6wja - Revision history

OCA at 14:26, 18 October 2023

OCA — Wed, 18 Oct 2023 14:26:42 GMT

←Older revision		Revision as of 14:26, 18 October 2023
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	<StructureSection load='6wja' size='340' side='right'caption='[[6wja]], [[Resolution\|resolution]] 2.09Å' scene=''>		<StructureSection load='6wja' size='340' side='right'caption='[[6wja]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6wja]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Psef5 Psef5~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WJA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6WJA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wja]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_protegens_Pf-5 Pseudomonas protegens Pf-5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WJA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WJA 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=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</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]] 2.094Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PFL_2971 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=220664 PSEF5])~~</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=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</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=6wja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wja OCA], [~~http~~://pdbe.org/6wja PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6wja RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6wja PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6wja 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=6wja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wja OCA], [https://pdbe.org/6wja PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wja RCSB], [https://www.ebi.ac.uk/pdbsum/6wja PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wja ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q4KCF6_PSEF5 Q4KCF6_PSEF5]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Psef5~~]]	+	[[Category: Pseudomonas protegens Pf-5]]
-	[[Category: Howell~~, P L~~]]	+	[[Category: Howell PL]]
-	[[Category: Marmont~~, L S~~]]	+	[[Category: Marmont LS]]
-	[[Category: Pfoh, R]]	+	[[Category: Pfoh R]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Nad dependent]]~~	+
-	~~[[Category: Short chain dehydrogenase~~]]	+

OCA at 07:09, 2 September 2020

OCA — Wed, 02 Sep 2020 07:09:55 GMT

←Older revision		Revision as of 07:09, 2 September 2020
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	==UDP-GlcNAc C4-epimerase mutant S121A/Y146F from Pseudomonas protegens in complex with UDP-GalNAc==		==UDP-GlcNAc C4-epimerase mutant S121A/Y146F from Pseudomonas protegens in complex with UDP-GalNAc==
-	<StructureSection load='6wja' size='340' side='right'caption='[[6wja]]' scene=''>	+	<StructureSection load='6wja' size='340' side='right'caption='[[6wja]], [[Resolution\|resolution]] 2.09Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WJA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WJA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6wja]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Psef5 Psef5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WJA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WJA FirstGlance]. <br>
-	</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=6wja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wja OCA], [http://pdbe.org/6wja PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wja RCSB], [http://www.ebi.ac.uk/pdbsum/6wja PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wja ProSAT]</span></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=UD2:URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE'>UD2</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PFL_2971 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=220664 PSEF5])</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=6wja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wja OCA], [http://pdbe.org/6wja PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wja RCSB], [http://www.ebi.ac.uk/pdbsum/6wja PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wja ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Pel is a GalNAc-rich bacterial polysaccharide that contributes to the structure and function of Pseudomonas aeruginosa biofilms. The pelABCDEFG operon is highly conserved among diverse bacterial species, and Pel may therefore be a widespread biofilm determinant. Previous annotation of pel gene clusters has helped us identify an additional gene, pelX, that is present adjacent to pelABCDEFG in >100 different bacterial species. The pelX gene is predicted to encode a member of the short-chain dehydrogenase/reductase (SDR) superfamily, but its potential role in Pel-dependent biofilm formation is unknown. Herein, we have used Pseudomonas protegens Pf-5 as a model to elucidate PelX function as Pseudomonas aeruginosa lacks a pelX homologue in its pel gene cluster. We found that P. protegens forms Pel-dependent biofilms; however, despite expression of pelX under these conditions, biofilm formation was unaffected in a DeltapelX strain. This observation led us to identify a pelX paralogue, PFL_5533, which we designate here PgnE, that appears to be functionally redundant to pelX In line with this, a DeltapelX DeltapgnE double mutant was substantially impaired in its ability to form Pel-dependent biofilms. To understand the molecular basis for this observation, we determined the structure of PelX to 2.1 A resolution. The structure revealed that PelX resembles UDP-GlcNAc C4-epimerases. Using (1)H NMR analysis, we show that PelX catalyzes the epimerization between UDP-GlcNAc and UDP-GalNAc. Our results indicate that Pel-dependent biofilm formation requires a UDP-GlcNAc C4-epimerase that generates the UDP-GalNAc precursors required by the Pel synthase machinery for polymer production.
		+
		+	PelX is a UDP-N-acetylglucosamine C4-epimerase involved in Pel polysaccharide-dependent biofilm formation.,Marmont LS, Whitfield GB, Pfoh R, Williams RJ, Randall TE, Ostaszewski A, Razvi E, Groves RA, Robinson H, Nitz M, Parsek MR, Lewis IA, Whitney JC, Harrison JJ, Howell PL J Biol Chem. 2020 Aug 21;295(34):11949-11962. doi: 10.1074/jbc.RA120.014555. Epub, 2020 Jun 29. PMID:32601062<ref>PMID:32601062</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6wja" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Howell PL]]	+	[[Category: Psef5]]
-	[[Category: Marmont LS]]	+	[[Category: Howell, P L]]
-	[[Category: Pfoh R]]	+	[[Category: Marmont, L S]]
		+	[[Category: Pfoh, R]]
		+	[[Category: Complex]]
		+	[[Category: Isomerase]]
		+	[[Category: Nad dependent]]
		+	[[Category: Short chain dehydrogenase]]

OCA at 14:09, 8 July 2020

OCA — Wed, 08 Jul 2020 14:09:08 GMT

←Older revision		Revision as of 14:09, 8 July 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6wja is ~~ON HOLD until Paper Publication~~	+	==UDP-GlcNAc C4-epimerase mutant S121A/Y146F from Pseudomonas protegens in complex with UDP-GalNAc==
-		+	<StructureSection load='6wja' size='340' side='right'caption='[[6wja]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WJA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6WJA FirstGlance]. <br>
-	~~Description~~:	+	</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=6wja FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wja OCA], [http://pdbe.org/6wja PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6wja RCSB], [http://www.ebi.ac.uk/pdbsum/6wja PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6wja ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Howell PL]]
		+	[[Category: Marmont LS]]
		+	[[Category: Pfoh R]]

OCA at 04:40, 27 May 2020

OCA — Wed, 27 May 2020 04:40:14 GMT

←Older revision		Revision as of 04:40, 27 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 22 Apr 2020 04:17:26 GMT

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

←Older revision

Revision as of 04:17, 22 April 2020

OCA: New page: '''Unreleased structure''' The entry 6wja is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Apr 2020 04:17:24 GMT

New page: '''Unreleased structure''' The entry 6wja is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6wja is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]