5opj - Revision history

OCA at 16:57, 13 December 2023

OCA — Wed, 13 Dec 2023 16:57:32 GMT

←Older revision		Revision as of 16:57, 13 December 2023
Line 1:		Line 1:

-	==~~Rhamnogalacturonan lyase~~==	+	==Beta-L-arabinofuranosidase==
-	<StructureSection load='5opj' size='340' side='right' caption='[[5opj]], [[Resolution\|resolution]] 2.05Å' scene=''>	+	<StructureSection load='5opj' size='340' side='right'caption='[[5opj]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5opj]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_thetaiotaomicron"_distaso_1912 "bacillus~~ thetaiotaomicron~~" distaso 1912~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OPJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OPJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5opj]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron Bacteroides thetaiotaomicron]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OPJ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=AHR:ALPHA~~-~~L-ARABINOFURANOSE'>AHR</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.05Å</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=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">SAMN02910322_03495 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])~~</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=5opj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5opj OCA], [https://pdbe.org/5opj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5opj RCSB], [https://www.ebi.ac.uk/pdbsum/5opj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5opj 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=5opj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5opj OCA], [~~http~~://pdbe.org/5opj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5opj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5opj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5opj ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8AAW3_BACTN Q8AAW3_BACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ thetaiotaomicron ~~distaso 1912~~]]	+	[[Category: Bacteroides thetaiotaomicron]]
-	[[Category: ~~Basle, A~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Gilbert, H J]]~~	+	[[Category: Basle A]]
-	~~[[Category: Luis,~~ A S]]	+	[[Category: Gilbert HJ]]
-	[[Category: ~~Arabinan~~]]	+	[[Category: Luis AS]]
-	[[Category: ~~B theta]]~~	+
-	~~[[Category: Beta arbinofuranosidase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Pectin]]~~	+
-	~~[[Category: Rhamnogalacturonan i~~]]	+

OCA at 07:04, 12 December 2018

OCA — Wed, 12 Dec 2018 07:04:51 GMT

←Older revision		Revision as of 07:04, 12 December 2018
Line 3:		Line 3:
	<StructureSection load='5opj' size='340' side='right' caption='[[5opj]], [[Resolution\|resolution]] 2.05Å' scene=''>		<StructureSection load='5opj' size='340' side='right' caption='[[5opj]], [[Resolution\|resolution]] 2.05Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5opj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OPJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5opj]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_thetaiotaomicron"_distaso_1912 "bacillus thetaiotaomicron" distaso 1912]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OPJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SAMN02910322_03495 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=818 "Bacillus thetaiotaomicron" Distaso 1912])</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=5opj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5opj OCA], [http://pdbe.org/5opj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5opj RCSB], [http://www.ebi.ac.uk/pdbsum/5opj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5opj 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=5opj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5opj OCA], [http://pdbe.org/5opj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5opj RCSB], [http://www.ebi.ac.uk/pdbsum/5opj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5opj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The major nutrients available to human colonic Bacteroides species are glycans, exemplified by pectins, a network of covalently linked plant cell wall polysaccharides containing galacturonic acid (GalA). Metabolism of complex carbohydrates by the Bacteroides genus is orchestrated by polysaccharide utilization loci (PULs). In Bacteroides thetaiotaomicron, a human colonic bacterium, the PULs activated by different pectin domains have been identified; however, the mechanism by which these loci contribute to the degradation of these GalA-containing polysaccharides is poorly understood. Here we show that each PUL orchestrates the metabolism of specific pectin molecules, recruiting enzymes from two previously unknown glycoside hydrolase families. The apparatus that depolymerizes the backbone of rhamnogalacturonan-I is particularly complex. This system contains several glycoside hydrolases that trim the remnants of other pectin domains attached to rhamnogalacturonan-I, and nine enzymes that contribute to the degradation of the backbone that makes up a rhamnose-GalA repeating unit. The catalytic properties of the pectin-degrading enzymes are optimized to protect the glycan cues that activate the specific PULs ensuring a continuous supply of inducing molecules throughout growth. The contribution of Bacteroides spp. to metabolism of the pectic network is illustrated by cross-feeding between organisms.
		+
		+	Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides.,Luis AS, Briggs J, Zhang X, Farnell B, Ndeh D, Labourel A, Basle A, Cartmell A, Terrapon N, Stott K, Lowe EC, McLean R, Shearer K, Schuckel J, Venditto I, Ralet MC, Henrissat B, Martens EC, Mosimann SC, Abbott DW, Gilbert HJ Nat Microbiol. 2018 Feb;3(2):210-219. doi: 10.1038/s41564-017-0079-1. Epub 2017, Dec 18. PMID:29255254<ref>PMID:29255254</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5opj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus thetaiotaomicron distaso 1912]]
	[[Category: Basle, A]]		[[Category: Basle, A]]
	[[Category: Gilbert, H J]]		[[Category: Gilbert, H J]]

OCA at 06:20, 28 February 2018

OCA — Wed, 28 Feb 2018 06:20:12 GMT

←Older revision		Revision as of 06:20, 28 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5opj ~~is ON HOLD~~	+	==Rhamnogalacturonan lyase==
-		+	<StructureSection load='5opj' size='340' side='right' caption='[[5opj]], [[Resolution\|resolution]] 2.05Å' scene=''>
-	~~Authors~~: ~~Basle, A~~.~~, Luis, A~~.S.~~, Gilbert, H~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5opj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OPJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OPJ FirstGlance]. <br>
-	~~Description~~: ~~Rhamnogalacturonan lyase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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>
-	[[~~Category~~: ~~Gilbert~~, H.J]]	+	<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=5opj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5opj OCA], [http://pdbe.org/5opj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5opj RCSB], [http://www.ebi.ac.uk/pdbsum/5opj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5opj ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Luis~~, A.S]]	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Basle, A]]		[[Category: Basle, A]]
		+	[[Category: Gilbert, H J]]
		+	[[Category: Luis, A S]]
		+	[[Category: Arabinan]]
		+	[[Category: B theta]]
		+	[[Category: Beta arbinofuranosidase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Pectin]]
		+	[[Category: Rhamnogalacturonan i]]

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

OCA — Wed, 27 Sep 2017 12:41:05 GMT

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

←Older revision

Revision as of 12:41, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5opj is ON HOLD Authors: Basle, A., Luis, A.S., Gilbert, H.J. Description: Rhamnogalacturonan lyase Category: Unreleased Structures [[Category:...

OCA — Wed, 27 Sep 2017 12:41:04 GMT

New page: '''Unreleased structure''' The entry 5opj is ON HOLD Authors: Basle, A., Luis, A.S., Gilbert, H.J. Description: Rhamnogalacturonan lyase Category: Unreleased Structures [[Category:...

New page

'''Unreleased structure'''

The entry 5opj is ON HOLD

Authors: Basle, A., Luis, A.S., Gilbert, H.J.

Description: Rhamnogalacturonan lyase
[[Category: Unreleased Structures]]
[[Category: Gilbert, H.J]]
[[Category: Luis, A.S]]
[[Category: Basle, A]]