5u8w - Revision history

OCA at 13:23, 4 October 2023

OCA — Wed, 04 Oct 2023 13:23:15 GMT

←Older revision		Revision as of 13:23, 4 October 2023
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	<StructureSection load='5u8w' size='340' side='right'caption='[[5u8w]], [[Resolution\|resolution]] 1.79Å' scene=''>		<StructureSection load='5u8w' size='340' side='right'caption='[[5u8w]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u8w]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pseab Pseab~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U8W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U8W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u8w]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_UCBPP-PA14 Pseudomonas aeruginosa UCBPP-PA14]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U8W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U8W FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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]] 1.79Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5u8u\|5u8u]]~~, [[~~5u8v~~\|~~5u8v~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~lpdG, PA14_43970 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=208963 PSEAB])</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=5u8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u8w OCA], [https://pdbe.org/5u8w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u8w RCSB], [https://www.ebi.ac.uk/pdbsum/5u8w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u8w ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[http~~:~~//en.wikipedia.org/wiki/Dihydrolipoyl_dehydrogenase Dihydrolipoyl dehydrogenase]~~, ~~with EC number [http://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.8.1.4 1.8.1.4]~~ </~~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=5u8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u8w OCA], [~~http~~://pdbe.org/5u8w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u8w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u8w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u8w ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A0H2Z9F5_PSEAB A0A0H2Z9F5_PSEAB]
	<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: Dihydrolipoyl dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseab~~]]	+	[[Category: Pseudomonas aeruginosa UCBPP-PA14]]
-	[[Category: Glasser~~, N R~~]]	+	[[Category: Glasser NR]]
-	[[Category: Hoy~~, J A~~]]	+	[[Category: Hoy JA]]
-	[[Category: Newman~~, D K~~]]	+	[[Category: Newman DK]]
-	[[Category: Wang~~, B X]]~~	+	[[Category: Wang BX]]
-	~~[[Category: Dihydrolipoamide dehydrogenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 16:43, 20 November 2019

OCA — Wed, 20 Nov 2019 16:43:20 GMT

←Older revision		Revision as of 16:43, 20 November 2019
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	==Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NADH==		==Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NADH==
-	<StructureSection load='5u8w' size='340' side='right' caption='[[5u8w]], [[Resolution\|resolution]] 1.79Å' scene=''>	+	<StructureSection load='5u8w' size='340' side='right'caption='[[5u8w]], [[Resolution\|resolution]] 1.79Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u8w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U8W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U8W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u8w]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseab Pseab]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U8W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U8W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5u8u\|5u8u]], [[5u8v\|5u8v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5u8u\|5u8u]], [[5u8v\|5u8v]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">lpdG, PA14_43970 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208963 PSEAB])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrolipoyl_dehydrogenase Dihydrolipoyl dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.4 1.8.1.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrolipoyl_dehydrogenase Dihydrolipoyl dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.4 1.8.1.4] </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=5u8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u8w OCA], [http://pdbe.org/5u8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u8w RCSB], [http://www.ebi.ac.uk/pdbsum/5u8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u8w 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=5u8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u8w OCA], [http://pdbe.org/5u8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u8w RCSB], [http://www.ebi.ac.uk/pdbsum/5u8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u8w ProSAT]</span></td></tr>
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	</StructureSection>		</StructureSection>
	[[Category: Dihydrolipoyl dehydrogenase]]		[[Category: Dihydrolipoyl dehydrogenase]]
		+	[[Category: Large Structures]]
		+	[[Category: Pseab]]
	[[Category: Glasser, N R]]		[[Category: Glasser, N R]]
	[[Category: Hoy, J A]]		[[Category: Hoy, J A]]

OCA at 07:35, 9 March 2017

OCA — Thu, 09 Mar 2017 07:35:10 GMT

←Older revision		Revision as of 07:35, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5u8w is ~~ON HOLD until Paper~~ Publication	+	==Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NADH==
		+	<StructureSection load='5u8w' size='340' side='right' caption='[[5u8w]], [[Resolution\|resolution]] 1.79Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5u8w]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U8W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U8W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5u8u\|5u8u]], [[5u8v\|5u8v]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dihydrolipoyl_dehydrogenase Dihydrolipoyl dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.4 1.8.1.4] </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=5u8w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u8w OCA], [http://pdbe.org/5u8w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u8w RCSB], [http://www.ebi.ac.uk/pdbsum/5u8w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u8w ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phenazines are a class of redox-active molecules produced by diverse bacteria and archaea. Many of the biological functions of phenazines, such as mediating signaling, iron acquisition, and redox homeostasis, derive from their redox activity. While prior studies have focused on extracellular phenazine oxidation by oxygen and iron, here we report a search for reductants and catalysts of intracellular phenazine reduction in Pseudomonas aeruginosa Enzymatic assays in cell-free lysate, together with crude fractionation and chemical inhibition, indicate that P. aeruginosa contains multiple enzymes that catalyze the reduction of the endogenous phenazines pyocyanin and phenazine-1-carboxylic acid in both cytosolic and membrane fractions. We used chemical inhibitors to target general enzyme classes and found that an inhibitor of flavoproteins and heme-containing proteins, diphenyleneiodonium, effectively inhibited phenazine reduction in vitro, suggesting that most phenazine reduction derives from these enzymes. Using natively purified proteins, we demonstrate that the pyruvate and alpha-ketoglutarate dehydrogenase complexes directly catalyze phenazine reduction with pyruvate or alpha-ketoglutarate as electron donors. Both complexes transfer electrons to phenazines through the common subunit dihydrolipoamide dehydrogenase, a flavoprotein encoded by the gene lpdG Although we were unable to co-crystalize LpdG with an endogenous phenazine, we report its X-ray crystal structure in the apo form (refined to 1.35 A), bound to NAD+ (1.45 A), and bound to NADH (1.79 A). In contrast to the notion that phenazines support intracellular redox homeostasis by oxidizing NADH, our work suggests that phenazines may substitute for NAD+ in LpdG and other enzymes, achieving the same end by a different mechanism.

-	~~Authors: Glasser, N.R~~., Wang~~, B.X.~~, Hoy, J.A.~~, Newman, D~~.K.	+	The pyruvate and alpha-ketoglutarate dehydrogenase complexes of Pseudomonas aeruginosa catalyze pyocyanin and phenazine-1-carboxylic acid reduction via the subunit dihydrolipoamide dehydrogenase.,Glasser NR, Wang BX, Hoy JA, Newman DK J Biol Chem. 2017 Feb 7. pii: jbc.M116.772848. doi: 10.1074/jbc.M116.772848. PMID:28174304<ref>PMID:28174304</ref>

-	~~Description~~: ~~Dihydrolipoamide~~ dehydrogenase ~~(LpdG) from Pseudomonas aeruginosa bound to NADH~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Newman, D.K]]	+	<div class="pdbe-citations 5u8w" style="background-color:#fffaf0;"></div>
-	[[Category: Wang, B.X]]	+	== References ==
-	[[Category: ~~Hoy, J.A~~]]	+	<references/>
-	[[Category: ~~Glasser, N.R~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Dihydrolipoyl dehydrogenase]]
		+	[[Category: Glasser, N R]]
		+	[[Category: Hoy, J A]]
		+	[[Category: Newman, D K]]
		+	[[Category: Wang, B X]]
		+	[[Category: Dihydrolipoamide dehydrogenase]]
		+	[[Category: Oxidoreductase]]

OCA at 15:32, 4 January 2017

OCA — Wed, 04 Jan 2017 15:32:00 GMT

←Older revision		Revision as of 15:32, 4 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5u8w is ON HOLD	+	The entry 5u8w is ON HOLD until Paper Publication

	Authors: Glasser, N.R., Wang, B.X., Hoy, J.A., Newman, D.K.		Authors: Glasser, N.R., Wang, B.X., Hoy, J.A., Newman, D.K.

OCA at 15:12, 2 January 2017

OCA — Mon, 02 Jan 2017 15:12:18 GMT

←Older revision		Revision as of 15:12, 2 January 2017
Line 3:		Line 3:
	The entry 5u8w is ON HOLD		The entry 5u8w is ON HOLD

-	Authors: ~~Nathaniel R~~ Glasser, ~~Benjamin X~~ Wang, ~~Julie A~~ Hoy, ~~Dianne K~~ Newman	+	Authors: Glasser, N.R., Wang, B.X., Hoy, J.A., Newman, D.K.

	Description: Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NADH		Description: Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NADH
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Nathaniel R Glasser~~, ~~Benjamin X~~ Wang, ~~Julie A~~ Hoy, ~~Dianne K Newman~~]]	+	[[Category: Newman, D.K]]
		+	[[Category: Wang, B.X]]
		+	[[Category: Hoy, J.A]]
		+	[[Category: Glasser, N.R]]

OCA: Protected "5u8w" [edit=sysop:move=sysop]

OCA — Thu, 22 Dec 2016 20:33:35 GMT

Protected "5u8w" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:33, 22 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u8w is ON HOLD Authors: Nathaniel R Glasser, Benjamin X Wang, Julie A Hoy, Dianne K Newman Description: Dihydrolipoamide dehydrogenase (LpdG) from...

OCA — Thu, 22 Dec 2016 20:33:33 GMT

New page: '''Unreleased structure''' The entry 5u8w is ON HOLD Authors: Nathaniel R Glasser, Benjamin X Wang, Julie A Hoy, Dianne K Newman Description: Dihydrolipoamide dehydrogenase (LpdG) from...

New page

'''Unreleased structure'''

The entry 5u8w is ON HOLD

Authors: Nathaniel R Glasser, Benjamin X Wang, Julie A Hoy, Dianne K Newman

Description: Dihydrolipoamide dehydrogenase (LpdG) from Pseudomonas aeruginosa bound to NADH
[[Category: Unreleased Structures]]
[[Category: Nathaniel R Glasser, Benjamin X Wang, Julie A Hoy, Dianne K Newman]]