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==Crystal structure of SCLam, a non-specific endo-beta-1,3(4)-glucanase from family GH16== | ==Crystal structure of SCLam, a non-specific endo-beta-1,3(4)-glucanase from family GH16== | ||
<StructureSection load='6xof' size='340' side='right'caption='[[6xof]]' scene=''> | <StructureSection load='6xof' size='340' side='right'caption='[[6xof]], [[Resolution|resolution]] 1.50Å' 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=6XOF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XOF FirstGlance]. <br> | <table><tr><td colspan='2'>[[6xof]] 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=6XOF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XOF 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=6xof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xof OCA], [https://pdbe.org/6xof PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xof RCSB], [https://www.ebi.ac.uk/pdbsum/6xof PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xof 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></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=6xof FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xof OCA], [https://pdbe.org/6xof PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xof RCSB], [https://www.ebi.ac.uk/pdbsum/6xof PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xof ProSAT]</span></td></tr> | |||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:33556371</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6xof" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Glucan endo-1,3-beta-D-glucosidase]] | |||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Bernardes A]] | [[Category: Uncultivated bacterium]] | ||
[[Category: Liberato | [[Category: Bernardes, A]] | ||
[[Category: Polikarpov I]] | [[Category: Liberato, M V]] | ||
[[Category: Squina F]] | [[Category: Polikarpov, I]] | ||
[[Category: Squina, F]] | |||
[[Category: Beta-glucan]] | |||
[[Category: Endo-1]] | |||
[[Category: Hydrolase]] | |||
[[Category: Metagenomic]] | |||
Revision as of 09:27, 25 August 2021
Crystal structure of SCLam, a non-specific endo-beta-1,3(4)-glucanase from family GH16Crystal structure of SCLam, a non-specific endo-beta-1,3(4)-glucanase from family GH16
Structural highlights
Publication Abstract from PubMedGlycoside 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. References
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