OCA at 07:07, 5 December 2018

OCA — Wed, 05 Dec 2018 07:07:42 GMT

←Older revision		Revision as of 07:07, 5 December 2018
Line 1:		Line 1:

-	==~~GH5~~ with ~~ligand XXXG2FDNP~~==	+	==Structure of an endo-Xyloglucanase from Cellvibrio japonicus complexed with XXXG(2F)-beta-DNP==
	<StructureSection load='6ha9' size='340' side='right' caption='[[6ha9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='6ha9' size='340' side='right' caption='[[6ha9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ha9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HA9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ha9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Celju Celju]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HA9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NFG:2,4-DINITROPHENYL+2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANOSIDE'>NFG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NFG:2,4-DINITROPHENYL+2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANOSIDE'>NFG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Cellulase Cellulase~~], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.4 3.2.1.4] </span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cel5D, CJA_3010 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=498211 CELJU])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xyloglucan-specific_endo-beta-1,4-glucanase Xyloglucan-specific endo-beta-1,4-glucanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.151 3.2.1.151] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ha9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ha9 OCA], [http://pdbe.org/6ha9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ha9 RCSB], [http://www.ebi.ac.uk/pdbsum/6ha9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ha9 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ha9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ha9 OCA], [http://pdbe.org/6ha9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ha9 RCSB], [http://www.ebi.ac.uk/pdbsum/6ha9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ha9 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Xyloglucan (XyG) is a complex polysaccharide that is ubiquitous and often abundant in the cell walls of terrestrial plants. XyG metabolism is therefore a key component of the global carbon cycle, and hence XyG enzymology is of significant fundamental and applied importance in biomass conversion. To facilitate structure-function analyses of XyG-specific endo-glucanases, we have synthesized a 2',4'-dinitrophenyl 2-deoxy-2-fluoro-beta-glycoside mechanism-based inhibitor based on the highly branched XyG repeating motif XXXG (Xyl3Glc4: ([alpha-d-Xylp-(1-->6)]-beta-d-Glcp-(1-->4)-[alpha-d-Xylp-(1-->6)]-beta-d-Glcp-(1 -->4)-[alpha-d-Xylp-(1-->6)]-beta-d-Glcp-(1-->4)-d-Glcp. Key steps in the chemo-enzymatic synthesis included selective enzyme hydrolysis of XyG polysaccharide to produce the core heptasaccharide, per-O-acetylation, alpha-bromination, reductive glycal formation, electrophilic fluorination, SNAr glycosylation, and Zemplen deprotection. The resulting compound, XXXG(2F)-beta-DNP, specifically labelled the active sites of several endo-(xylo)glucanases by accumulation of a covalent glycosyl-enzyme intermediate, as revealed by intact protein mass spectrometry. Crystallography of a complex with a Cellvibrio japonicus Glycoside Hydrolase Family 5 (GH5) endo-xyloglucanase corroborated the covalent nature of the intermediate, and further revealed the anticipated specificity for the catalytic nucleophile of this anomeric-configuration-retaining glycosidase. This specificity complements that of an analogous XXXG N-bromoacetylglycosylamine inhibitor, which labelled the catalytic acid-base sidechain in the same enzyme [Attia, et al., Biotechnol. Biofuels, 2018, 11, 45]. We anticipate that these inhibitors may find continued use in mechanistic analyses of endo-(xylo)glucanases from diverse GH families.
		+
		+	Synthesis and application of a highly branched, mechanism-based 2-deoxy-2-fluoro-oligosaccharide inhibitor of endo-xyloglucanases.,Jain N, Attia MA, Offen WA, Davies GJ, Brumer H Org Biomol Chem. 2018 Nov 21;16(45):8732-8741. doi: 10.1039/c8ob02250j. PMID:30387796<ref>PMID:30387796</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ha9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cellulase~~]]	+	[[Category: Celju]]
		+	[[Category: Xyloglucan-specific endo-beta-1,4-glucanase]]
	[[Category: Davies, G J]]		[[Category: Davies, G J]]
	[[Category: Offen, W A]]		[[Category: Offen, W A]]

OCA at 07:54, 3 October 2018

OCA — Wed, 03 Oct 2018 07:54:37 GMT

←Older revision		Revision as of 07:54, 3 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ha9 is ~~ON HOLD~~	+	==GH5 with ligand XXXG2FDNP==
-		+	<StructureSection load='6ha9' size='340' side='right' caption='[[6ha9]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ha9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HA9 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NFG:2,4-DINITROPHENYL+2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANOSIDE'>NFG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cellulase Cellulase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.4 3.2.1.4] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ha9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ha9 OCA], [http://pdbe.org/6ha9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ha9 RCSB], [http://www.ebi.ac.uk/pdbsum/6ha9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ha9 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cellulase]]
		+	[[Category: Davies, G J]]
		+	[[Category: Offen, W A]]
		+	[[Category: 4-glucanase]]
		+	[[Category: Endo-beta-1]]
		+	[[Category: Glycoside hydrolase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Xyloglucan]]

OCA: Protected "6ha9" [edit=sysop:move=sysop]

OCA — Wed, 15 Aug 2018 15:02:18 GMT

Protected "6ha9" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:02, 15 August 2018

OCA: New page: '''Unreleased structure''' The entry 6ha9 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 15 Aug 2018 15:02:17 GMT

New page: '''Unreleased structure''' The entry 6ha9 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ha9 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6ha9 - Revision history

OCA at 07:07, 5 December 2018

OCA at 07:54, 3 October 2018

OCA: Protected "6ha9" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6ha9 is ON HOLD Authors: Description: Category: Unreleased Structures