5j90 - Revision history

OCA at 10:54, 6 September 2023

OCA — Wed, 06 Sep 2023 10:54:46 GMT

←Older revision		Revision as of 10:54, 6 September 2023
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	<StructureSection load='5j90' size='340' side='right'caption='[[5j90]], [[Resolution\|resolution]] 1.39Å' scene=''>		<StructureSection load='5j90' size='340' side='right'caption='[[5j90]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j90]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cytophaga_johnsonae Cytophaga johnsonae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J90 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5J90 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j90]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Flavobacterium_johnsoniae_UW101 Flavobacterium johnsoniae UW101]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J90 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J90 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</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]] 1.3932Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5j5u\|5j5u]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Fjoh_4558 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=376686 Cytophaga johnsonae])~~</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=5j90 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j90 OCA], [https://pdbe.org/5j90 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j90 RCSB], [https://www.ebi.ac.uk/pdbsum/5j90 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j90 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=5j90 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j90 OCA], [~~http~~://pdbe.org/5j90 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5j90 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5j90 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5j90 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A5FB66_FLAJ1 A5FB66_FLAJ1]
	<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: ~~Cytophaga johnsonae~~]]	+	[[Category: Flavobacterium johnsoniae UW101]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Koropatkin~~, N M]]~~	+	[[Category: Koropatkin NM]]
-	~~[[Category: Bacteroidete]]~~	+
-	~~[[Category: Chitin-binding]]~~	+
-	~~[[Category: Chitin-binding protein]]~~	+
-	~~[[Category: Flavobacterium johnsoniae]]~~	+
-	~~[[Category: Susd homolog~~]]	+

OCA at 07:34, 10 June 2020

OCA — Wed, 10 Jun 2020 07:34:25 GMT

←Older revision		Revision as of 07:34, 10 June 2020
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	==Structure of Fjoh_4558, a chitin-binding SusD homolog from Flavobacterium johnsoniae==		==Structure of Fjoh_4558, a chitin-binding SusD homolog from Flavobacterium johnsoniae==
-	<StructureSection load='5j90' size='340' side='right' caption='[[5j90]], [[Resolution\|resolution]] 1.39Å' scene=''>	+	<StructureSection load='5j90' size='340' side='right'caption='[[5j90]], [[Resolution\|resolution]] 1.39Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5j90]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J90 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5J90 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5j90]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cytophaga_johnsonae Cytophaga johnsonae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J90 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J90 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j5u\|5j5u]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j5u\|5j5u]]</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=5j90 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j90 OCA], [http://pdbe.org/5j90 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j90 RCSB], [http://www.ebi.ac.uk/pdbsum/5j90 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j90 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Fjoh_4558 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=376686 Cytophaga johnsonae])</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=5j90 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j90 OCA], [http://pdbe.org/5j90 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j90 RCSB], [http://www.ebi.ac.uk/pdbsum/5j90 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j90 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: Cytophaga johnsonae]]
		+	[[Category: Large Structures]]
	[[Category: Koropatkin, N M]]		[[Category: Koropatkin, N M]]
	[[Category: Bacteroidete]]		[[Category: Bacteroidete]]

OCA at 09:25, 10 March 2017

OCA — Fri, 10 Mar 2017 09:25:38 GMT

←Older revision		Revision as of 09:25, 10 March 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5j90 is ~~ON HOLD until Paper~~ Publication	+	==Structure of Fjoh_4558, a chitin-binding SusD homolog from Flavobacterium johnsoniae==
		+	<StructureSection load='5j90' size='340' side='right' caption='[[5j90]], [[Resolution\|resolution]] 1.39Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5j90]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J90 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J90 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5j5u\|5j5u]]</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=5j90 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j90 OCA], [http://pdbe.org/5j90 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j90 RCSB], [http://www.ebi.ac.uk/pdbsum/5j90 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j90 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Chitin is the second most abundant polysaccharide on earth and as such a great target for bioconversion applications. The phylum Bacteroidetes is one of nature's most ubiquitous bacterial lineages and is essential in the global carbon cycle with many members being highly efficient degraders of complex carbohydrates. However, despite their specialist reputation in carbohydrate conversion, mechanisms for degrading recalcitrant crystalline polysaccharides such as chitin and cellulose are hitherto unknown. RESULTS: Here we describe a complete functional analysis of a novel polysaccharide utilization locus (PUL) in the soil Bacteroidete Flavobacterium johnsoniae, tailored for conversion of chitin. The F. johnsoniae chitin utilization locus (ChiUL) consists of eleven contiguous genes encoding carbohydrate capture and transport proteins, enzymes, and a two-component sensor-regulator system. The key chitinase (ChiA) encoded by ChiUL is atypical in terms of known Bacteroidetes-affiliated PUL mechanisms as it is not anchored to the outer cell membrane and consists of multiple catalytic domains. We demonstrate how the extraordinary hydrolytic efficiency of ChiA derives from synergy between its multiple chitinolytic (endo- and exo-acting) and previously unidentified chitin-binding domains. Reverse genetics show that ChiA and PUL-encoded proteins involved in sugar binding, import, and chitin sensing are essential for efficient chitin utilization. Surprisingly, the ChiUL encodes two pairs of SusC/D-like outer membrane proteins. Ligand-binding and structural studies revealed functional differences between the two SusD-like proteins that enhance scavenging of chitin from the environment. The combined results from this study provide insight into the mechanisms employed by Bacteroidetes to degrade recalcitrant polysaccharides and reveal important novel aspects of the PUL paradigm. CONCLUSIONS: By combining reverse genetics to map essential PUL genes, structural studies on outer membrane chitin-binding proteins, and enzymology, we provide insight into the mechanisms employed by Bacteroidetes to degrade recalcitrant polysaccharides and introduce a new saccharolytic mechanism used by the phylum Bacteroidetes. The presented discovery and analysis of the ChiUL will greatly benefit future enzyme discovery efforts as well as studies regarding enzymatic intramolecular synergism.

-	~~Authors:~~ Koropatkin, N.M.	+	A polysaccharide utilization locus from Flavobacterium johnsoniae enables conversion of recalcitrant chitin.,Larsbrink J, Zhu Y, Kharade SS, Kwiatkowski KJ, Eijsink VG, Koropatkin NM, McBride MJ, Pope PB Biotechnol Biofuels. 2016 Nov 28;9:260. eCollection 2016. PMID:27933102<ref>PMID:27933102</ref>

-	~~Description: Structure of Fjoh_4558~~, a ~~chitin~~-binding ~~SusD homolog from Flavobacterium johnsoniae~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: ~~Koropatkin, N.M~~]]	+	<div class="pdbe-citations 5j90" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Koropatkin, N M]]
		+	[[Category: Bacteroidete]]
		+	[[Category: Chitin-binding]]
		+	[[Category: Chitin-binding protein]]
		+	[[Category: Flavobacterium johnsoniae]]
		+	[[Category: Susd homolog]]

OCA at 13:13, 1 June 2016

OCA — Wed, 01 Jun 2016 13:13:35 GMT

←Older revision		Revision as of 13:13, 1 June 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5j90 is ON HOLD	+	The entry 5j90 is ON HOLD until Paper Publication

	Authors: Koropatkin, N.M.		Authors: Koropatkin, N.M.

OCA: Protected "5j90" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:41:46 GMT

Protected "5j90" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:41, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5j90 is ON HOLD Authors: Koropatkin, N.M. Description: Structure of Fjoh_4558, a chitin-binding SusD homolog from Flavobacterium johnsoniae [[Categ...

OCA — Wed, 11 May 2016 01:41:45 GMT

New page: '''Unreleased structure''' The entry 5j90 is ON HOLD Authors: Koropatkin, N.M. Description: Structure of Fjoh_4558, a chitin-binding SusD homolog from Flavobacterium johnsoniae [[Categ...

New page

'''Unreleased structure'''

The entry 5j90 is ON HOLD

Authors: Koropatkin, N.M.

Description: Structure of Fjoh_4558, a chitin-binding SusD homolog from Flavobacterium johnsoniae
[[Category: Unreleased Structures]]
[[Category: Koropatkin, N.M]]