6yyi - Revision history

OCA at 13:38, 24 January 2024

OCA — Wed, 24 Jan 2024 13:38:25 GMT

←Older revision		Revision as of 13:38, 24 January 2024
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	<StructureSection load='6yyi' size='340' side='right'caption='[[6yyi]], [[Resolution\|resolution]] 2.67Å' scene=''>		<StructureSection load='6yyi' size='340' side='right'caption='[[6yyi]], [[Resolution\|resolution]] 2.67Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<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>	+	<table><tr><td colspan='2'>[[6yyi]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyoglomus_thermophilum_H-6-12 Dictyoglomus thermophilum H-6-12]. 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 [https://proteopedia.org/fgij/fg.htm?mol=6YYI FirstGlance]. <br>
-	</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>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.67Å</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='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='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'>[https://proteopedia.org/fgij/fg.htm?mol=6yyi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yyi OCA], [https://pdbe.org/6yyi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yyi RCSB], [https://www.ebi.ac.uk/pdbsum/6yyi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yyi ProSAT]</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>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B5YB78_DICT6 B5YB78_DICT6]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6yyi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6yyi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Xylosidase 3D structures\|Xylosidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dict6~~]]	+	[[Category: Dictyoglomus thermophilum H-6-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Xylan 1,4-beta-xylosidase]]~~	+	[[Category: Bretagne D]]
-	[[Category: Bretagne, D]]	+	[[Category: Daniellou R]]
-	[[Category: Daniellou, R]]	+	[[Category: Lafite P]]
-	[[Category: Lafite, P]]	+
-	~~[[Category: Carbohydrate substrate complex]]~~	+
-	~~[[Category: Hydrolase~~]]	+

OCA at 06:53, 9 December 2020

OCA — Wed, 09 Dec 2020 06:53:18 GMT

←Older revision		Revision as of 06:53, 9 December 2020
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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]]

OCA at 07:48, 2 December 2020

OCA — Wed, 02 Dec 2020 07:48:10 GMT

←Older revision		Revision as of 07:48, 2 December 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6yyi is ON HOLD until Paper Publication~~	+	==Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum bound to beta-D-xylopyranose==
-		+	<StructureSection load='6yyi' size='340' side='right'caption='[[6yyi]]' scene=''>
-	~~Authors: Lafite, P., Daniellou, R., Bretagne, D.~~	+	== 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>
-	~~Description:~~ Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum bound to beta-D-xylopyranose	+	</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>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Lafite~~, P]]	+	__TOC__
-	[[Category: Bretagne, D]]	+	</StructureSection>
-	[[Category: Daniellou, R]]	+	[[Category: Large Structures]]
		+	[[Category: Bretagne D]]
		+	[[Category: Daniellou R]]
		+	[[Category: Lafite P]]

OCA at 05:05, 10 June 2020

OCA — Wed, 10 Jun 2020 05:05:09 GMT

←Older revision		Revision as of 05:05, 10 June 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6yyi is ON HOLD	+	The entry 6yyi is ON HOLD until Paper Publication

	Authors: Lafite, P., Daniellou, R., Bretagne, D.		Authors: Lafite, P., Daniellou, R., Bretagne, D.

OCA: Protected "6yyi" [edit=sysop:move=sysop]

OCA — Wed, 13 May 2020 04:16:47 GMT

Protected "6yyi" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:16, 13 May 2020

OCA: New page: '''Unreleased structure''' The entry 6yyi is ON HOLD Authors: Lafite, P., Daniellou, R., Bretagne, D. Description: Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum...

OCA — Wed, 13 May 2020 04:16:46 GMT

New page: '''Unreleased structure''' The entry 6yyi is ON HOLD Authors: Lafite, P., Daniellou, R., Bretagne, D. Description: Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum...

New page

'''Unreleased structure'''

The entry 6yyi is ON HOLD

Authors: Lafite, P., Daniellou, R., Bretagne, D.

Description: Crystal structure of beta-D-xylosidase from Dictyoglomus thermophilum bound to beta-D-xylopyranose
[[Category: Unreleased Structures]]
[[Category: Lafite, P]]
[[Category: Bretagne, D]]
[[Category: Daniellou, R]]