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| | <StructureSection load='6xql' size='340' side='right'caption='[[6xql]], [[Resolution|resolution]] 1.97Å' scene=''> | | <StructureSection load='6xql' size='340' side='right'caption='[[6xql]], [[Resolution|resolution]] 1.97Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6xql]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultivated_bacterium Uncultivated bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6xql]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XQL FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.97Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6xof|6xof]], [[6xqg|6xqg]], [[6xqh|6xqh]], [[6xqf|6xqf]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">sclam ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=77133 uncultivated bacterium])</td></tr> | + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Glucan_endo-1,3-beta-D-glucosidase Glucan endo-1,3-beta-D-glucosidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.39 3.2.1.39] </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=6xql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xql OCA], [https://pdbe.org/6xql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xql RCSB], [https://www.ebi.ac.uk/pdbsum/6xql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xql ProSAT]</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=6xql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xql OCA], [https://pdbe.org/6xql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xql RCSB], [https://www.ebi.ac.uk/pdbsum/6xql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xql ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/A0A0B5H9B3_9BACT A0A0B5H9B3_9BACT] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6xql" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6xql" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Glucanase 3D structures|Glucanase 3D structures]] |
| | + | *[[Laminarase 3D structures|Laminarase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Glucan endo-1,3-beta-D-glucosidase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Uncultivated bacterium]] | + | [[Category: Uncultured bacterium]] |
| - | [[Category: Liberato, M V]] | + | [[Category: Liberato MV]] |
| - | [[Category: Squina, F]] | + | [[Category: Squina F]] |
| - | [[Category: Endo-1]]
| + | |
| - | [[Category: Glycoside hydrolase]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Metagenome]]
| + | |
| - | [[Category: Transglycosylation]]
| + | |
| Structural highlights
Function
A0A0B5H9B3_9BACT
Publication Abstract from PubMed
Glycoside hydrolases (GHs) are involved in the degradation of a wide diversity of carbohydrates and present several biotechnological applications. Many GH families are composed of enzymes with a single well-defined specificity. In contrast, enzymes from the GH16 family can act on a range of different polysaccharides, including beta-glucans and galactans. SCLam, a GH16 member derived from a soil metagenome, an endo-beta-1,3(4)-glucanase (EC 3.2.1.6), can cleave both beta-1,3 and beta-1,4 glycosidic bonds in glucans, such as laminarin, barley beta-glucan, and cello-oligosaccharides. A similar cleavage pattern was previously reported for other GH16 family members. However, the molecular mechanisms for this dual cleavage activity on (1,3)- and (1,4)-beta-D-glycosidic bonds by laminarinases have not been elucidated. In this sense, we determined the X-ray structure of a presumably inactive form of SCLam cocrystallized with different oligosaccharides. The solved structures revealed general bound products that are formed owing to residual activities of hydrolysis and transglycosylation. Biochemical and biophysical analyses and molecular dynamics simulations help to rationalize differences in activity toward different substrates. Our results depicted a bulky aromatic residue near the catalytic site critical to select the preferable configuration of glycosidic bonds in the binding cleft. Altogether, these data contribute to understanding the structural basis of recognition and hydrolysis of beta-1,3 and beta-1,4 glycosidic linkages of the laminarinase enzyme class, which is valuable for future studies on the GH16 family members and applications related to biomass conversion into feedstocks and bioproducts.
Insights into the dual cleavage activity of the GH16 laminarinase enzyme class on beta-1,3 and beta-1,4 glycosidic bonds.,Liberato MV, Teixeira Prates E, Goncalves TA, Bernardes A, Vilela N, Fattori J, Ematsu GC, Chinaglia M, Machi Gomes ER, Migliorini Figueira AC, Damasio A, Polikarpov I, Skaf MS, Squina FM J Biol Chem. 2021 Jan-Jun;296:100385. doi: 10.1016/j.jbc.2021.100385. Epub 2021, Feb 5. PMID:33556371[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Liberato MV, Teixeira Prates E, Goncalves TA, Bernardes A, Vilela N, Fattori J, Ematsu GC, Chinaglia M, Machi Gomes ER, Migliorini Figueira AC, Damasio A, Polikarpov I, Skaf MS, Squina FM. Insights into the dual cleavage activity of the GH16 laminarinase enzyme class on beta-1,3 and beta-1,4 glycosidic bonds. J Biol Chem. 2021 Jan-Jun;296:100385. doi: 10.1016/j.jbc.2021.100385. Epub 2021, Feb 5. PMID:33556371 doi:http://dx.doi.org/10.1016/j.jbc.2021.100385
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