5fq0 - Revision history

OCA at 13:18, 26 July 2023

OCA — Wed, 26 Jul 2023 13:18:04 GMT

←Older revision		Revision as of 13:18, 26 July 2023
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	<StructureSection load='5fq0' size='340' side='right'caption='[[5fq0]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5fq0' size='340' side='right'caption='[[5fq0]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fq0]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Halsx Halsx~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQ0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FQ0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fq0]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Halomonas_sp. Halomonas sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FQ0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>~~, ~~<scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5fpx\|5fpx]]~~, ~~[[5fpz\|5fpz]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=5fq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq0 OCA], [~~http~~://pdbe.org/5fq0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fq0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fq0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fq0 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=5fq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq0 OCA], [https://pdbe.org/5fq0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fq0 RCSB], [https://www.ebi.ac.uk/pdbsum/5fq0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fq0 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A182DWD1_HALSX A0A182DWD1_HALSX]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Halsx~~]]	+	[[Category: Halomonas sp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Abbott~~, D W~~]]	+	[[Category: Abbott DW]]
-	[[Category: Abe~~, K T~~]]	+	[[Category: Abe KT]]
-	[[Category: Barr, C]]	+	[[Category: Barr C]]
-	[[Category: Boraston~~, A B~~]]	+	[[Category: Boraston AB]]
-	[[Category: Hehemann~~, J H~~]]	+	[[Category: Hehemann JH]]
-	[[Category: Hobbs~~, J K~~]]	+	[[Category: Hobbs JK]]
-	[[Category: Hof, F]]	+	[[Category: Hof F]]
-	[[Category: Lee~~, S M~~]]	+	[[Category: Lee SM]]
-	[[Category: McLean, R]]	+	[[Category: McLean R]]
-	[[Category: Robb, M]]	+	[[Category: Robb M]]
-	~~[[Category: Alginate]]~~	+
-	~~[[Category: Cupin]]~~	+
-	~~[[Category: Kdgf]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Pectin]]~~	+
-	~~[[Category: Uronate sugar metabolism~~]]	+

OCA at 07:31, 6 May 2020

OCA — Wed, 06 May 2020 07:31:43 GMT

←Older revision		Revision as of 07:31, 6 May 2020
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	==The structure of KdgF from Halomonas sp.==		==The structure of KdgF from Halomonas sp.==
-	<StructureSection load='5fq0' size='340' side='right' caption='[[5fq0]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5fq0' size='340' side='right'caption='[[5fq0]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fq0]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FQ0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fq0]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Halsx Halsx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FQ0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fpx\|5fpx]], [[5fpz\|5fpz]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fpx\|5fpx]], [[5fpz\|5fpz]]</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=5fq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq0 OCA], [http://pdbe.org/5fq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fq0 RCSB], [http://www.ebi.ac.uk/pdbsum/5fq0 PDBsum]</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=5fq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq0 OCA], [http://pdbe.org/5fq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fq0 RCSB], [http://www.ebi.ac.uk/pdbsum/5fq0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fq0 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: Halsx]]
		+	[[Category: Large Structures]]
	[[Category: Abbott, D W]]		[[Category: Abbott, D W]]
	[[Category: Abe, K T]]		[[Category: Abe, K T]]

OCA at 08:38, 1 June 2016

OCA — Wed, 01 Jun 2016 08:38:14 GMT

←Older revision		Revision as of 08:38, 1 June 2016
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	<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=5fq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq0 OCA], [http://pdbe.org/5fq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fq0 RCSB], [http://www.ebi.ac.uk/pdbsum/5fq0 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=5fq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq0 OCA], [http://pdbe.org/5fq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fq0 RCSB], [http://www.ebi.ac.uk/pdbsum/5fq0 PDBsum]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Uronates are charged sugars that form the basis of two abundant sources of biomass-pectin and alginate-found in the cell walls of terrestrial plants and marine algae, respectively. These polysaccharides represent an important source of carbon to those organisms with the machinery to degrade them. The microbial pathways of pectin and alginate metabolism are well studied and essentially parallel; in both cases, unsaturated monouronates are produced and processed into the key metabolite 2-keto-3-deoxygluconate (KDG). The enzymes required to catalyze each step have been identified within pectinolytic and alginolytic microbes; yet the function of a small ORF, kdgF, which cooccurs with the genes for these enzymes, is unknown. Here we show that KdgF catalyzes the conversion of pectin- and alginate-derived 4,5-unsaturated monouronates to linear ketonized forms, a step in uronate metabolism that was previously thought to occur spontaneously. Using enzyme assays, NMR, mutagenesis, and deletion of kdgF, we show that KdgF proteins from both pectinolytic and alginolytic bacteria catalyze the ketonization of unsaturated monouronates and contribute to efficient production of KDG. We also report the X-ray crystal structures of two KdgF proteins and propose a mechanism for catalysis. The discovery of the function of KdgF fills a 50-y-old gap in the knowledge of uronate metabolism. Our findings have implications not only for the understanding of an important metabolic pathway, but also the role of pectinolysis in plant-pathogen virulence and the growing interest in the use of pectin and alginate as feedstocks for biofuel production.
		+
		+	KdgF, the missing link in the microbial metabolism of uronate sugars from pectin and alginate.,Hobbs JK, Lee SM, Robb M, Hof F, Barr C, Abe KT, Hehemann JH, McLean R, Abbott DW, Boraston AB Proc Natl Acad Sci U S A. 2016 May 16. pii: 201524214. PMID:27185956<ref>PMID:27185956</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5fq0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:44, 13 May 2016

OCA — Fri, 13 May 2016 19:44:15 GMT

←Older revision		Revision as of 19:44, 13 May 2016
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-	'''Unreleased structure'''

-	The ~~entry~~ 5fq0 ~~is ON HOLD~~	+	==The structure of KdgF from Halomonas sp.==
-		+	<StructureSection load='5fq0' size='340' side='right' caption='[[5fq0]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~: ~~Hobbs, J~~.K.~~, Lee, S~~.M.~~, Robb, M~~.~~, Hof, F~~.~~, Barr, C~~., ~~Abe~~, K.T., ~~Hehemann, J~~.H., ~~McLean, R~~., ~~Abbott, D~~.W., ~~Boraston, A~~.B.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5fq0]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FQ0 FirstGlance]. <br>
-	~~Description~~: ~~The structure of KdgF from Halomonas sp.~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fpx\|5fpx]], [[5fpz\|5fpz]]</td></tr>
-	[[Category: ~~Mclean~~, R]]	+	<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=5fq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fq0 OCA], [http://pdbe.org/5fq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fq0 RCSB], [http://www.ebi.ac.uk/pdbsum/5fq0 PDBsum]</span></td></tr>
-	[[Category: ~~Abe~~, K.T]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Abbott, D W]]
		+	[[Category: Abe, K T]]
		+	[[Category: Barr, C]]
		+	[[Category: Boraston, A B]]
		+	[[Category: Hehemann, J H]]
		+	[[Category: Hobbs, J K]]
	[[Category: Hof, F]]		[[Category: Hof, F]]
-	~~[[Category: Barr, C]]~~	+	[[Category: Lee, S M]]
-	~~[[Category: Boraston, A.B]]~~	+	[[Category: McLean, R]]
-	~~[[Category: Abbott, D.W]]~~	+
-	~~[[Category: Hehemann, J.H]]~~	+
-	[[Category: Lee, S.M]]	+
-	[[Category: ~~Hobbs~~, ~~J.K~~]]	+
	[[Category: Robb, M]]		[[Category: Robb, M]]
		+	[[Category: Alginate]]
		+	[[Category: Cupin]]
		+	[[Category: Kdgf]]
		+	[[Category: Lyase]]
		+	[[Category: Pectin]]
		+	[[Category: Uronate sugar metabolism]]

OCA at 00:39, 10 March 2016

OCA — Thu, 10 Mar 2016 00:39:34 GMT

←Older revision		Revision as of 00:39, 10 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fq0 is ON HOLD ~~until sometime in the future~~	+	The entry 5fq0 is ON HOLD

	Authors: Hobbs, J.K., Lee, S.M., Robb, M., Hof, F., Barr, C., Abe, K.T., Hehemann, J.H., McLean, R., Abbott, D.W., Boraston, A.B.		Authors: Hobbs, J.K., Lee, S.M., Robb, M., Hof, F., Barr, C., Abe, K.T., Hehemann, J.H., McLean, R., Abbott, D.W., Boraston, A.B.

OCA: Protected "5fq0" [edit=sysop:move=sysop]

OCA — Wed, 16 Dec 2015 13:00:57 GMT

Protected "5fq0" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:00, 16 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fq0 is ON HOLD until sometime in the future Authors: Hobbs, J.K., Lee, S.M., Robb, M., Hof, F., Barr, C., Abe, K.T., Hehemann, J.H., McLean, R., Ab...

OCA — Wed, 16 Dec 2015 13:00:56 GMT

New page: '''Unreleased structure''' The entry 5fq0 is ON HOLD until sometime in the future Authors: Hobbs, J.K., Lee, S.M., Robb, M., Hof, F., Barr, C., Abe, K.T., Hehemann, J.H., McLean, R., Ab...

New page

'''Unreleased structure'''

The entry 5fq0 is ON HOLD until sometime in the future

Authors: Hobbs, J.K., Lee, S.M., Robb, M., Hof, F., Barr, C., Abe, K.T., Hehemann, J.H., McLean, R., Abbott, D.W., Boraston, A.B.

Description: The structure of KdgF from Halomonas sp.
[[Category: Unreleased Structures]]
[[Category: Mclean, R]]
[[Category: Abe, K.T]]
[[Category: Hof, F]]
[[Category: Barr, C]]
[[Category: Boraston, A.B]]
[[Category: Abbott, D.W]]
[[Category: Hehemann, J.H]]
[[Category: Lee, S.M]]
[[Category: Hobbs, J.K]]
[[Category: Robb, M]]