3nn4 - Revision history

OCA at 06:42, 3 April 2024

OCA — Wed, 03 Apr 2024 06:42:06 GMT

←Older revision		Revision as of 06:42, 3 April 2024
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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=3nn4 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=3nn4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Chlorite dismutase (Cld) is a unique heme enzyme which transforms chlorite to chloride and molecular oxygen (reaction: ClO(2)(-)-->Cl(-)+O(2)). Since bacteria with Cld play significant roles in the bioremediation of industrially contaminated sites and also in wastewater treatment, it is of high interest to understand the molecular mechanism of chlorite detoxification. Here we investigate a highly active Cld from Candidatus Nitrospira defluvii (NdCld), a key nitrifier in biological wastewater treatment, using a comprehensive structural, biochemical and bioinformatics approach. We determined the crystal structure of Cld from Candidatus Nitrospira defluvii and showed that functional NdCld is a homopentamer possessing a fold found in other Clds and Cld-like enzymes. To investigate the Cld function in more detail, site-directed mutagenesis of a catalytically important residue (Arg173) was performed and two enzyme mutants were structurally and biochemically characterized. Arginine 173 is demonstrated to play a key role in (i) controlling of ligand and substrate access and binding and (ii) in chlorite dismutation reaction. The flexible residue modulates the electrostatic potential and size of the active site entrance and might be involved in keeping transiently formed hypochlorite in place for final molecular oxygen and chloride formation. Furthermore, using a structure-based sequence alignment, we show that the residue corresponding to Arg173 is conserved in all known active forms of Cld and propose it as a marker for Cld activity in yet uncharacterized Cld-like proteins. Finally, our analysis indicates that all Clds and Cld-like enzymes employ a non-covalently bound heme as a cofactor.
-
-	Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue.,Kostan J, Sjoblom B, Maixner F, Mlynek G, Furtmuller PG, Obinger C, Wagner M, Daims H, Djinovic-Carugo K J Struct Biol. 2010 Jun 22. PMID:20600954<ref>PMID:20600954</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3nn4" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 00:32, 28 December 2023

OCA — Thu, 28 Dec 2023 00:32:40 GMT

←Older revision		Revision as of 00:32, 28 December 2023
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	<StructureSection load='3nn4' size='340' side='right'caption='[[3nn4]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3nn4' size='340' side='right'caption='[[3nn4]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nn4]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"candidatus_nitrospira_defluvii"_spieck_et_al._2006 "candidatus nitrospira~~ defluvii~~" spieck et al. 2006~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NN4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3NN4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nn4]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Nitrospira_defluvii Nitrospira defluvii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NN4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NN4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.7Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3nn1\|3nn1]], [[3nn2\|3nn2]], [[3nn3\|3nn3]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Chlorite_O(2)-lyase Chlorite O(2)-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.49 1.13.11.49]~~ </~~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=3nn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nn4 OCA], [https://pdbe.org/3nn4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nn4 RCSB], [https://www.ebi.ac.uk/pdbsum/3nn4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nn4 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=3nn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nn4 OCA], [~~http~~://pdbe.org/3nn4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3nn4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3nn4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3nn4 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B3U4H7_9BACT B3U4H7_9BACT]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Candidatus nitrospira defluvii spieck et al. 2006]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Daims, H]]	+	[[Category: Nitrospira defluvii]]
-	[[Category: Djinovic-Carugo, K]]	+	[[Category: Daims H]]
-	[[Category: Furtmueller~~, P G~~]]	+	[[Category: Djinovic-Carugo K]]
-	[[Category: Kostan, J]]	+	[[Category: Furtmueller PG]]
-	[[Category: Maixner, F]]	+	[[Category: Kostan J]]
-	[[Category: Mlynek, G]]	+	[[Category: Maixner F]]
-	[[Category: Obinger, C]]	+	[[Category: Mlynek G]]
-	[[Category: Sjoeblom, B]]	+	[[Category: Obinger C]]
-	[[Category: Wagner, M]]	+	[[Category: Sjoeblom B]]
-	~~[[Category: Chlorite dismutation]]~~	+	[[Category: Wagner M]]
-	~~[[Category: Ferredoxin like fold]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Periplasmatic~~]]	+

OCA at 08:05, 4 November 2020

OCA — Wed, 04 Nov 2020 08:05:35 GMT

←Older revision		Revision as of 08:05, 4 November 2020
Line 1:		Line 1:

	==Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant==		==Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant==
-	<StructureSection load='3nn4' size='340' side='right' caption='[[3nn4]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='3nn4' size='340' side='right'caption='[[3nn4]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nn4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"candidatus_nitrospira_defluvii"_spieck_et_al._2006 "candidatus nitrospira defluvii" spieck et al. 2006]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NN4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3NN4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nn4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"candidatus_nitrospira_defluvii"_spieck_et_al._2006 "candidatus nitrospira defluvii" spieck et al. 2006]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NN4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3NN4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nn1\|3nn1]], [[3nn2\|3nn2]], [[3nn3\|3nn3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nn1\|3nn1]], [[3nn2\|3nn2]], [[3nn3\|3nn3]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chlorite_O(2)-lyase Chlorite O(2)-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.49 1.13.11.49] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chlorite_O(2)-lyase Chlorite O(2)-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.49 1.13.11.49] </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=3nn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nn4 OCA], [http://pdbe.org/3nn4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nn4 RCSB], [http://www.ebi.ac.uk/pdbsum/3nn4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nn4 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=3nn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nn4 OCA], [http://pdbe.org/3nn4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nn4 RCSB], [http://www.ebi.ac.uk/pdbsum/3nn4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nn4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Candidatus nitrospira defluvii spieck et al. 2006]]		[[Category: Candidatus nitrospira defluvii spieck et al. 2006]]
		+	[[Category: Large Structures]]
	[[Category: Daims, H]]		[[Category: Daims, H]]
	[[Category: Djinovic-Carugo, K]]		[[Category: Djinovic-Carugo, K]]

OCA at 10:17, 30 January 2019

OCA — Wed, 30 Jan 2019 10:17:48 GMT

←Older revision		Revision as of 10:17, 30 January 2019
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nn/3nn4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nn/3nn4_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 04:55, 5 August 2016

OCA — Fri, 05 Aug 2016 04:55:44 GMT

←Older revision		Revision as of 04:55, 5 August 2016
Line 1:		Line 1:
		+
	==Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant==		==Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant==
	<StructureSection load='3nn4' size='340' side='right' caption='[[3nn4]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='3nn4' size='340' side='right' caption='[[3nn4]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3nn4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Candidatus_nitrospira_defluvii Candidatus~~ nitrospira defluvii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NN4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NN4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3nn4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/"candidatus_nitrospira_defluvii"_spieck_et_al._2006 "candidatus nitrospira defluvii" spieck et al. 2006]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NN4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NN4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nn1\|3nn1]], [[3nn2\|3nn2]], [[3nn3\|3nn3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nn1\|3nn1]], [[3nn2\|3nn2]], [[3nn3\|3nn3]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chlorite_O(2)-lyase Chlorite O(2)-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.49 1.13.11.49] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chlorite_O(2)-lyase Chlorite O(2)-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.49 1.13.11.49] </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=3nn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nn4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nn4 RCSB], [http://www.ebi.ac.uk/pdbsum/3nn4 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=3nn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nn4 OCA], [http://pdbe.org/3nn4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3nn4 RCSB], [http://www.ebi.ac.uk/pdbsum/3nn4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3nn4 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		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=3nn4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		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 3nn4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Candidatus nitrospira defluvii]]	+	[[Category: Candidatus nitrospira defluvii spieck et al. 2006]]
	[[Category: Daims, H]]		[[Category: Daims, H]]
	[[Category: Djinovic-Carugo, K]]		[[Category: Djinovic-Carugo, K]]

OCA at 07:14, 19 December 2014

OCA — Fri, 19 Dec 2014 07:14:02 GMT

←Older revision		Revision as of 07:14, 19 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3nn4\| PDB=3nn4 \| SCENE= }}~~	+	==Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant==
-	===Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant===	+	<StructureSection load='3nn4' size='340' side='right' caption='[[3nn4]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20600954}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3nn4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Candidatus_nitrospira_defluvii Candidatus nitrospira defluvii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NN4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NN4 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3nn1\|3nn1]], [[3nn2\|3nn2]], [[3nn3\|3nn3]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Chlorite_O(2)-lyase Chlorite O(2)-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.13.11.49 1.13.11.49] </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=3nn4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nn4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3nn4 RCSB], [http://www.ebi.ac.uk/pdbsum/3nn4 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/nn/3nn4_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 ==
		+	Chlorite dismutase (Cld) is a unique heme enzyme which transforms chlorite to chloride and molecular oxygen (reaction: ClO(2)(-)-->Cl(-)+O(2)). Since bacteria with Cld play significant roles in the bioremediation of industrially contaminated sites and also in wastewater treatment, it is of high interest to understand the molecular mechanism of chlorite detoxification. Here we investigate a highly active Cld from Candidatus Nitrospira defluvii (NdCld), a key nitrifier in biological wastewater treatment, using a comprehensive structural, biochemical and bioinformatics approach. We determined the crystal structure of Cld from Candidatus Nitrospira defluvii and showed that functional NdCld is a homopentamer possessing a fold found in other Clds and Cld-like enzymes. To investigate the Cld function in more detail, site-directed mutagenesis of a catalytically important residue (Arg173) was performed and two enzyme mutants were structurally and biochemically characterized. Arginine 173 is demonstrated to play a key role in (i) controlling of ligand and substrate access and binding and (ii) in chlorite dismutation reaction. The flexible residue modulates the electrostatic potential and size of the active site entrance and might be involved in keeping transiently formed hypochlorite in place for final molecular oxygen and chloride formation. Furthermore, using a structure-based sequence alignment, we show that the residue corresponding to Arg173 is conserved in all known active forms of Cld and propose it as a marker for Cld activity in yet uncharacterized Cld-like proteins. Finally, our analysis indicates that all Clds and Cld-like enzymes employ a non-covalently bound heme as a cofactor.

-	~~==About this Structure==~~	+	Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium "Candidatus Nitrospira defluvii": Identification of a catalytically important amino acid residue.,Kostan J, Sjoblom B, Maixner F, Mlynek G, Furtmuller PG, Obinger C, Wagner M, Daims H, Djinovic-Carugo K J Struct Biol. 2010 Jun 22. PMID:20600954<ref>PMID:20600954</ref>
-	~~[[3nn4]] is a 5 chain structure with sequence~~ from ~~[http://en.wikipedia.org/wiki/Candidatus_nitrospira_defluvii~~ Candidatus ~~nitrospira~~ defluvii~~]. Full crystallographic information is available from [http~~:~~//oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=3NN4 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:020600954</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Candidatus nitrospira defluvii]]		[[Category: Candidatus nitrospira defluvii]]
-	[[Category: Daims, H.]]	+	[[Category: Daims, H]]
-	[[Category: Djinovic-Carugo, K.]]	+	[[Category: Djinovic-Carugo, K]]
-	[[Category: Furtmueller, P G.]]	+	[[Category: Furtmueller, P G]]
-	[[Category: Kostan, J.]]	+	[[Category: Kostan, J]]
-	[[Category: Maixner, F.]]	+	[[Category: Maixner, F]]
-	[[Category: Mlynek, G.]]	+	[[Category: Mlynek, G]]
-	[[Category: Obinger, C.]]	+	[[Category: Obinger, C]]
-	[[Category: Sjoeblom, B.]]	+	[[Category: Sjoeblom, B]]
-	[[Category: Wagner, M.]]	+	[[Category: Wagner, M]]
	[[Category: Chlorite dismutation]]		[[Category: Chlorite dismutation]]
	[[Category: Ferredoxin like fold]]		[[Category: Ferredoxin like fold]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Periplasmatic]]		[[Category: Periplasmatic]]

OCA: Protected "3nn4" [edit=sysop:move=sysop]

OCA — Wed, 24 Apr 2013 11:55:45 GMT

Protected "3nn4" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:55, 24 April 2013

OCA at 11:55, 24 April 2013

OCA — Wed, 24 Apr 2013 11:55:41 GMT

←Older revision		Revision as of 11:55, 24 April 2013
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-	{{Seed}}
-	[[Image:3nn4.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3nn4", creates the "Structure Box" on the page.
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-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-	-->
	{{STRUCTURE_3nn4\| PDB=3nn4 \| SCENE= }}		{{STRUCTURE_3nn4\| PDB=3nn4 \| SCENE= }}
-
	===Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant===		===Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20600954}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20600954 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_20600954}}		{{ABSTRACT_PUBMED_20600954}}

	==About this Structure==		==About this Structure==
-	~~3NN4~~ is a 5 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Candidatus_nitrospira_defluvii Candidatus nitrospira defluvii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NN4 OCA].	+	[[3nn4]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Candidatus_nitrospira_defluvii Candidatus nitrospira defluvii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NN4 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20600954~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020600954</ref><references group="xtra"/><references/>
	[[Category: Candidatus nitrospira defluvii]]		[[Category: Candidatus nitrospira defluvii]]
	[[Category: Daims, H.]]		[[Category: Daims, H.]]
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	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Periplasmatic]]		[[Category: Periplasmatic]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 4 08:22:05 2010''

OCA at 04:15, 4 August 2010

OCA — Wed, 04 Aug 2010 04:15:27 GMT

←Older revision		Revision as of 04:15, 4 August 2010
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	{{Seed}}		{{Seed}}
-	[[Image:3nn4.~~jpg~~\|left\|200px]]	+	[[Image:3nn4.png\|left\|200px]]

	<!--		<!--
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	[[Category: Periplasmatic]]		[[Category: Periplasmatic]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jul 28 12~~:42:35 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 4 08:22:05 2010''

OCA at 08:35, 28 July 2010

OCA — Wed, 28 Jul 2010 08:35:54 GMT

←Older revision		Revision as of 08:35, 28 July 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3nn4.jpg\|left\|200px]]

-	The ~~entry 3nn4~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3nn4", 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_3nn4\| PDB=3nn4 \| SCENE= }}

-	~~Authors: Kostan, J., Sjoeblom, B., Maixner, F., Mlynek, G., Furtmueller, P.G., Obinger, C., Wagner, M., Daims, H., Djinovic-Carugo, K.~~	+	===Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant===

-	Description: Structure of chlorite dismutase from Candidatus Nitrospira defluvii R173K mutant

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul ~~14 16~~:07:57 2010''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20600954}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20600954 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20600954}}
		+
		+	==About this Structure==
		+	3NN4 is a 5 chains structure with sequences from [http://en.wikipedia.org/wiki/Candidatus_nitrospira_defluvii Candidatus nitrospira defluvii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NN4 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20600954</ref><references group="xtra"/>
		+	[[Category: Candidatus nitrospira defluvii]]
		+	[[Category: Daims, H.]]
		+	[[Category: Djinovic-Carugo, K.]]
		+	[[Category: Furtmueller, P G.]]
		+	[[Category: Kostan, J.]]
		+	[[Category: Maixner, F.]]
		+	[[Category: Mlynek, G.]]
		+	[[Category: Obinger, C.]]
		+	[[Category: Sjoeblom, B.]]
		+	[[Category: Wagner, M.]]
		+	[[Category: Chlorite dismutation]]
		+	[[Category: Ferredoxin like fold]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Periplasmatic]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 28 12:42:35 2010''