6yyi
From Proteopedia
(Difference between revisions)
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==Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum bound to beta-D-xylopyranose== | ==Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum bound to beta-D-xylopyranose== | ||
| - | <StructureSection load='6yyi' size='340' side='right'caption='[[6yyi]]' scene=''> | + | <StructureSection load='6yyi' size='340' side='right'caption='[[6yyi]], [[Resolution|resolution]] 2.67Å' 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=6YYI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YYI FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6yyi]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Dict6 Dict6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YYI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YYI FirstGlance]. <br> |
| - | </td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6yyi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yyi OCA], [http://pdbe.org/6yyi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yyi RCSB], [http://www.ebi.ac.uk/pdbsum/6yyi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yyi 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=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr> |
| + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">DICTH_1792 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=309799 DICT6])</td></tr> | ||
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xylan_1,4-beta-xylosidase Xylan 1,4-beta-xylosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.37 3.2.1.37] </span></td></tr> | ||
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6yyi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yyi OCA], [http://pdbe.org/6yyi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yyi RCSB], [http://www.ebi.ac.uk/pdbsum/6yyi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yyi ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Dictyoglomus thermophilum beta-d-xylosidase DtXyl is attractive as a potential thermostable biocatalyst able to produce biologically active ginsenosides intermediates from beta-(1,2)-D-xylosylated compounds, including Notoginsenoside-R1. DtXyl was expressed as an active N-terminal His-tagged protein, and its crystal structure was solved in presence or absence of d-xylose product. Modelling of notoginsenoside R1 in DtXyl active site led to the identification of several hydrophobic residues interacting in close contact to the substrate hydrophobic core. Unlike other residues involved in substrate binding, these residues are not conserved among GH39 xylosidase family, and their physico-chemical properties can be correlated to the efficient binding and subsequent hydrolysis of Notoginsenoside R1. | ||
| + | |||
| + | Crystal structure of Dictyoglomus thermophilum beta-d-xylosidase DtXyl unravels the structural determinants for efficient notoginsenoside R1 hydrolysis.,Bretagne D, Paris A, de Vaumas R, Lafite P, Daniellou R Biochimie. 2020 Nov 23;181:34-41. doi: 10.1016/j.biochi.2020.11.017. PMID:33242495<ref>PMID:33242495</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6yyi" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| + | [[Category: Dict6]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| - | [[Category: Bretagne D]] | + | [[Category: Xylan 1,4-beta-xylosidase]] |
| - | [[Category: Daniellou R]] | + | [[Category: Bretagne, D]] |
| - | [[Category: Lafite P]] | + | [[Category: Daniellou, R]] |
| + | [[Category: Lafite, P]] | ||
| + | [[Category: Carbohydrate substrate complex]] | ||
| + | [[Category: Hydrolase]] | ||
Revision as of 06:53, 9 December 2020
Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum bound to beta-D-xylopyranose
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