6o15 - Revision history

OCA at 07:02, 11 October 2023

OCA — Wed, 11 Oct 2023 07:02:56 GMT

←Older revision		Revision as of 07:02, 11 October 2023
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	<StructureSection load='6o15' size='340' side='right'caption='[[6o15]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='6o15' size='340' side='right'caption='[[6o15]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6o15]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O15 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6O15 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6o15]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O15 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NAD:NICOTINAMIDE~~-~~ADENINE-DINUCLEOTIDE'>NAD</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.35Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~yjhC, b4280, JW5769 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=83333 ECOLI])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6o15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o15 OCA], [~~http~~://pdbe.org/6o15 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6o15 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6o15 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6o15 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=6o15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o15 OCA], [https://pdbe.org/6o15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o15 RCSB], [https://www.ebi.ac.uk/pdbsum/6o15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o15 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/YJHC_ECOLI YJHC_ECOLI]
	<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: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Davies~~, J S~~]]	+	[[Category: Davies JS]]
-	[[Category: Dobson~~, R C~~]]	+	[[Category: Dobson RC]]
-	[[Category: Horne~~, C R~~]]	+	[[Category: Horne CR]]
-	[[Category: Kind, L]]	+	[[Category: Kind L]]
-	~~[[Category: Gfo/idh/moca]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 07:13, 15 April 2020

OCA — Wed, 15 Apr 2020 07:13:57 GMT

←Older revision		Revision as of 07:13, 15 April 2020
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	<StructureSection load='6o15' size='340' side='right'caption='[[6o15]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='6o15' size='340' side='right'caption='[[6o15]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6o15]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O15 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6O15 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6o15]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O15 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6O15 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6o15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o15 OCA], [http://pdbe.org/6o15 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o15 RCSB], [http://www.ebi.ac.uk/pdbsum/6o15 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o15 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yjhC, b4280, JW5769 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6o15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o15 OCA], [http://pdbe.org/6o15 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o15 RCSB], [http://www.ebi.ac.uk/pdbsum/6o15 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o15 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: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Davies, J S]]		[[Category: Davies, J S]]

OCA at 06:50, 27 November 2019

OCA — Wed, 27 Nov 2019 06:50:48 GMT

←Older revision		Revision as of 06:50, 27 November 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6o15 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of a putative oxidoreductase YjhC from Escherichia coli in complex with NAD(H)==
		+	<StructureSection load='6o15' size='340' side='right'caption='[[6o15]], [[Resolution\|resolution]] 1.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6o15]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O15 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O15 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6o15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o15 OCA], [http://pdbe.org/6o15 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o15 RCSB], [http://www.ebi.ac.uk/pdbsum/6o15 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o15 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Human pathogenic and commensal bacteria have evolved the ability to scavenge host-derived sialic acids and subsequently degrade them as a source of nutrition. Expression of the Escherichia coli yjhBC operon is controlled by the repressor protein nanR, which regulates the core machinery responsible for the import and catabolic processing of sialic acid. The role of the yjhBC encoded proteins is not known-here, we demonstrate that the enzyme YjhC is an oxidoreductase/dehydrogenase involved in bacterial sialic acid degradation. First, we demonstrate in vivo using knockout experiments that YjhC is broadly involved in carbohydrate metabolism, including that of N-acetyl-d-glucosamine, N-acetyl-d-galactosamine and N-acetylneuraminic acid. Differential scanning fluorimetry demonstrates that YjhC binds N-acetylneuraminic acid and its lactone variant, along with NAD(H), which is consistent with its role as an oxidoreductase. Next, we solved the crystal structure of YjhC in complex with the NAD(H) cofactor to 1.35 A resolution. The protein fold belongs to the Gfo/Idh/MocA protein family. The dimeric assembly observed in the crystal form is confirmed through solution studies. Ensemble refinement reveals a flexible loop region that may play a key role during catalysis, providing essential contacts to stabilize the substrate-a unique feature to YjhC among closely related structures. Guided by the structure, in silico docking experiments support the binding of sialic acid and several common derivatives in the binding pocket, which has an overall positive charge distribution. Taken together, our results verify the role of YjhC as a bona fide oxidoreductase/dehydrogenase and provide the first evidence to support its involvement in sialic acid metabolism.

-	~~Authors~~:	+	On the structure and function of Escherichia coli YjhC: An oxidoreductase involved in bacterial sialic acid metabolism.,Horne CR, Kind L, Davies JS, Dobson RCJ Proteins. 2019 Nov 7. doi: 10.1002/prot.25846. PMID:31697432<ref>PMID:31697432</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6o15" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Davies, J S]]
		+	[[Category: Dobson, R C]]
		+	[[Category: Horne, C R]]
		+	[[Category: Kind, L]]
		+	[[Category: Gfo/idh/moca]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Rossmann fold]]

OCA at 07:09, 2 October 2019

OCA — Wed, 02 Oct 2019 07:09:06 GMT

←Older revision		Revision as of 07:09, 2 October 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6o15 is ON HOLD	+	The entry 6o15 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 14:59, 14 August 2019

OCA — Wed, 14 Aug 2019 14:59:30 GMT

←Older revision		Revision as of 14:59, 14 August 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6o15 is ON HOLD ~~until Paper Publication~~	+	The entry 6o15 is ON HOLD

	Authors:		Authors:

OCA: Protected "6o15" [edit=sysop:move=sysop]

OCA — Wed, 27 Feb 2019 13:49:09 GMT

Protected "6o15" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:49, 27 February 2019

OCA: New page: '''Unreleased structure''' The entry 6o15 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Feb 2019 13:49:07 GMT

New page: '''Unreleased structure''' The entry 6o15 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6o15 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]