5zyn - Revision history

OCA at 09:10, 22 November 2023

OCA — Wed, 22 Nov 2023 09:10:20 GMT

←Older revision		Revision as of 09:10, 22 November 2023
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	==Fumarate reductase==		==Fumarate reductase==
-	<StructureSection load='5zyn' size='340' side='right' caption='[[5zyn]], [[Resolution\|resolution]] 1.75Å' scene=''>	+	<StructureSection load='5zyn' size='340' side='right'caption='[[5zyn]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zyn]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZYN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZYN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zyn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZYN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZYN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=FAD:FLAVIN~~-~~ADENINE+DINUCLEOTIDE'>FAD</scene>~~, ~~<scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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]] 1.75Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~OSM1, YJR051W, J1659 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=559292 Baker~~'~~s yeast])</td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.6 1.3.1.6]~~ </~~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=5zyn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zyn OCA], [https://pdbe.org/5zyn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zyn RCSB], [https://www.ebi.ac.uk/pdbsum/5zyn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zyn 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=5zyn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zyn OCA], [~~http~~://pdbe.org/5zyn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zyn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zyn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zyn ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/OSM1_YEAST OSM1_YEAST]] Irreversibly catalyzes the reduction of fumarate to succinate. Together with the second isozyme of soluble fumarate reductase (FRD1), essential for anaerobic growth. Involved in maintaining redox balance during oxygen deficiency conditions. Reduction of fumarate is the main source of succinate during fermentation, and under anaerobic conditions, the formation of succinate is strictly required for the reoxidation of FADH(2).<ref>PMID:12949191</ref> <ref>PMID:17345583</ref> <ref>PMID:9587404</ref> <ref>PMID:9711846</ref>	+	[https://www.uniprot.org/uniprot/OSM1_YEAST OSM1_YEAST] Irreversibly catalyzes the reduction of fumarate to succinate. Together with the second isozyme of soluble fumarate reductase (FRD1), essential for anaerobic growth. Involved in maintaining redox balance during oxygen deficiency conditions. Reduction of fumarate is the main source of succinate during fermentation, and under anaerobic conditions, the formation of succinate is strictly required for the reoxidation of FADH(2).<ref>PMID:12949191</ref> <ref>PMID:17345583</ref> <ref>PMID:9587404</ref> <ref>PMID:9711846</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baker's yeast~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Oxidoreductase~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Kim~~, C M~~]]	+	[[Category: Kim CM]]
-	[[Category: Park~~, H H]]~~	+	[[Category: Park HH]]
-	~~[[Category: Fumarate reductase~~]]	+

OCA at 07:07, 12 December 2018

OCA — Wed, 12 Dec 2018 07:07:32 GMT

←Older revision		Revision as of 07:07, 12 December 2018
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	<StructureSection load='5zyn' size='340' side='right' caption='[[5zyn]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='5zyn' size='340' side='right' caption='[[5zyn]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zyn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZYN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZYN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zyn]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZYN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZYN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OSM1, YJR051W, J1659 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.6 1.3.1.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.6 1.3.1.6] </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=5zyn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zyn OCA], [http://pdbe.org/5zyn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zyn RCSB], [http://www.ebi.ac.uk/pdbsum/5zyn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zyn 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=5zyn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zyn OCA], [http://pdbe.org/5zyn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zyn RCSB], [http://www.ebi.ac.uk/pdbsum/5zyn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zyn ProSAT]</span></td></tr>
Line 10:		Line 11:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/OSM1_YEAST OSM1_YEAST]] Irreversibly catalyzes the reduction of fumarate to succinate. Together with the second isozyme of soluble fumarate reductase (FRD1), essential for anaerobic growth. Involved in maintaining redox balance during oxygen deficiency conditions. Reduction of fumarate is the main source of succinate during fermentation, and under anaerobic conditions, the formation of succinate is strictly required for the reoxidation of FADH(2).<ref>PMID:12949191</ref> <ref>PMID:17345583</ref> <ref>PMID:9587404</ref> <ref>PMID:9711846</ref>		[[http://www.uniprot.org/uniprot/OSM1_YEAST OSM1_YEAST]] Irreversibly catalyzes the reduction of fumarate to succinate. Together with the second isozyme of soluble fumarate reductase (FRD1), essential for anaerobic growth. Involved in maintaining redox balance during oxygen deficiency conditions. Reduction of fumarate is the main source of succinate during fermentation, and under anaerobic conditions, the formation of succinate is strictly required for the reoxidation of FADH(2).<ref>PMID:12949191</ref> <ref>PMID:17345583</ref> <ref>PMID:9587404</ref> <ref>PMID:9711846</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Osm1 and Frd1 are soluble fumarate reductases from yeast that are critical for allowing survival under anaerobic conditions. Although they maintain redox balance during anaerobiosis, the underlying mechanism is not understood. Here, we report the crystal structure of a eukaryotic soluble fumarate reductase, which is unique among soluble fumarate reductases as it lacks a heme domain. Structural and enzymatic analyses indicate that Osm1 has a specific binding pocket for flavin molecules, including FAD, FMN, and riboflavin, catalyzing their oxidation while reducing fumarate to succinate. Moreover, ER-resident Osm1 can transfer electrons from the Ero1 FAD cofactor to fumarate either by free FAD or by a direct interaction, allowing de novo disulfide bond formation in the absence of oxygen. We conclude that soluble eukaryotic fumarate reductases can maintain an oxidizing environment under anaerobic conditions, either by oxidizing cellular flavin cofactors or by a direct interaction with flavoenzymes such as Ero1.
		+
		+	Molecular basis of maintaining an oxidizing environment under anaerobiosis by soluble fumarate reductase.,Kim S, Kim CM, Son YJ, Choi JY, Siegenthaler RK, Lee Y, Jang TH, Song J, Kang H, Kaiser CA, Park HH Nat Commun. 2018 Nov 19;9(1):4867. doi: 10.1038/s41467-018-07285-9. PMID:30451826<ref>PMID:30451826</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zyn" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Kim, C M]]		[[Category: Kim, C M]]
	[[Category: Park, H H]]		[[Category: Park, H H]]
	[[Category: Fumarate reductase]]		[[Category: Fumarate reductase]]

OCA at 07:39, 3 October 2018

OCA — Wed, 03 Oct 2018 07:39:18 GMT

←Older revision		Revision as of 07:39, 3 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zyn is ~~ON HOLD until Paper Publication~~	+	==Fumarate reductase==
-		+	<StructureSection load='5zyn' size='340' side='right' caption='[[5zyn]], [[Resolution\|resolution]] 1.75Å' scene=''>
-	~~Authors~~: ~~Park~~, H.H., ~~Kim~~, C.M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zyn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZYN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZYN FirstGlance]. <br>
-	~~Description~~: ~~Fumarate~~ reductase	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.6 1.3.1.6] </span></td></tr>
-	[[Category: Park, H.H]]	+	<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=5zyn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zyn OCA], [http://pdbe.org/5zyn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zyn RCSB], [http://www.ebi.ac.uk/pdbsum/5zyn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zyn ProSAT]</span></td></tr>
-	[[Category: ~~Kim, C.M~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/OSM1_YEAST OSM1_YEAST]] Irreversibly catalyzes the reduction of fumarate to succinate. Together with the second isozyme of soluble fumarate reductase (FRD1), essential for anaerobic growth. Involved in maintaining redox balance during oxygen deficiency conditions. Reduction of fumarate is the main source of succinate during fermentation, and under anaerobic conditions, the formation of succinate is strictly required for the reoxidation of FADH(2).<ref>PMID:12949191</ref> <ref>PMID:17345583</ref> <ref>PMID:9587404</ref> <ref>PMID:9711846</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Oxidoreductase]]
		+	[[Category: Kim, C M]]
		+	[[Category: Park, H H]]
		+	[[Category: Fumarate reductase]]

OCA at 06:03, 26 September 2018

OCA — Wed, 26 Sep 2018 06:03:46 GMT

←Older revision		Revision as of 06:03, 26 September 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Park, H.H., Kim, C.M.		Authors: Park, H.H., Kim, C.M.

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

OCA — Wed, 30 May 2018 03:57:20 GMT

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

←Older revision

Revision as of 03:57, 30 May 2018

OCA: New page: '''Unreleased structure''' The entry 5zyn is ON HOLD Authors: Park, H.H., Kim, C.M. Description: Fumarate reductase Category: Unreleased Structures Category: Park, H.H [[Catego...

OCA — Wed, 30 May 2018 03:57:19 GMT

New page: '''Unreleased structure''' The entry 5zyn is ON HOLD Authors: Park, H.H., Kim, C.M. Description: Fumarate reductase Category: Unreleased Structures Category: Park, H.H [[Catego...

New page

'''Unreleased structure'''

The entry 5zyn is ON HOLD

Authors: Park, H.H., Kim, C.M.

Description: Fumarate reductase
[[Category: Unreleased Structures]]
[[Category: Park, H.H]]
[[Category: Kim, C.M]]