1lko - Revision history

OCA at 07:33, 14 February 2024

OCA — Wed, 14 Feb 2024 07:33:49 GMT

←Older revision		Revision as of 07:33, 14 February 2024
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	<StructureSection load='1lko' size='340' side='right'caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='1lko' size='340' side='right'caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_29579 Atcc 29579~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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]] 1.63Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1lkm\|1lkm]], [[1lkp\|1lkp]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [https://pdbe.org/1lko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [https://www.ebi.ac.uk/pdbsum/1lko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lko 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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [https://pdbe.org/1lko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [https://www.ebi.ac.uk/pdbsum/1lko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lko ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH]] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).	+	[https://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</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=1lko 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=1lko ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Rubrerythrin (Rbr) is a 44-kDa homodimeric protein, found in many air-sensitive bacteria and archaea, which contains a unique combination of a rubredoxin-like [Fe(SCys)(4)] site and a non-sulfur, oxo/dicarboxylato-bridged diiron site. The diiron site structure resembles those found in O2-activating diiron enzymes. However, Rbr instead appears to function as a hydrogen peroxide reductase (peroxidase). The diferrous site in all-ferrous Rbr (Rbr(red)) shows a much greater reactivity with H2O2 than does the diferric site in all-ferric Rbr (Rbr(ox)), but only the latter structure has been reported. Here we report the X-ray crystal structures of the recombinant Rbr(red) from the sulfate reducing bacterium, Desulfovibrio vulgaris, as well as its azide adduct (Rbr(red)N3). We have also redetermined the structure of Rbr(ox) to a higher resolution than previously reported. The structural differences between Rbr(ox) and Rbr(red) are localized entirely at the diiron site. The most striking structural change upon reduction of the diferric to the diferrous site of Rbr is a 1.8-A movement of one iron away from a unique glutamate carboxylate ligand and toward a trans-disposed histidine side chain, which replaces the glutamate as a ligand. This movement increases the inter-iron distance from 3.3 to 4 A. Rbr(red)N(3) shows this same iron movement and His-->Glu ligand replacement relative to Rbr(ox), and, in addition, an azide coordinated to the diiron site in a cis mu-1,3 fashion, replacing two solvent ligands in Rbr(red). Relative to those in O2-activating enzymes, the bridging carboxylate ligation of the Rbr diiron site is less flexible upon diferric/diferrous interconversion. The diferrous site is also much more rigid, symmetrical, and solvent-exposed than those in O2-activating enzymes. On the basis of these unique structural features, a mechanism is proposed for facile reduction of hydrogen peroxide by Rbr involving a cis mu-eta(2) H2O2 diferrous intermediate.
-
-	X-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase.,Jin S, Kurtz DM Jr, Liu ZJ, Rose J, Wang BC J Am Chem Soc. 2002 Aug 21;124(33):9845-55. PMID:12175244<ref>PMID:12175244</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1lko" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 29579~~]]	+	[[Category: Desulfovibrio vulgaris]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jin, S]]	+	[[Category: Jin S]]
-	[[Category: Kurtz~~, D M~~]]	+	[[Category: Kurtz Jr DM]]
-	[[Category: Liu~~, Z J~~]]	+	[[Category: Liu ZJ]]
-	[[Category: Rose, J]]	+	[[Category: Rose J]]
-	[[Category: Wang~~, B C]]~~	+	[[Category: Wang BC]]
-	~~[[Category: Diiron]]~~	+
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Four-helix bundle]]~~	+
-	~~[[Category: Reduced form]]~~	+
-	~~[[Category: Rubredoxin-like]]~~	+
-	~~[[Category: Rubrerythrin~~]]	+

OCA at 06:45, 18 August 2021

OCA — Wed, 18 Aug 2021 06:45:57 GMT

←Older revision		Revision as of 06:45, 18 August 2021
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	<StructureSection load='1lko' size='340' side='right'caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='1lko' size='340' side='right'caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1LKO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LKO FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lkm\|1lkm]], [[1lkp\|1lkp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lkm\|1lkm]], [[1lkp\|1lkp]]</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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [~~http~~://pdbe.org/1lko PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1lko PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1lko 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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [https://pdbe.org/1lko PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [https://www.ebi.ac.uk/pdbsum/1lko PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lko ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH]] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).	+	[[https://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH]] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 12:26, 13 November 2019

OCA — Wed, 13 Nov 2019 12:26:32 GMT

←Older revision		Revision as of 12:26, 13 November 2019
Line 1:		Line 1:

	==Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form==		==Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form==
-	<StructureSection load='1lko' size='340' side='right' caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>	+	<StructureSection load='1lko' size='340' side='right'caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKO FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKO FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 29579]]		[[Category: Atcc 29579]]
		+	[[Category: Large Structures]]
	[[Category: Jin, S]]		[[Category: Jin, S]]
	[[Category: Kurtz, D M]]		[[Category: Kurtz, D M]]

OCA at 08:02, 31 January 2018

OCA — Wed, 31 Jan 2018 08:02:05 GMT

←Older revision		Revision as of 08:02, 31 January 2018
Line 1:		Line 1:
		+
	==Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form==		==Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form==
	<StructureSection load='1lko' size='340' side='right' caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='1lko' size='340' side='right' caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lkm\|1lkm]], [[1lkp\|1lkp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lkm\|1lkm]], [[1lkp\|1lkp]]</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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [http://pdbe.org/1lko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [http://www.ebi.ac.uk/pdbsum/1lko 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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [http://pdbe.org/1lko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [http://www.ebi.ac.uk/pdbsum/1lko PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1lko ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lk/1lko_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lk/1lko_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 17:19, 9 February 2016

OCA — Tue, 09 Feb 2016 17:19:16 GMT

←Older revision		Revision as of 17:19, 9 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=1lko ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:26, 11 September 2015

OCA — Fri, 11 Sep 2015 00:26:39 GMT

←Older revision		Revision as of 00:26, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1lko' size='340' side='right' caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='1lko' size='340' side='right' caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Desulfovibrio_vulgaris Desulfovibrio vulgaris~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_29579 Atcc 29579]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKO FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lkm\|1lkm]], [[1lkp\|1lkp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lkm\|1lkm]], [[1lkp\|1lkp]]</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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [http://www.ebi.ac.uk/pdbsum/1lko 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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [http://pdbe.org/1lko PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [http://www.ebi.ac.uk/pdbsum/1lko PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		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 1lko" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Desulfovibrio vulgaris~~]]	+	[[Category: Atcc 29579]]
	[[Category: Jin, S]]		[[Category: Jin, S]]
	[[Category: Kurtz, D M]]		[[Category: Kurtz, D M]]

OCA at 08:19, 25 December 2014

OCA — Thu, 25 Dec 2014 08:19:54 GMT

←Older revision		Revision as of 08:19, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKO FirstGlance]. <br>		<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKO FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lkm\|1lkm]], [[1lkp\|1lkp]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lkm\|1lkm]], [[1lkp\|1lkp]]</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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [http://www.ebi.ac.uk/pdbsum/1lko 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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [http://www.ebi.ac.uk/pdbsum/1lko PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RUBY_DESVH RUBY_DESVH]] May provide oxidative stress protection via catalytic reduction of intracellular hydrogen peroxide (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
-	[[Category: Jin, S.]]	+	[[Category: Jin, S]]
-	[[Category: Kurtz, D M.]]	+	[[Category: Kurtz, D M]]
-	[[Category: Liu, Z J.]]	+	[[Category: Liu, Z J]]
-	[[Category: Rose, J.]]	+	[[Category: Rose, J]]
-	[[Category: Wang, B C.]]	+	[[Category: Wang, B C]]
	[[Category: Diiron]]		[[Category: Diiron]]
	[[Category: Electron transport]]		[[Category: Electron transport]]

OCA at 14:34, 28 September 2014

OCA — Sun, 28 Sep 2014 14:34:07 GMT

←Older revision		Revision as of 14:34, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1lko.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form==
		+	<StructureSection load='1lko' size='340' side='right' caption='[[1lko]], [[Resolution\|resolution]] 1.63Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1lko]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1LKO FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lkm\|1lkm]], [[1lkp\|1lkp]]</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=1lko FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lko OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1lko RCSB], [http://www.ebi.ac.uk/pdbsum/1lko 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/lk/1lko_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 ==
		+	Rubrerythrin (Rbr) is a 44-kDa homodimeric protein, found in many air-sensitive bacteria and archaea, which contains a unique combination of a rubredoxin-like [Fe(SCys)(4)] site and a non-sulfur, oxo/dicarboxylato-bridged diiron site. The diiron site structure resembles those found in O2-activating diiron enzymes. However, Rbr instead appears to function as a hydrogen peroxide reductase (peroxidase). The diferrous site in all-ferrous Rbr (Rbr(red)) shows a much greater reactivity with H2O2 than does the diferric site in all-ferric Rbr (Rbr(ox)), but only the latter structure has been reported. Here we report the X-ray crystal structures of the recombinant Rbr(red) from the sulfate reducing bacterium, Desulfovibrio vulgaris, as well as its azide adduct (Rbr(red)N3). We have also redetermined the structure of Rbr(ox) to a higher resolution than previously reported. The structural differences between Rbr(ox) and Rbr(red) are localized entirely at the diiron site. The most striking structural change upon reduction of the diferric to the diferrous site of Rbr is a 1.8-A movement of one iron away from a unique glutamate carboxylate ligand and toward a trans-disposed histidine side chain, which replaces the glutamate as a ligand. This movement increases the inter-iron distance from 3.3 to 4 A. Rbr(red)N(3) shows this same iron movement and His-->Glu ligand replacement relative to Rbr(ox), and, in addition, an azide coordinated to the diiron site in a cis mu-1,3 fashion, replacing two solvent ligands in Rbr(red). Relative to those in O2-activating enzymes, the bridging carboxylate ligation of the Rbr diiron site is less flexible upon diferric/diferrous interconversion. The diferrous site is also much more rigid, symmetrical, and solvent-exposed than those in O2-activating enzymes. On the basis of these unique structural features, a mechanism is proposed for facile reduction of hydrogen peroxide by Rbr involving a cis mu-eta(2) H2O2 diferrous intermediate.

-	~~{{STRUCTURE_1lko\| PDB=1lko \| SCENE= }}~~	+	X-ray crystal structures of reduced rubrerythrin and its azide adduct: a structure-based mechanism for a non-heme diiron peroxidase.,Jin S, Kurtz DM Jr, Liu ZJ, Rose J, Wang BC J Am Chem Soc. 2002 Aug 21;124(33):9845-55. PMID:12175244<ref>PMID:12175244</ref>

-	~~===Crystal structure~~ of ~~Desulfovibrio vulgaris rubrerythrin all-iron(II) form===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12175244}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1lko]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012175244<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
	[[Category: Jin, S.]]		[[Category: Jin, S.]]

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

OCA — Wed, 05 Dec 2012 20:09:08 GMT

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

←Older revision

Revision as of 20:09, 5 December 2012

OCA at 20:09, 5 December 2012

OCA — Wed, 05 Dec 2012 20:09:05 GMT

←Older revision		Revision as of 20:09, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1lko.png\|left\|200px]]		[[Image:1lko.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1lko", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1lko\| PDB=1lko \| SCENE= }}		{{STRUCTURE_1lko\| PDB=1lko \| SCENE= }}

	===Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form===		===Crystal structure of Desulfovibrio vulgaris rubrerythrin all-iron(II) form===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12175244}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12175244 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12175244}}		{{ABSTRACT_PUBMED_12175244}}

	==About this Structure==		==About this Structure==
-	~~1LKO~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA].	+	[[1lko]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Desulfovibrio_vulgaris Desulfovibrio vulgaris]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LKO OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12175244~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012175244</ref><references group="xtra"/>
	[[Category: Desulfovibrio vulgaris]]		[[Category: Desulfovibrio vulgaris]]
	[[Category: Jin, S.]]		[[Category: Jin, S.]]
-	[[Category: ~~Jr.~~, D M~~.Kurtz~~.]]	+	[[Category: Kurtz, D M.]]
	[[Category: Liu, Z J.]]		[[Category: Liu, Z J.]]
	[[Category: Rose, J.]]		[[Category: Rose, J.]]
	[[Category: Wang, B C.]]		[[Category: Wang, B C.]]
	[[Category: Diiron]]		[[Category: Diiron]]
		+	[[Category: Electron transport]]
	[[Category: Four-helix bundle]]		[[Category: Four-helix bundle]]
	[[Category: Reduced form]]		[[Category: Reduced form]]
	[[Category: Rubredoxin-like]]		[[Category: Rubredoxin-like]]
	[[Category: Rubrerythrin]]		[[Category: Rubrerythrin]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:28:23 2009''