6e2a - Revision history

OCA at 06:17, 11 October 2023

2023-10-11T06:17:39Z

←Older revision		Revision as of 06:17, 11 October 2023
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	<StructureSection load='6e2a' size='340' side='right'caption='[[6e2a]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6e2a' size='340' side='right'caption='[[6e2a]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e2a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pseae Pseae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E2A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E2A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e2a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa_PAO1 Pseudomonas aeruginosa PAO1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E2A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E2A FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PA1024 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=208964 PSEAE])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Nitronate_monooxygenase Nitronate monooxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.16 1.13.12.16]~~ </~~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=6e2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e2a OCA], [https://pdbe.org/6e2a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e2a RCSB], [https://www.ebi.ac.uk/pdbsum/6e2a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e2a 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=6e2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e2a OCA], [https://pdbe.org/6e2a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e2a RCSB], [https://www.ebi.ac.uk/pdbsum/6e2a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e2a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~2NPD_PSEAE 2NPD_PSEAE]~~] Catalyzes the ~~oxidative denitrification~~ of ~~nitronates to their~~ corresponding ~~aldehydes~~ and ~~nitrites~~.<ref>PMID:~~16682407~~</ref>	+	[https://www.uniprot.org/uniprot/NQRED_PSEAE NQRED_PSEAE] Catalyzes the NADH-dependent reduction of a broad spectrum of quinone substrates, generating the corresponding hydroquinones. Highly prefers NADH to NADPH as a reducing substrate. Also displays a small NADH oxidase activity. Does not exhibit nitronate monooxygenase activity; is inactive against propionate 3-nitronate, 3-nitropropionate, nitroethane, 1-nitropropane, 2-nitropropane, and the anionic forms ethylnitronate, propyl-1-nitronate, and propyl-2-nitronate. Has no azoreductase activity since it is not able to reduce the azo dye methyl red with NADH. May be required to maintain an appropriate [NAD(+)]/[NADH] ratio for the catabolism of fatty acids in P.aeruginosa PAO1.<ref>PMID:27502282</ref>
	<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: ~~Nitronate monooxygenase]]~~	+	[[Category: Pseudomonas aeruginosa PAO1]]
-	~~[[Category: Pseae~~]]	+	[[Category: Agniswamy J]]
-	[[Category: Agniswamy, J]]	+	[[Category: Ball J]]
-	[[Category: Ball, J]]	+	[[Category: Gadda G]]
-	[[Category: Gadda, G]]	+	[[Category: Reis RAG]]
-	[[Category: Reis~~, R A.G~~]]	+	[[Category: Weber I]]
-	[[Category: Weber, I]]	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Nad+ complex]]~~	+
-	~~[[Category: Nadh:quinone reductase]]~~	+
-	~~[[Category: Oxidative stress]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Quinone~~]]	+

OCA at 10:18, 18 March 2021

2021-03-18T10:18:13Z

←Older revision		Revision as of 10:18, 18 March 2021
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	<StructureSection load='6e2a' size='340' side='right'caption='[[6e2a]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6e2a' size='340' side='right'caption='[[6e2a]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e2a]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E2A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6E2A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e2a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E2A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E2A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA1024 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA1024 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Nitronate_monooxygenase Nitronate monooxygenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.16 1.13.12.16] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitronate_monooxygenase Nitronate monooxygenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.16 1.13.12.16] </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=6e2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e2a OCA], [~~http~~://pdbe.org/6e2a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6e2a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6e2a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6e2a 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=6e2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e2a OCA], [https://pdbe.org/6e2a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e2a RCSB], [https://www.ebi.ac.uk/pdbsum/6e2a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e2a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/2NPD_PSEAE 2NPD_PSEAE]] Catalyzes the oxidative denitrification of nitronates to their corresponding aldehydes and nitrites.<ref>PMID:16682407</ref>	+	[[https://www.uniprot.org/uniprot/2NPD_PSEAE 2NPD_PSEAE]] Catalyzes the oxidative denitrification of nitronates to their corresponding aldehydes and nitrites.<ref>PMID:16682407</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 08:37, 27 November 2019

2019-11-27T08:37:53Z

←Older revision		Revision as of 08:37, 27 November 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6e2a is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of NADH:quinone reductase PA1024 from Pseudomonas aeruginosa PAO1 in complex with NAD+==
		+	<StructureSection load='6e2a' size='340' side='right'caption='[[6e2a]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6e2a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pseae Pseae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E2A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E2A FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PA1024 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=208964 PSEAE])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitronate_monooxygenase Nitronate monooxygenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.12.16 1.13.12.16] </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=6e2a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e2a OCA], [http://pdbe.org/6e2a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e2a RCSB], [http://www.ebi.ac.uk/pdbsum/6e2a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e2a ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/2NPD_PSEAE 2NPD_PSEAE]] Catalyzes the oxidative denitrification of nitronates to their corresponding aldehydes and nitrites.<ref>PMID:16682407</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the NADH:quinone oxidoreductase PA1024 has been solved in complex with NAD(+) to 2.2 A resolution. The nicotinamide C4 is 3.6 A from the FMN N5 atom, with a suitable orientation for facile hydride transfer. NAD(+) binds in a folded conformation at the interface of the TIM-barrel domain and the extended domain of the enzyme. Comparison of the enzyme-NAD(+) structure with that of the ligand-free enzyme revealed a different conformation of a short loop (75-86) that is part of the NAD(+) -binding pocket. P78, P82, and P84 provide internal rigidity to the loop, whereas Q80 serves as an active site latch that secures the NAD(+) within the binding pocket. An interrupted helix consisting of two alpha-helices connected by a small three-residue loop binds the pyrophosphate moiety of NAD(+) . The adenine moiety of NAD(+) appears to pi-pi stack with Y261. Steric constraints between the adenosine ribose of NAD(+) , P78, and Q80, control the strict specificity of the enzyme for NADH. Charged residues do not play a role in the specificity of PA1024 for the NADH substrate.

-	~~Authors~~:	+	Steric hindrance controls pyridine nucleotide specificity of a flavin-dependent NADH:quinone oxidoreductase.,Ball J, Reis RAG, Agniswamy J, Weber IT, Gadda G Protein Sci. 2019 Jan;28(1):167-175. doi: 10.1002/pro.3514. Epub 2018 Oct 31. PMID:30246917<ref>PMID:30246917</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6e2a" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Monooxygenase 3D structures\|Monooxygenase 3D structures]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Nitronate monooxygenase]]
		+	[[Category: Pseae]]
		+	[[Category: Agniswamy, J]]
		+	[[Category: Ball, J]]
		+	[[Category: Gadda, G]]
		+	[[Category: Reis, R A.G]]
		+	[[Category: Weber, I]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Nad+ complex]]
		+	[[Category: Nadh:quinone reductase]]
		+	[[Category: Oxidative stress]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Quinone]]

OCA at 19:48, 9 August 2018

2018-08-09T19:48:36Z

←Older revision		Revision as of 19:48, 9 August 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6e2a is ON HOLD	+	The entry 6e2a is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6e2a" [edit=sysop:move=sysop]

2018-07-18T05:41:26Z

Protected "6e2a" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:41, 18 July 2018

OCA: New page: '''Unreleased structure''' The entry 6e2a is ON HOLD Authors: Description: Category: Unreleased Structures

2018-07-18T05:41:25Z

New page: '''Unreleased structure''' The entry 6e2a is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6e2a is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]