 FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7bm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bm6 OCA], [https://pdbe.org/7bm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bm6 RCSB], [https://www.ebi.ac.uk/pdbsum/7bm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bm6 ProSAT]</span></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MAV:ALPHA-D-MANNOPYRANURONIC+ACID'>MAV</scene>, <scene name='pdbligand=MAW:4-DEOXY-ALPHA-L-ERYTHRO-HEX-4-ENOPYRANURONIC+ACID'>MAW</scene></td></tr> |
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">alyA3, zobellia_2624 ([https://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'>[https://en.wikipedia.org/wiki/Poly(beta-D-mannuronate)_lyase Poly(beta-D-mannuronate) lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.2.3 4.2.2.3] </span></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7bm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bm6 OCA], [https://pdbe.org/7bm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bm6 RCSB], [https://www.ebi.ac.uk/pdbsum/7bm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bm6 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Alginate is a major compound of brown macroalgae and as such an important carbon and energy source for heterotrophic marine bacteria. Despite the rather simple composition of alginate only comprising mannuronate and guluronate units, these bacteria feature complex alginolytic systems that can contain up to seven alginate lyases. This reflects the necessity of large enzyme systems for the complete degradation of the abundant substrate. Numerous alginate lyases have been characterized. They belong to different polysaccharide lyase (PL) families, but only one crystal structure of a family 17 (PL17) alginate lyase has been reported to date, namely Alg17c from the gammaproteobacterium Saccharophagus degradans. Biochemical and structural characterizations are helpful to link sequence profiles to function, evolution of functions and niche-specific characteristics. Here we combined detailed biochemical and crystallographic analysis of AlyA3, a PL17 alginate lyase from the marine flavobacteria Zobellia galactanivorans DsijT, providing the first structure of a PL17 in the Bacteroidetes phylum. AlyA3 is exo-lytic and highly specific of mannuronate stretches. As part of an "alginate utilizing locus", its activity is complementary to that of other characterized alginate lyases from the same bacterium. Structural comparison with Alg17c highlights a common mode of action for exo-lytic cleavage of the substrate, strengthening our understanding of the PL17 catalytic mechanism. We show that unlike Alg17c, AlyA3 contains an inserted flexible loop at the entrance to the catalytic groove, likely involved in substrate recognition, processivity and turn over. | ||
| + | |||
| + | Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium Zobellia galactanivorans DsijT.,Jouanneau D, Klau LJ, Larocque R, Jaffrennou A, Duval G, Le Duff N, Roret T, Jeudy A, Aachmann FL, Czjzek M, Thomas F Glycobiology. 2021 Jun 28. pii: 6302544. doi: 10.1093/glycob/cwab058. PMID:34184062<ref>PMID:34184062</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7bm6" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Cytophaga drobachiensis barbeyron et al. 1998]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Czjzek M]] | + | [[Category: Czjzek, M]] |
| - | [[Category: Jeudy A]] | + | [[Category: Duff, N Le]] |
| - | [[Category: Jouanneau D]] | + | [[Category: Jeudy, A]] |
| - | [[Category: | + | [[Category: Jouanneau, D]] |
| - | [[Category: | + | [[Category: Roret, T]] |
| + | [[Category: Alginate lyase]] | ||
| + | [[Category: Delta-guluronate complex]] | ||
| + | [[Category: Exo-acting marine enzyme]] | ||
| + | [[Category: Family pl17]] | ||
| + | [[Category: Hydrolase]] | ||
Revision as of 06:27, 1 December 2021
Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium Zobellia galactanivorans DsijT
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