5l1n - Revision history

OCA at 12:47, 4 October 2023

OCA — Wed, 04 Oct 2023 12:47:01 GMT

←Older revision		Revision as of 12:47, 4 October 2023
Line 1:		Line 1:

	==Pyrococcus horikoshii CoA Disulfide Reductase Quadruple Mutant==		==Pyrococcus horikoshii CoA Disulfide Reductase Quadruple Mutant==
-	<StructureSection load='5l1n' size='340' side='right' caption='[[5l1n]], [[Resolution\|resolution]] 3.60Å' scene=''>	+	<StructureSection load='5l1n' size='340' side='right'caption='[[5l1n]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l1n]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5L1N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l1n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5L1N FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=COA:COENZYME+A'>COA</scene~~>, ~~<scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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]] 3.6Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>PH0572 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~70601 Pyrococcus horikoshii])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/CoA-disulfide_reductase CoA-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.14 1.8.1.14]~~ </~~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=5l1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1n OCA], [https://pdbe.org/5l1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5l1n RCSB], [https://www.ebi.ac.uk/pdbsum/5l1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1n 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=5l1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1n OCA], [~~http~~://pdbe.org/5l1n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5l1n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5l1n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1n ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~CDR_PYRHO CDR_PYRHO~~]~~] Acts as a coenzyme A disulfide reductase. Specific for CoA disulfide. Shows a slow~~ NAD(P)H ~~oxidase activity in~~ the ~~presence~~ of ~~high concentrations~~ of ~~substrate-level FAD~~. ~~This demonstrates that it is not~~ likely ~~to act as an NADH oxidase~~ in vivo.	+	[https://www.uniprot.org/uniprot/NCPPR_PYRHO NCPPR_PYRHO] Catalyzes the NAD(P)H-dependent reduction of polysulfide, CoA-polysulfides, and CoA persulfide, as well as the reduction of a range of other small persulfides, including TNB and glutathione persulfides. The likely in vivo substrates are di-, poly-, and persulfide derivatives of coenzyme A, although polysulfide itself is also efficiently reduced (PubMed:23530771). Shows coenzyme A disulfide reductase (CoADR) activity with both NADH and NADPH, with a preference for NADPH (PubMed:15720393). May also play a role in the reduction of elemental sulfur (PubMed:23530771).<ref>PMID:15720393</ref> <ref>PMID:23530771</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~CoA-disulfide reductase~~]]	+	[[Category: Large Structures]]
-	[[Category: Pyrococcus horikoshii]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	[[Category: Chen, B]]	+	[[Category: Chen B]]
-	[[Category: ~~III, E J.~~Crane]]	+	[[Category: Crane III EJ]]
-	[[Category: Sazinsky~~, M H~~]]	+	[[Category: Sazinsky MH]]
-	[[Category: Sea, K]]	+	[[Category: Sea K]]
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Sulfur metabolism half-sites reactivity~~]]	+

OCA at 07:27, 25 July 2018

OCA — Wed, 25 Jul 2018 07:27:56 GMT

←Older revision		Revision as of 07:27, 25 July 2018
Line 3:		Line 3:
	<StructureSection load='5l1n' size='340' side='right' caption='[[5l1n]], [[Resolution\|resolution]] 3.60Å' scene=''>		<StructureSection load='5l1n' size='340' side='right' caption='[[5l1n]], [[Resolution\|resolution]] 3.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5l1n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5L1N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5l1n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5L1N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PH0572 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/CoA-disulfide_reductase CoA-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.14 1.8.1.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/CoA-disulfide_reductase CoA-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.14 1.8.1.14] </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=5l1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1n OCA], [http://pdbe.org/5l1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l1n RCSB], [http://www.ebi.ac.uk/pdbsum/5l1n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1n 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=5l1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1n OCA], [http://pdbe.org/5l1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l1n RCSB], [http://www.ebi.ac.uk/pdbsum/5l1n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1n ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CDR_PYRHO CDR_PYRHO]] Acts as a coenzyme A disulfide reductase. Specific for CoA disulfide. Shows a slow NAD(P)H oxidase activity in the presence of high concentrations of substrate-level FAD. This demonstrates that it is not likely to act as an NADH oxidase in vivo.		[[http://www.uniprot.org/uniprot/CDR_PYRHO CDR_PYRHO]] Acts as a coenzyme A disulfide reductase. Specific for CoA disulfide. Shows a slow NAD(P)H oxidase activity in the presence of high concentrations of substrate-level FAD. This demonstrates that it is not likely to act as an NADH oxidase in vivo.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Within the family of pyridine nucleotide disulfide oxidoreductase (PNDOR), enzymes are a group of single-cysteine containing FAD-dependent reductases that utilize a tightly bound coenzyme A to assist in the NAD(P)H-dependent reduction of di-, per-, and polysulfide substrates in bacteria and archaea. For many of these homodimeric enzymes, it has proved difficult to determine the substrate specificity and metabolic function based on sequence and genome analysis alone. Coenzyme A-disulfide reductase (CoADR) isolated from Pyrococcus horikoshii (phCoADR) reduces Co-A per- and polysulfides, but, unlike other highly homologous members of this group, is a poor CoA disulfide reductase. The phCoADR structure has a narrower access channel for CoA substrates, which suggested that this restriction might be responsible for the enzyme's poor activity toward the bulky CoA disulfide substrate. To test this hypothesis, the substrate channel was widened by making four mutations along the channel wall (Y65A, Y66A, P67G, and H367G). The structure of the quadruple mutant shows a widened substrate channel, which is supported by a fourfold increase in kcat for the NAD(P)H-dependent reduction of CoA disulfide and enhanced activity toward the substrate at lower temperatures. Anaerobic titrations of the enzyme with NADH revealed a half-site reactivity not observed with the wild-type enzyme in which one subunit of the enzyme could be fully reduced to an EH4 state, while the other remained in an EH2 or EH2.NADH state. These results suggest that for these closely related enzymes, substrate channel morphology is an important determinant of substrate specificity, and homology modeling will be the preferred technique for predicting function among PNDORs.
		+
		+	A broader active site in Pyrococcus horikoshii CoA disulfide reductase accommodates larger substrates and reveals evidence of subunit asymmetry.,Sea K, Lee J, To D, Chen B, Sazinsky MH, Crane EJ 3rd FEBS Open Bio. 2018 Jun 9;8(7):1083-1092. doi: 10.1002/2211-5463.12439., eCollection 2018 Jul. PMID:29988575<ref>PMID:29988575</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5l1n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Coenzyme A-Disulfide Reductase\|Coenzyme A-Disulfide Reductase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: CoA-disulfide reductase]]		[[Category: CoA-disulfide reductase]]
		+	[[Category: Pyrococcus horikoshii]]
	[[Category: Chen, B]]		[[Category: Chen, B]]
	[[Category: III, E J.Crane]]		[[Category: III, E J.Crane]]

OCA at 10:34, 7 October 2017

OCA — Sat, 07 Oct 2017 10:34:15 GMT

←Older revision		Revision as of 10:34, 7 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5l1n is ~~ON HOLD until Paper Publication~~	+	==Pyrococcus horikoshii CoA Disulfide Reductase Quadruple Mutant==
-		+	<StructureSection load='5l1n' size='340' side='right' caption='[[5l1n]], [[Resolution\|resolution]] 3.60Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5l1n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5L1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5L1N FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/CoA-disulfide_reductase CoA-disulfide reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.8.1.14 1.8.1.14] </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=5l1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5l1n OCA], [http://pdbe.org/5l1n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5l1n RCSB], [http://www.ebi.ac.uk/pdbsum/5l1n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5l1n ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CDR_PYRHO CDR_PYRHO]] Acts as a coenzyme A disulfide reductase. Specific for CoA disulfide. Shows a slow NAD(P)H oxidase activity in the presence of high concentrations of substrate-level FAD. This demonstrates that it is not likely to act as an NADH oxidase in vivo.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: CoA-disulfide reductase]]
		+	[[Category: Chen, B]]
		+	[[Category: III, E J.Crane]]
		+	[[Category: Sazinsky, M H]]
		+	[[Category: Sea, K]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Sulfur metabolism half-sites reactivity]]

OCA at 12:56, 14 September 2016

OCA — Wed, 14 Sep 2016 12:56:39 GMT

←Older revision		Revision as of 12:56, 14 September 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5l1n is ON HOLD	+	The entry 5l1n is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5l1n" [edit=sysop:move=sysop]

OCA — Wed, 10 Aug 2016 13:59:38 GMT

Protected "5l1n" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:59, 10 August 2016

OCA: New page: '''Unreleased structure''' The entry 5l1n is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 Aug 2016 13:59:37 GMT

New page: '''Unreleased structure''' The entry 5l1n is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5l1n is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]