5lmc - Revision history

OCA at 18:34, 18 October 2023

OCA — Wed, 18 Oct 2023 18:34:34 GMT

←Older revision		Revision as of 18:34, 18 October 2023
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	<StructureSection load='5lmc' size='340' side='right'caption='[[5lmc]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='5lmc' size='340' side='right'caption='[[5lmc]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lmc]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5LMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lmc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LMC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.9Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d02\|4d02]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5lmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmc OCA], [https://pdbe.org/5lmc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lmc RCSB], [https://www.ebi.ac.uk/pdbsum/5lmc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmc ProSAT]</span></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=5lmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmc OCA], [~~http~~://pdbe.org/5lmc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5lmc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5lmc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmc ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/NORV_ECOLI NORV_ECOLI]] Anaerobic nitric oxide reductase; uses NADH to detoxify nitric oxide (NO), protecting several 4Fe-4S NO-sensitive enzymes. Has at least 2 reductase partners, only one of which (NorW, flavorubredoxin reductase) has been identified. NO probably binds to the di-iron center; electrons enter from the reductase at rubredoxin and are transferred sequentially to the FMN center and the di-iron center. Also able to function as an aerobic oxygen reductase.<ref>PMID:11751865</ref> <ref>PMID:12101220</ref>	+	[https://www.uniprot.org/uniprot/NORV_ECOLI NORV_ECOLI] Anaerobic nitric oxide reductase; uses NADH to detoxify nitric oxide (NO), protecting several 4Fe-4S NO-sensitive enzymes. Has at least 2 reductase partners, only one of which (NorW, flavorubredoxin reductase) has been identified. NO probably binds to the di-iron center; electrons enter from the reductase at rubredoxin and are transferred sequentially to the FMN center and the di-iron center. Also able to function as an aerobic oxygen reductase.<ref>PMID:11751865</ref> <ref>PMID:12101220</ref>
	<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: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Borges~~, P T~~]]	+	[[Category: Borges PT]]
-	[[Category: Carrondo~~, M A~~]]	+	[[Category: Carrondo MA]]
-	[[Category: Frazao, C]]	+	[[Category: Frazao C]]
-	[[Category: Romao~~, C V~~]]	+	[[Category: Romao CV]]
-	[[Category: Teixeira, M]]	+	[[Category: Teixeira M]]
-	[[Category: Vicente~~, J B]]~~	+	[[Category: Vicente JB]]
-	~~[[Category: Diiron center]]~~	+
-	~~[[Category: Flavodiiron protein]]~~	+
-	~~[[Category: Flavorubredoxin]]~~	+
-	~~[[Category: Nitric oxide reductase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:42, 12 August 2020

OCA — Wed, 12 Aug 2020 10:42:31 GMT

←Older revision		Revision as of 10:42, 12 August 2020
Line 1:		Line 1:

	==Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms from its rubredoxin domain==		==Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms from its rubredoxin domain==
-	<StructureSection load='5lmc' size='340' side='right' caption='[[5lmc]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='5lmc' size='340' side='right'caption='[[5lmc]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5lmc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMC OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5LMC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5lmc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5LMC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d02\|4d02]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d02\|4d02]]</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=5lmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmc OCA], [http://pdbe.org/5lmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmc RCSB], [http://www.ebi.ac.uk/pdbsum/5lmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmc ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">norV, flrD, ygaI, ygaJ, ygaK, b2710, JW2680 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5lmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmc OCA], [http://pdbe.org/5lmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmc RCSB], [http://www.ebi.ac.uk/pdbsum/5lmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Borges, P T]]		[[Category: Borges, P T]]
	[[Category: Carrondo, M A]]		[[Category: Carrondo, M A]]

OCA at 17:17, 19 October 2016

OCA — Wed, 19 Oct 2016 17:17:39 GMT

←Older revision		Revision as of 17:17, 19 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5lmc is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms from its rubredoxin domain==
		+	<StructureSection load='5lmc' size='340' side='right' caption='[[5lmc]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5lmc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LMC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4d02\|4d02]]</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=5lmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmc OCA], [http://pdbe.org/5lmc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmc RCSB], [http://www.ebi.ac.uk/pdbsum/5lmc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmc ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/NORV_ECOLI NORV_ECOLI]] Anaerobic nitric oxide reductase; uses NADH to detoxify nitric oxide (NO), protecting several 4Fe-4S NO-sensitive enzymes. Has at least 2 reductase partners, only one of which (NorW, flavorubredoxin reductase) has been identified. NO probably binds to the di-iron center; electrons enter from the reductase at rubredoxin and are transferred sequentially to the FMN center and the di-iron center. Also able to function as an aerobic oxygen reductase.<ref>PMID:11751865</ref> <ref>PMID:12101220</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Flavodiiron proteins (FDPs) are present in organisms from all domains of life and have been described so far to be involved in the detoxification of oxygen or nitric oxide, acting as O2 and/or NO reductases. The Escherichia coli FDP, named flavorubredoxin (FlRd) is the most extensively studied FDP. Biochemical and in vivo studies revealed that FlRd is involved in NO detoxification, as part of the bacterial defense mechanisms against reactive nitrogen species. E. coli FlRd has a clear preference for NO as substrate in vitro, exhibiting a very low reactivity towards O2. To contribute to the understanding of the structural features defining this substrate selectivity, we determined the crystallographic structure of E. coli FlRd, both in the as-isolated and reduced states. The overall tetrameric structure revealed a highly conserved flavodiiron core domain, with a metallo-beta-lactamase-like domain containing a diiron center and a flavodoxin domain with a FMN cofactor. The metal center in the oxidized state has a mu-hydroxo bridge coordinating the two irons, while in the reduced state this moiety is not detected. Since only the flavodiiron domain was observed in these crystal structures, the structure of the rubredoxin domain was determined by NMR. Tunnels for the substrates were identified, and through Molecular Dynamics simulations no differences for O2 or NO permeation were found. The present data represents the first structure for a NO-selective FDP.

-	~~Authors:~~ Romao, ~~C.V.~~, Borges, P~~.T.~~, ~~Vicente~~, ~~J.B.~~, Carrondo, ~~M.A.~~, Teixeira, M., Frazao, C.	+	Structure of Escherichia coli Flavodiiron nitric oxide reductase.,Romao CV, Vicente JB, Borges PT, Victor BL, Lamosa P, Silva E, Pereira L, Bandeiras TM, Soares CM, Carrondo MA, Turner D, Teixeira M, Frazao C J Mol Biol. 2016 Oct 7. pii: S0022-2836(16)30423-5. doi:, 10.1016/j.jmb.2016.10.008. PMID:27725182<ref>PMID:27725182</ref>

-	~~Description: Oxidized flavodiiron core of Escherichia coli flavorubredoxin~~, ~~including~~ the Fe-~~4SG atoms from its rubredoxin domain~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	[[Category: Borges, P.T]]	+	<div class="pdbe-citations 5lmc" style="background-color:#fffaf0;"></div>
-	~~[[Category: Romao, C.V~~]]	+	== References ==
-	[[Category: Carrondo, M.A]]	+	<references/>
-	~~[[Category: Vicente, J.B]]~~	+	__TOC__
-	~~[[Category: Teixeira, M~~]]	+	</StructureSection>
		+	[[Category: Borges, P T]]
		+	[[Category: Carrondo, M A]]
	[[Category: Frazao, C]]		[[Category: Frazao, C]]
		+	[[Category: Romao, C V]]
		+	[[Category: Teixeira, M]]
		+	[[Category: Vicente, J B]]
		+	[[Category: Diiron center]]
		+	[[Category: Flavodiiron protein]]
		+	[[Category: Flavorubredoxin]]
		+	[[Category: Nitric oxide reductase]]
		+	[[Category: Oxidoreductase]]

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

OCA — Wed, 10 Aug 2016 14:38:39 GMT

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

←Older revision

Revision as of 14:38, 10 August 2016

OCA: New page: '''Unreleased structure''' The entry 5lmc is ON HOLD until Paper Publication Authors: Romao, C.V., Borges, P.T., Vicente, J.B., Carrondo, M.A., Teixeira, M., Frazao, C. Description: Ox...

OCA — Wed, 10 Aug 2016 14:38:38 GMT

New page: '''Unreleased structure''' The entry 5lmc is ON HOLD until Paper Publication Authors: Romao, C.V., Borges, P.T., Vicente, J.B., Carrondo, M.A., Teixeira, M., Frazao, C. Description: Ox...

New page

'''Unreleased structure'''

The entry 5lmc is ON HOLD until Paper Publication

Authors: Romao, C.V., Borges, P.T., Vicente, J.B., Carrondo, M.A., Teixeira, M., Frazao, C.

Description: Oxidized flavodiiron core of Escherichia coli flavorubredoxin, including the Fe-4SG atoms from its rubredoxin domain
[[Category: Unreleased Structures]]
[[Category: Borges, P.T]]
[[Category: Romao, C.V]]
[[Category: Carrondo, M.A]]
[[Category: Vicente, J.B]]
[[Category: Teixeira, M]]
[[Category: Frazao, C]]