1gny - Revision history

OCA at 06:28, 1 May 2024

OCA — Wed, 01 May 2024 06:28:22 GMT

←Older revision		Revision as of 06:28, 1 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GNY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GNY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.63Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [https://pdbe.org/1gny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [https://www.ebi.ac.uk/pdbsum/1gny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gny 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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [https://pdbe.org/1gny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [https://www.ebi.ac.uk/pdbsum/1gny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gny ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/XY10C_CELJA XY10C_CELJA] Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.<ref>PMID:14670951</ref> <ref>PMID:7492333</ref>		[https://www.uniprot.org/uniprot/XY10C_CELJA XY10C_CELJA] Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.<ref>PMID:14670951</ref> <ref>PMID:7492333</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The recycling of photosynthetically fixed carbon by the action of microbial glycoside hydrolases is a key biological process. The consortium of degradative enzymes involved in this process frequently display catalytic modules appended to one or more noncatalytic carbohydrate-binding modules (CBMs). CBMs play a central role in the optimization of the catalytic activity of plant cell wall hydrolases through their binding to specific plant structural polysaccharides. Despite their pivotal role in the biodegradation of plant biomass, the mechanism by which these proteins recognize their target ligands is unclear. This report describes the structure of a xylan-binding CBM (CBM15) in complex with its ligand. This module, derived from Pseudomonas cellulosa xylanase Xyn10C, binds to both soluble xylan and xylooligosaccharides. The three-dimensional crystal structure of CBM15 bound to xylopentaose has been solved by x-ray crystallography to a resolution of 1.6 A. The protein displays a similar beta-jelly roll fold to that observed in many other families of binding-modules. A groove, 20-25 A in length, on the concave surface of one of the beta-sheets presents two tryptophan residues, the faces of which are orientated at approximately 240 degrees to one another. These form-stacking interactions with the n and n+2 sugars of xylopentaose complementing the approximate 3-fold helical structure of this ligand in the binding cleft of CBM15. In four of the five observed binding subsites, the 2' and 3' hydroxyls of the bound ligand are solvent-exposed, providing an explanation for the capacity of this xylan-binding CBM to accommodate the highly decorated xylans found in the plant cell wall.
-
-	Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation.,Szabo L, Jamal S, Xie H, Charnock SJ, Bolam DN, Gilbert HJ, Davies GJ J Biol Chem. 2001 Dec 28;276(52):49061-5. Epub 2001 Oct 11. PMID:11598143<ref>PMID:11598143</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1gny" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:00, 11 January 2023

OCA — Wed, 11 Jan 2023 08:00:42 GMT

←Older revision		Revision as of 08:00, 11 January 2023
Line 3:		Line 3:
	<StructureSection load='1gny' size='340' side='right'caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='1gny' size='340' side='right'caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"cellvibrio_cellulosa"_nagy_et_al._2002 "cellvibrio cellulosa" nagy et al. 2002~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GNY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [https://pdbe.org/1gny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [https://www.ebi.ac.uk/pdbsum/1gny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gny 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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [https://pdbe.org/1gny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [https://www.ebi.ac.uk/pdbsum/1gny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gny ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/XY10C_CELJA XY10C_CELJA]] Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.<ref>PMID:14670951</ref> <ref>PMID:7492333</ref>	+	[https://www.uniprot.org/uniprot/XY10C_CELJA XY10C_CELJA] Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.<ref>PMID:14670951</ref> <ref>PMID:7492333</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cellvibrio ~~cellulosa nagy et al. 2002]]~~	+	[[Category: Cellvibrio japonicus]]
-	~~[[Category: Endo-1,4-beta-xylanase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bolam~~, D N~~]]	+	[[Category: Bolam DN]]
-	[[Category: Charnock~~, S J~~]]	+	[[Category: Charnock SJ]]
-	[[Category: Davies~~, G J~~]]	+	[[Category: Davies GJ]]
-	[[Category: Gilbert~~, H J~~]]	+	[[Category: Gilbert HJ]]
-	[[Category: Jamal, S]]	+	[[Category: Jamal S]]
-	[[Category: Szabo, S]]	+	[[Category: Szabo S]]
-	[[Category: Xie, H]]	+	[[Category: Xie H]]
-	~~[[Category: Carbohydrate-binding module]]~~	+
-	~~[[Category: Catalysis]]~~	+
-	~~[[Category: Xylan]]~~	+
-	~~[[Category: Xylanase]]~~	+
-	~~[[Category: Xylooligosaccharide~~]]	+

OCA at 11:02, 31 March 2021

OCA — Wed, 31 Mar 2021 11:02:50 GMT

←Older revision		Revision as of 11:02, 31 March 2021
Line 3:		Line 3:
	<StructureSection load='1gny' size='340' side='right'caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='1gny' size='340' side='right'caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca.weizmann.ac~~.~~il/oca-docs~~/fgij/fg.htm?mol=1GNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"cellvibrio_cellulosa"_nagy_et_al._2002 "cellvibrio cellulosa" nagy et al. 2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GNY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [~~http~~://pdbe.org/1gny PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1gny PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1gny 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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [https://pdbe.org/1gny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [https://www.ebi.ac.uk/pdbsum/1gny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gny ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/XY10C_CELJA XY10C_CELJA]] Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.<ref>PMID:14670951</ref> <ref>PMID:7492333</ref>	+	[[https://www.uniprot.org/uniprot/XY10C_CELJA XY10C_CELJA]] Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.<ref>PMID:14670951</ref> <ref>PMID:7492333</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cellvibrio cellulosa nagy et al. 2002]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 08:40, 26 June 2019

OCA — Wed, 26 Jun 2019 08:40:52 GMT

←Older revision		Revision as of 08:40, 26 June 2019
Line 1:		Line 1:

	==xylan-binding module CBM15==		==xylan-binding module CBM15==
-	<StructureSection load='1gny' size='340' side='right' caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>	+	<StructureSection load='1gny' size='340' side='right'caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GNY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GNY FirstGlance]. <br>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
		+	[[Category: Large Structures]]
	[[Category: Bolam, D N]]		[[Category: Bolam, D N]]
	[[Category: Charnock, S J]]		[[Category: Charnock, S J]]

OCA at 04:38, 21 September 2017

OCA — Thu, 21 Sep 2017 04:38:28 GMT

←Older revision		Revision as of 04:38, 21 September 2017
Line 1:		Line 1:
-	==~~XYLAN~~-~~BINDING MODULE~~ CBM15==	+
		+	==xylan-binding module CBM15==
	<StructureSection load='1gny' size='340' side='right' caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='1gny' size='340' side='right' caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/"cellvibrio_cellulosa"_nagy_et_al._2002 "cellvibrio cellulosa" nagy et al. 2002]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GNY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [http://pdbe.org/1gny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [http://www.ebi.ac.uk/pdbsum/1gny PDBsum]</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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [http://pdbe.org/1gny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [http://www.ebi.ac.uk/pdbsum/1gny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gny ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cellvibrio cellulosa nagy et al. 2002]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Bolam, D N]]		[[Category: Bolam, D N]]

OCA at 09:28, 11 September 2015

OCA — Fri, 11 Sep 2015 09:28:18 GMT

←Older revision		Revision as of 09:28, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1gny' size='340' side='right' caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='1gny' size='340' side='right' caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Cellvibrio_japonicus Cellvibrio japonicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"cellvibrio_cellulosa"_nagy_et_al._2002 "cellvibrio cellulosa" nagy et al. 2002]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GNY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</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/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [http://www.ebi.ac.uk/pdbsum/1gny PDBsum]</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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [http://pdbe.org/1gny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [http://www.ebi.ac.uk/pdbsum/1gny PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/XY10C_CELJA XY10C_CELJA]] Endo-acting xylanase which specifically cleaves internal linkages on the xylan backbone, releasing xylooligosaccharides. Is able to hydrolyze oat spelt xylan, the arabinoxylans from wheat and rye, and glucuronoxylan. Also displays very low activity against xylooligosaccharides. During the xylan degradation process, Xyn10C may act on the soluble xylans and long xylooligosaccharides products released by the secreted xylanases Xyn11A, Xyn11B and Xyn10A.<ref>PMID:14670951</ref> <ref>PMID:7492333</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1gny" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cellvibrio ~~japonicus~~]]	+	[[Category: Cellvibrio cellulosa nagy et al. 2002]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
	[[Category: Bolam, D N]]		[[Category: Bolam, D N]]

OCA at 23:54, 22 December 2014

OCA — Mon, 22 Dec 2014 23:54:27 GMT

←Older revision		Revision as of 23:54, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GNY FirstGlance]. <br>		<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GNY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [http://www.ebi.ac.uk/pdbsum/1gny PDBsum]</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=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [http://www.ebi.ac.uk/pdbsum/1gny PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	[[Category: Cellvibrio japonicus]]		[[Category: Cellvibrio japonicus]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
-	[[Category: Bolam, D N.]]	+	[[Category: Bolam, D N]]
-	[[Category: Charnock, S J.]]	+	[[Category: Charnock, S J]]
-	[[Category: Davies, G J.]]	+	[[Category: Davies, G J]]
-	[[Category: Gilbert, H J.]]	+	[[Category: Gilbert, H J]]
-	[[Category: Jamal, S.]]	+	[[Category: Jamal, S]]
-	[[Category: Szabo, S.]]	+	[[Category: Szabo, S]]
-	[[Category: Xie, H.]]	+	[[Category: Xie, H]]
	[[Category: Carbohydrate-binding module]]		[[Category: Carbohydrate-binding module]]
	[[Category: Catalysis]]		[[Category: Catalysis]]

OCA at 13:39, 28 September 2014

OCA — Sun, 28 Sep 2014 13:39:57 GMT

←Older revision		Revision as of 13:39, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1gny.~~png~~\|~~left\|200px~~]]	+	==XYLAN-BINDING MODULE CBM15==
		+	<StructureSection load='1gny' size='340' side='right' caption='[[1gny]], [[Resolution\|resolution]] 1.63Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1gny]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1GNY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=XYP:BETA-D-XYLOPYRANOSE'>XYP</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Endo-1,4-beta-xylanase Endo-1,4-beta-xylanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.8 3.2.1.8] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1gny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gny OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1gny RCSB], [http://www.ebi.ac.uk/pdbsum/1gny PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The recycling of photosynthetically fixed carbon by the action of microbial glycoside hydrolases is a key biological process. The consortium of degradative enzymes involved in this process frequently display catalytic modules appended to one or more noncatalytic carbohydrate-binding modules (CBMs). CBMs play a central role in the optimization of the catalytic activity of plant cell wall hydrolases through their binding to specific plant structural polysaccharides. Despite their pivotal role in the biodegradation of plant biomass, the mechanism by which these proteins recognize their target ligands is unclear. This report describes the structure of a xylan-binding CBM (CBM15) in complex with its ligand. This module, derived from Pseudomonas cellulosa xylanase Xyn10C, binds to both soluble xylan and xylooligosaccharides. The three-dimensional crystal structure of CBM15 bound to xylopentaose has been solved by x-ray crystallography to a resolution of 1.6 A. The protein displays a similar beta-jelly roll fold to that observed in many other families of binding-modules. A groove, 20-25 A in length, on the concave surface of one of the beta-sheets presents two tryptophan residues, the faces of which are orientated at approximately 240 degrees to one another. These form-stacking interactions with the n and n+2 sugars of xylopentaose complementing the approximate 3-fold helical structure of this ligand in the binding cleft of CBM15. In four of the five observed binding subsites, the 2' and 3' hydroxyls of the bound ligand are solvent-exposed, providing an explanation for the capacity of this xylan-binding CBM to accommodate the highly decorated xylans found in the plant cell wall.

-	~~{{STRUCTURE_1gny\| PDB=1gny \| SCENE= }}~~	+	Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation.,Szabo L, Jamal S, Xie H, Charnock SJ, Bolam DN, Gilbert HJ, Davies GJ J Biol Chem. 2001 Dec 28;276(52):49061-5. Epub 2001 Oct 11. PMID:11598143<ref>PMID:11598143</ref>

-	~~===XYLAN-BINDING MODULE CBM15===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11598143}}~~	+	== References ==
-		+	<references/>
-	==~~About this Structure~~==	+	__TOC__
-	~~[[1gny]] is a 1 chain structure with sequence from [http:~~//~~en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA].~~	+	</StructureSection>
	[[Category: Cellvibrio japonicus]]		[[Category: Cellvibrio japonicus]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]

OCA: Protected "1gny" [edit=sysop:move=sysop]

OCA — Wed, 21 Nov 2012 16:14:59 GMT

Protected "1gny" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:14, 21 November 2012

OCA at 16:14, 21 November 2012

OCA — Wed, 21 Nov 2012 16:14:56 GMT

←Older revision		Revision as of 16:14, 21 November 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1gny.png\|left\|200px]]		[[Image:1gny.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1gny", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
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	{{STRUCTURE_1gny\| PDB=1gny \| SCENE= }}		{{STRUCTURE_1gny\| PDB=1gny \| SCENE= }}

	===XYLAN-BINDING MODULE CBM15===		===XYLAN-BINDING MODULE CBM15===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11598143}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11598143 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_11598143}}		{{ABSTRACT_PUBMED_11598143}}

	==About this Structure==		==About this Structure==
-	~~1GNY is a~~ [[~~Single protein~~]] structure of sequence from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA].	+	[[1gny]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cellvibrio_japonicus Cellvibrio japonicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GNY OCA].
-		+
-	~~==Reference==~~	+
-	Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation., Szabo L, Jamal S, Xie H, Charnock SJ, Bolam DN, Gilbert HJ, Davies GJ, J Biol Chem. 2001 Dec 28;276(52):49061-5. Epub 2001 Oct 11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11598143 11598143]	+
	[[Category: Cellvibrio japonicus]]		[[Category: Cellvibrio japonicus]]
	[[Category: Endo-1,4-beta-xylanase]]		[[Category: Endo-1,4-beta-xylanase]]
-	[[Category: Single protein]]
	[[Category: Bolam, D N.]]		[[Category: Bolam, D N.]]
	[[Category: Charnock, S J.]]		[[Category: Charnock, S J.]]
Line 39:		Line 23:
	[[Category: Xylanase]]		[[Category: Xylanase]]
	[[Category: Xylooligosaccharide]]		[[Category: Xylooligosaccharide]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 1 05:34:58 2008''