5nok - Revision history

OCA at 13:16, 15 November 2023

2023-11-15T13:16:02Z

←Older revision		Revision as of 13:16, 15 November 2023
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	<StructureSection load='5nok' size='340' side='right'caption='[[5nok]], [[Resolution\|resolution]] 2.24Å' scene=''>		<StructureSection load='5nok' size='340' side='right'caption='[[5nok]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nok]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5NOK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nok]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_cellulosilyticus_DSM_14838 Bacteroides cellulosilyticus DSM 14838]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NOK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MES:2-(N~~-~~MORPHOLINO)-ETHANESULFONIC+ACID'>MES</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]] 2.24Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=5nok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nok OCA], [~~http~~://pdbe.org/5nok PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5nok RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5nok PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5nok 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=5nok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nok OCA], [https://pdbe.org/5nok PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5nok RCSB], [https://www.ebi.ac.uk/pdbsum/5nok PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5nok ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E2N9D0_9BACE E2N9D0_9BACE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides cellulosilyticus DSM 14838]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Basle, A]]	+	[[Category: Basle A]]
-	[[Category: Cartmell, A]]	+	[[Category: Cartmell A]]
-	[[Category: Gilbert~~, H J~~]]	+	[[Category: Gilbert HJ]]
-	[[Category: Henrissat, B]]	+	[[Category: Henrissat B]]
-	[[Category: Munoz-Munoz, J]]	+	[[Category: Munoz-Munoz J]]
-	[[Category: Terrapon, N]]	+	[[Category: Terrapon N]]
-	~~[[Category: Arabinogalactan]]~~	+
-	~~[[Category: Glucuronic acid]]~~	+
-	~~[[Category: L-rhamnose]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Polysaccharide lyase~~]]	+

OCA at 12:08, 26 August 2020

2020-08-26T12:08:59Z

←Older revision		Revision as of 12:08, 26 August 2020
Line 1:		Line 1:

	==Polysaccharide Lyase BACCELL_00875==		==Polysaccharide Lyase BACCELL_00875==
-	<StructureSection load='5nok' size='340' side='right' caption='[[5nok]], [[Resolution\|resolution]] 2.24Å' scene=''>	+	<StructureSection load='5nok' size='340' side='right'caption='[[5nok]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5nok]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NOK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5nok]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5NOK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=5nok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nok OCA], [http://pdbe.org/5nok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nok RCSB], [http://www.ebi.ac.uk/pdbsum/5nok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nok 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=5nok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nok OCA], [http://pdbe.org/5nok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nok RCSB], [http://www.ebi.ac.uk/pdbsum/5nok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nok ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Basle, A]]		[[Category: Basle, A]]
	[[Category: Cartmell, A]]		[[Category: Cartmell, A]]

OCA at 11:07, 24 August 2017

2017-08-24T11:07:00Z

←Older revision		Revision as of 11:07, 24 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5nok is ~~ON HOLD until Paper~~ Publication	+	==Polysaccharide Lyase BACCELL_00875==
		+	<StructureSection load='5nok' size='340' side='right' caption='[[5nok]], [[Resolution\|resolution]] 2.24Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5nok]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NOK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NOK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=5nok FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5nok OCA], [http://pdbe.org/5nok PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5nok RCSB], [http://www.ebi.ac.uk/pdbsum/5nok PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5nok ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represents a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis we screened the potential enzymatic functions of hypothetical proteins encoded by genes of Bacteroides thetaiotaomicron that were up-regulated by arabinogalactan proteins or AGPs. Although AGPs are ubiquitous in plants, there is a paucity of information on their detailed structure, the function of these glycans in planta, and the mechanisms by which they are depolymerized in microbial ecosystems. Here we have discovered a new polysaccharide lyase family that is specific for the l-rhamnose-alpha1,4-d-glucuronic acid linkage that caps the side chains of complex AGPs. The reaction product generated by the lyase, Delta4,5-unsaturated uronic acid, is removed from AGP by a glycoside hydrolase located in family GH105, producing the final product 4-deoxy-beta-l-threo-hex-4-enepyranosyl-uronic acid. The crystal structure of a member of the novel lyase family revealed a catalytic domain that displays an (alpha/alpha)6 barrel-fold. In the center of the barrel is a deep pocket, which, based on mutagenesis data and amino acid conservation, comprises the active site of the lyase. A tyrosine is the proposed catalytic base in the beta-elimination reaction. This study illustrates how highly complex glycans can be used as a scaffold to discover new enzyme families within microbial ecosystems where carbohydrate metabolism is a major evolutionary driver.

-	~~Authors: Cartmell, A~~., Munoz-Munoz, J., ~~Terrapon~~, N., Basle, A., Henrissat, B., Gilbert~~, H.~~J.	+	An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins.,Munoz-Munoz J, Cartmell A, Terrapon N, Basle A, Henrissat B, Gilbert HJ J Biol Chem. 2017 Aug 11;292(32):13271-13283. doi: 10.1074/jbc.M117.794578. Epub , 2017 Jun 21. PMID:28637865<ref>PMID:28637865</ref>

-	~~Description~~: ~~Polysaccharide Lyase BACCELL_00875~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5nok" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Basle, A]]
		+	[[Category: Cartmell, A]]
		+	[[Category: Gilbert, H J]]
	[[Category: Henrissat, B]]		[[Category: Henrissat, B]]
-	[[Category: Terrapon, N]]
	[[Category: Munoz-Munoz, J]]		[[Category: Munoz-Munoz, J]]
-	[[Category: ~~Cartmell~~, A]]	+	[[Category: Terrapon, N]]
-	[[Category: ~~Basle, A~~]]	+	[[Category: Arabinogalactan]]
-	[[Category: ~~Gilbert, H.J~~]]	+	[[Category: Glucuronic acid]]
		+	[[Category: L-rhamnose]]
		+	[[Category: Lyase]]
		+	[[Category: Polysaccharide lyase]]

OCA: Protected "5nok" [edit=sysop:move=sysop]

2017-04-19T09:44:36Z

Protected "5nok" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:44, 19 April 2017

OCA: New page: '''Unreleased structure''' The entry 5nok is ON HOLD until Paper Publication Authors: Cartmell, A., Munoz-Munoz, J., Terrapon, N., Basle, A., Henrissat, B., Gilbert, H.J. Description: ...

2017-04-19T09:44:35Z

New page: '''Unreleased structure''' The entry 5nok is ON HOLD until Paper Publication Authors: Cartmell, A., Munoz-Munoz, J., Terrapon, N., Basle, A., Henrissat, B., Gilbert, H.J. Description: ...

New page

'''Unreleased structure'''

The entry 5nok is ON HOLD until Paper Publication

Authors: Cartmell, A., Munoz-Munoz, J., Terrapon, N., Basle, A., Henrissat, B., Gilbert, H.J.

Description: Polysaccharide Lyase BACCELL_00875
[[Category: Unreleased Structures]]
[[Category: Henrissat, B]]
[[Category: Terrapon, N]]
[[Category: Munoz-Munoz, J]]
[[Category: Cartmell, A]]
[[Category: Basle, A]]
[[Category: Gilbert, H.J]]