1ycf - Revision history

OCA at 08:56, 14 February 2024

OCA — Wed, 14 Feb 2024 08:56:32 GMT

←Older revision		Revision as of 08:56, 14 February 2024
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	<StructureSection load='1ycf' size='340' side='right'caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1ycf' size='340' side='right'caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_35608 Atcc 35608~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Moorella_thermoacetica Moorella thermoacetica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YCF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1e5d\|1e5d]], [[1ycg\|1ycg]], [[1ych\|1ych]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [https://pdbe.org/1ycf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [https://www.ebi.ac.uk/pdbsum/1ycf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ycf 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=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [https://pdbe.org/1ycf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [https://www.ebi.ac.uk/pdbsum/1ycf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ycf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/FPRA_MOOTA FPRA_MOOTA]] Has nitric oxide reductase activity in combination with Hrb; probably involved in nitrosative stress protection.	+	[https://www.uniprot.org/uniprot/FPRA_MOOTA FPRA_MOOTA] Has nitric oxide reductase activity in combination with Hrb; probably involved in nitrosative stress protection.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ycf ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ycf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Several members of a widespread class of bacterial and archaeal metalloflavoproteins, called FprA, likely function as scavenging nitric oxide reductases (S-NORs). However, the only published X-ray crystal structure of an FprA is for a protein characterized as a rubredoxin:dioxygen oxidoreductase (ROO) from Desulfovibrio gigas. Therefore, the crystal structure of Moorella thermoacetica FprA, which has been established to function as an S-NOR, was solved in three different states: as isolated, reduced, and reduced, NO-reacted. As is the case for D. gigas ROO, the M. thermoacetica FprA contains a solvent-bridged non-heme, non-sulfur diiron site with five-coordinate iron centers bridged by an aspartate, and terminal glutamate, aspartate, and histidine ligands. However, the M. thermoacetica FprA diiron site showed four His ligands, two to each iron, in all three states, whereas the D. gigas ROO diiron site was reported to contain only three His ligands, even though the fourth His residue is conserved. The Fe1-Fe2 distance within the diiron site of M. thermoacetica FprA remained at 3.2-3.4 A with little or no movement of the protein ligands in the three different states and with conservation of the two proximal open coordination sites. Molecular modeling indicated that each open coordination site can accommodate an end-on NO. This relatively rigid and symmetrical diiron site structure is consistent with formation of a diferrous dinitrosyl as the committed catalytic intermediate leading to formation of N(2)O. These results provide new insight into the structural features that fine-tune biological non-heme diiron sites for dioxygen activation vs nitric oxide reduction.
-
-	X-ray crystal structures of Moorella thermoacetica FprA. Novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase.,Silaghi-Dumitrescu R, Kurtz DM Jr, Ljungdahl LG, Lanzilotta WN Biochemistry. 2005 May 3;44(17):6492-501. PMID:15850383<ref>PMID:15850383</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ycf" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 35608]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kurtz, D M~~]]	+	[[Category: Moorella thermoacetica]]
-	[[Category: ~~Lanzilotta, W N~~]]	+	[[Category: Kurtz DM]]
-	[[Category: ~~Silaghi-Dumitrescu, R~~]]	+	[[Category: Lanzilotta WN]]
-	[[Category: ~~Diferrous~~-~~dinitrosyl]]~~	+	[[Category: Silaghi-Dumitrescu R]]
-	~~[[Category: Diron site structure]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Scavenging nitric oxide reductase~~]]	+

OCA at 06:33, 6 October 2021

OCA — Wed, 06 Oct 2021 06:33:12 GMT

←Older revision		Revision as of 06:33, 6 October 2021
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	<StructureSection load='1ycf' size='340' side='right'caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1ycf' size='340' side='right'caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_35608 Atcc 35608]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35608 Atcc 35608]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YCF FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e5d\|1e5d]], [[1ycg\|1ycg]], [[1ych\|1ych]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1e5d\|1e5d]], [[1ycg\|1ycg]], [[1ych\|1ych]]</div></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=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [~~http~~://pdbe.org/1ycf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ycf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ycf 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=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [https://pdbe.org/1ycf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [https://www.ebi.ac.uk/pdbsum/1ycf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ycf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/FPRA_MOOTA FPRA_MOOTA]] Has nitric oxide reductase activity in combination with Hrb; probably involved in nitrosative stress protection.	+	[[https://www.uniprot.org/uniprot/FPRA_MOOTA FPRA_MOOTA]] Has nitric oxide reductase activity in combination with Hrb; probably involved in nitrosative stress protection.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:12, 4 December 2019

OCA — Wed, 04 Dec 2019 11:12:17 GMT

←Older revision		Revision as of 11:12, 4 December 2019
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	==Oxidized (di-ferric) FprA from Moorella thermoacetica==		==Oxidized (di-ferric) FprA from Moorella thermoacetica==
-	<StructureSection load='1ycf' size='340' side='right' caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='1ycf' size='340' side='right'caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35608 Atcc 35608]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YCF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35608 Atcc 35608]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YCF FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 35608]]		[[Category: Atcc 35608]]
		+	[[Category: Large Structures]]
	[[Category: Kurtz, D M]]		[[Category: Kurtz, D M]]
	[[Category: Lanzilotta, W N]]		[[Category: Lanzilotta, W N]]

OCA at 06:34, 31 January 2018

OCA — Wed, 31 Jan 2018 06:34:29 GMT

←Older revision		Revision as of 06:34, 31 January 2018
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yc/1ycf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yc/1ycf_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 06:28, 21 September 2016

OCA — Wed, 21 Sep 2016 06:28:35 GMT

←Older revision		Revision as of 06:28, 21 September 2016
Line 1:		Line 1:
		+
	==Oxidized (di-ferric) FprA from Moorella thermoacetica==		==Oxidized (di-ferric) FprA from Moorella thermoacetica==
	<StructureSection load='1ycf' size='340' side='right' caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1ycf' size='340' side='right' caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e5d\|1e5d]], [[1ycg\|1ycg]], [[1ych\|1ych]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e5d\|1e5d]], [[1ycg\|1ycg]], [[1ych\|1ych]]</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=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [http://pdbe.org/1ycf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [http://www.ebi.ac.uk/pdbsum/1ycf PDBsum]</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=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [http://pdbe.org/1ycf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [http://www.ebi.ac.uk/pdbsum/1ycf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ycf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 05:51, 10 February 2016

OCA — Wed, 10 Feb 2016 05:51:05 GMT

←Older revision		Revision as of 05:51, 10 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ycf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:58, 11 September 2015

OCA — Fri, 11 Sep 2015 05:58:59 GMT

←Older revision		Revision as of 05:58, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1ycf' size='340' side='right' caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='1ycf' size='340' side='right' caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Moorella_thermoacetica Moorella thermoacetica~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YCF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_35608 Atcc 35608]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YCF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e5d\|1e5d]], [[1ycg\|1ycg]], [[1ych\|1ych]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e5d\|1e5d]], [[1ycg\|1ycg]], [[1ych\|1ych]]</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=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [http://www.ebi.ac.uk/pdbsum/1ycf PDBsum]</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=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [http://pdbe.org/1ycf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [http://www.ebi.ac.uk/pdbsum/1ycf PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FPRA_MOOTA FPRA_MOOTA]] Has nitric oxide reductase activity in combination with Hrb; probably involved in nitrosative stress protection.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 25:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1ycf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Moorella thermoacetica~~]]	+	[[Category: Atcc 35608]]
	[[Category: Kurtz, D M]]		[[Category: Kurtz, D M]]
	[[Category: Lanzilotta, W N]]		[[Category: Lanzilotta, W N]]

OCA at 08:57, 8 January 2015

OCA — Thu, 08 Jan 2015 08:57:16 GMT

←Older revision		Revision as of 08:57, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Moorella_thermoacetica Moorella thermoacetica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YCF FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Moorella_thermoacetica Moorella thermoacetica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YCF FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e5d\|1e5d]], [[1ycg\|1ycg]], [[1ych\|1ych]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e5d\|1e5d]], [[1ycg\|1ycg]], [[1ych\|1ych]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [http://www.ebi.ac.uk/pdbsum/1ycf PDBsum]</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=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [http://www.ebi.ac.uk/pdbsum/1ycf PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Moorella thermoacetica]]		[[Category: Moorella thermoacetica]]
-	[[Category: Kurtz, D M.]]	+	[[Category: Kurtz, D M]]
-	[[Category: Lanzilotta, W N.]]	+	[[Category: Lanzilotta, W N]]
-	[[Category: Silaghi-Dumitrescu, R.]]	+	[[Category: Silaghi-Dumitrescu, R]]
	[[Category: Diferrous-dinitrosyl]]		[[Category: Diferrous-dinitrosyl]]
	[[Category: Diron site structure]]		[[Category: Diron site structure]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Scavenging nitric oxide reductase]]		[[Category: Scavenging nitric oxide reductase]]

OCA at 19:23, 29 September 2014

OCA — Mon, 29 Sep 2014 19:23:38 GMT

←Older revision		Revision as of 19:23, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1ycf.~~png~~\|~~left~~\|200px]]	+	==Oxidized (di-ferric) FprA from Moorella thermoacetica==
		+	<StructureSection load='1ycf' size='340' side='right' caption='[[1ycf]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ycf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Moorella_thermoacetica Moorella thermoacetica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YCF FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FEO:MU-OXO-DIIRON'>FEO</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1e5d\|1e5d]], [[1ycg\|1ycg]], [[1ych\|1ych]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ycf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ycf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ycf RCSB], [http://www.ebi.ac.uk/pdbsum/1ycf PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yc/1ycf_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Several members of a widespread class of bacterial and archaeal metalloflavoproteins, called FprA, likely function as scavenging nitric oxide reductases (S-NORs). However, the only published X-ray crystal structure of an FprA is for a protein characterized as a rubredoxin:dioxygen oxidoreductase (ROO) from Desulfovibrio gigas. Therefore, the crystal structure of Moorella thermoacetica FprA, which has been established to function as an S-NOR, was solved in three different states: as isolated, reduced, and reduced, NO-reacted. As is the case for D. gigas ROO, the M. thermoacetica FprA contains a solvent-bridged non-heme, non-sulfur diiron site with five-coordinate iron centers bridged by an aspartate, and terminal glutamate, aspartate, and histidine ligands. However, the M. thermoacetica FprA diiron site showed four His ligands, two to each iron, in all three states, whereas the D. gigas ROO diiron site was reported to contain only three His ligands, even though the fourth His residue is conserved. The Fe1-Fe2 distance within the diiron site of M. thermoacetica FprA remained at 3.2-3.4 A with little or no movement of the protein ligands in the three different states and with conservation of the two proximal open coordination sites. Molecular modeling indicated that each open coordination site can accommodate an end-on NO. This relatively rigid and symmetrical diiron site structure is consistent with formation of a diferrous dinitrosyl as the committed catalytic intermediate leading to formation of N(2)O. These results provide new insight into the structural features that fine-tune biological non-heme diiron sites for dioxygen activation vs nitric oxide reduction.

-	~~{{STRUCTURE_1ycf\| PDB=1ycf \| SCENE= }}~~	+	X-ray crystal structures of Moorella thermoacetica FprA. Novel diiron site structure and mechanistic insights into a scavenging nitric oxide reductase.,Silaghi-Dumitrescu R, Kurtz DM Jr, Ljungdahl LG, Lanzilotta WN Biochemistry. 2005 May 3;44(17):6492-501. PMID:15850383<ref>PMID:15850383</ref>

-	~~===Oxidized (di-ferric) FprA from Moorella thermoacetica===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15850383}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1ycf]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Moorella_thermoacetica Moorella thermoacetica]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1YCF OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015850383<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Moorella thermoacetica]]		[[Category: Moorella thermoacetica]]
	[[Category: Kurtz, D M.]]		[[Category: Kurtz, D M.]]

OCA: Protected "1ycf" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 17:03:42 GMT

Protected "1ycf" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:03, 5 January 2013