2z9d - Revision history

OCA at 13:27, 1 November 2023

OCA — Wed, 01 Nov 2023 13:27:08 GMT

←Older revision		Revision as of 13:27, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='2z9d' size='340' side='right'caption='[[2z9d]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2z9d' size='340' side='right'caption='[[2z9d]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z9d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z9d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z9D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</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]] 2.1Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[2z98\|2z98]]~~, [[~~2z9b~~\|~~2z9b]], [[2z9c\|2z9c~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>azoR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Azobenzene_reductase Azobenzene reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.6 1.7.1.6]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [https://pdbe.org/2z9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [https://www.ebi.ac.uk/pdbsum/2z9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9d 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=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [https://pdbe.org/2z9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [https://www.ebi.ac.uk/pdbsum/2z9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/AZOR_ECOLI AZOR_ECOLI]] Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity. The enzyme can reduce ethyl red and methyl red, but is not able to convert sulfonated azo dyes.<ref>PMID:2168383</ref>	+	[https://www.uniprot.org/uniprot/AZOR_ECOLI AZOR_ECOLI] Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity. The enzyme can reduce ethyl red and methyl red, but is not able to convert sulfonated azo dyes.<ref>PMID:2168383</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: Azobenzene reductase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ito, K]]	+	[[Category: Ito K]]
-	~~[[Category: Azoreductase]]~~	+
-	~~[[Category: Flavoprotein]]~~	+
-	~~[[Category: Fmn]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:48, 8 December 2021

OCA — Wed, 08 Dec 2021 10:48:38 GMT

←Older revision		Revision as of 10:48, 8 December 2021
Line 1:		Line 1:

	==The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals==		==The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals==
-	<StructureSection load='2z9d' size='340' side='right' caption='[[2z9d]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2z9d' size='340' side='right'caption='[[2z9d]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z9d]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z9d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z9D FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z98\|2z98]], [[2z9b\|2z9b]], [[2z9c\|2z9c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2z98\|2z98]], [[2z9b\|2z9b]], [[2z9c\|2z9c]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">azoR ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">azoR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Azobenzene_reductase Azobenzene reductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.6 1.7.1.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Azobenzene_reductase Azobenzene reductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.6 1.7.1.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [~~http~~://pdbe.org/2z9d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z9d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9d 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=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [https://pdbe.org/2z9d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [https://www.ebi.ac.uk/pdbsum/2z9d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/AZOR_ECOLI AZOR_ECOLI]] Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity. The enzyme can reduce ethyl red and methyl red, but is not able to convert sulfonated azo dyes.<ref>PMID:2168383</ref>	+	[[https://www.uniprot.org/uniprot/AZOR_ECOLI AZOR_ECOLI]] Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity. The enzyme can reduce ethyl red and methyl red, but is not able to convert sulfonated azo dyes.<ref>PMID:2168383</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Azobenzene reductase]]		[[Category: Azobenzene reductase]]
		+	[[Category: Large Structures]]
	[[Category: Ito, K]]		[[Category: Ito, K]]
	[[Category: Azoreductase]]		[[Category: Azoreductase]]

OCA at 09:11, 17 October 2018

OCA — Wed, 17 Oct 2018 09:11:08 GMT

←Older revision		Revision as of 09:11, 17 October 2018
Line 1:		Line 1:
		+
	==The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals==		==The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals==
	<StructureSection load='2z9d' size='340' side='right' caption='[[2z9d]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2z9d' size='340' side='right' caption='[[2z9d]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">azoR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">azoR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Azobenzene_reductase Azobenzene reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.6 1.7.1.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Azobenzene_reductase Azobenzene reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.6 1.7.1.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [http://pdbe.org/2z9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [http://www.ebi.ac.uk/pdbsum/2z9d 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=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [http://pdbe.org/2z9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [http://www.ebi.ac.uk/pdbsum/2z9d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z9d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z9/2z9d_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z9/2z9d_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 20:55, 7 February 2016

OCA — Sun, 07 Feb 2016 20:55:23 GMT

←Older revision		Revision as of 20:55, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='2z9d' size='340' side='right' caption='[[2z9d]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2z9d' size='340' side='right' caption='[[2z9d]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z9d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z9D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z9d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z9D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z98\|2z98]], [[2z9b\|2z9b]], [[2z9c\|2z9c]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z98\|2z98]], [[2z9b\|2z9b]], [[2z9c\|2z9c]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">azoR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">azoR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Azobenzene_reductase Azobenzene reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.6 1.7.1.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Azobenzene_reductase Azobenzene reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.6 1.7.1.6] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [http://www.ebi.ac.uk/pdbsum/2z9d 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=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [http://pdbe.org/2z9d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [http://www.ebi.ac.uk/pdbsum/2z9d PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 19:
	<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=2z9d ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 29:
	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 2z9d" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Azobenzene reductase]]		[[Category: Azobenzene reductase]]
-	[[Category: Escherichia coli]]
	[[Category: Ito, K]]		[[Category: Ito, K]]
	[[Category: Azoreductase]]		[[Category: Azoreductase]]

OCA at 18:11, 24 December 2014

OCA — Wed, 24 Dec 2014 18:11:21 GMT

←Older revision		Revision as of 18:11, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z9d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z9D FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z9d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z9D FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z98\|2z98]], [[2z9b\|2z9b]], [[2z9c\|2z9c]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z98\|2z98]], [[2z9b\|2z9b]], [[2z9c\|2z9c]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">azoR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">azoR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Azobenzene_reductase Azobenzene reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.6 1.7.1.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Azobenzene_reductase Azobenzene reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.6 1.7.1.6] </span></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=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [http://www.ebi.ac.uk/pdbsum/2z9d 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=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [http://www.ebi.ac.uk/pdbsum/2z9d PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AZOR_ECOLI AZOR_ECOLI]] Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity. The enzyme can reduce ethyl red and methyl red, but is not able to convert sulfonated azo dyes.<ref>PMID:2168383</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	[[Category: Azobenzene reductase]]		[[Category: Azobenzene reductase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Ito, K.]]	+	[[Category: Ito, K]]
	[[Category: Azoreductase]]		[[Category: Azoreductase]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]

OCA at 05:28, 2 October 2014

OCA — Thu, 02 Oct 2014 05:28:32 GMT

←Older revision		Revision as of 05:28, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2z9d.~~png~~\|~~left~~\|200px]]	+	==The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals==
		+	<StructureSection load='2z9d' size='340' side='right' caption='[[2z9d]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z9d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z9D FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2z98\|2z98]], [[2z9b\|2z9b]], [[2z9c\|2z9c]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">azoR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Azobenzene_reductase Azobenzene reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.1.6 1.7.1.6] </span></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=2z9d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z9d OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z9d RCSB], [http://www.ebi.ac.uk/pdbsum/2z9d 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/z9/2z9d_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 ==
		+	AzoR is an FMN-dependent NADH-azoreductase isolated from Escherichia coli as a protein responsible for the degradation of azo compounds. We previously reported the crystal structure of the enzyme in the oxidized form. In the present study, different structures of AzoR were determined under several conditions to obtain clues to the reaction mechanism of the enzyme. AzoR in its reduced form revealed a twisted butterfly bend of the isoalloxazine ring of the FMN cofactor and a rearrangement of solvent molecules. The crystal structure of oxidized AzoR in a different space group and the structure of the enzyme in complex with the inhibitor dicoumarol were also determined. These structures indicate that the formation of a hydrophobic part around the isoalloxazine ring is important for substrate binding and an electrostatic interaction between Arg-59 and the carboxyl group of the azo compound causes a substrate preference for methyl red over p-methyl red. The substitution of Arg-59 with Ala enhanced the Vmax value for p-methyl red 27-fold with a 3.8-fold increase of the Km value. This result indicates that Arg-59 decides the substrate specificity of AzoR. The Vmax value for the p-methyl red reduction of the R59A mutant is comparable with that for the methyl red reduction of the wild-type enzyme, whereas the activity toward methyl red was retained. These findings indicate the expansion of AzoR substrate specificity by a single amino acid substitution. Furthermore, we built an authentic model of the AzoR-methyl red complex based on the results of the study.

-	~~{{STRUCTURE_2z9d\| PDB=2z9d \| SCENE= }}~~	+	Expansion of substrate specificity and catalytic mechanism of azoreductase by X-ray crystallography and site-directed mutagenesis.,Ito K, Nakanishi M, Lee WC, Zhi Y, Sasaki H, Zenno S, Saigo K, Kitade Y, Tanokura M J Biol Chem. 2008 May 16;283(20):13889-96. Epub 2008 Mar 12. PMID:18337254<ref>PMID:18337254</ref>

-	~~===The crystal structure~~ of ~~AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18337254}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2z9d]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018337254<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Azobenzene reductase]]		[[Category: Azobenzene reductase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "2z9d" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 18:47:24 GMT

Protected "2z9d" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:47, 7 January 2013

OCA at 18:47, 7 January 2013

OCA — Mon, 07 Jan 2013 18:47:18 GMT

←Older revision		Revision as of 18:47, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2z9d.png\|left\|200px]]		[[Image:2z9d.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z9d", 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_2z9d\| PDB=2z9d \| SCENE= }}		{{STRUCTURE_2z9d\| PDB=2z9d \| SCENE= }}

	===The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals===		===The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18337254}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18337254 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18337254}}		{{ABSTRACT_PUBMED_18337254}}

	==About this Structure==		==About this Structure==
-	~~2Z9D~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA].	+	[[2z9d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18337254~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018337254</ref><references group="xtra"/>
	[[Category: Azobenzene reductase]]		[[Category: Azobenzene reductase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
Line 32:		Line 20:
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:26:40 2009''

OCA at 14:26, 16 February 2009

OCA — Mon, 16 Feb 2009 14:26:42 GMT

←Older revision		Revision as of 14:26, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Z9D is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA].	+	2Z9D is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Z9D OCA].

	==Reference==		==Reference==
-	Expansion of Substrate Specificity and Catalytic Mechanism of Azoreductase by X-ray Crystallography and Site-directed Mutagenesis., Ito K, Nakanishi M, Lee WC, Zhi Y, Sasaki H, Zenno S, Saigo K, Kitade Y, Tanokura M, J Biol Chem. 2008 May 16;283(20):13889-13896. Epub 2008 Mar 12. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18337254 18337254]~~	+	<ref group="xtra">PMID:18337254</ref><references group="xtra"/>
	[[Category: Azobenzene reductase]]		[[Category: Azobenzene reductase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Ito, K.]]		[[Category: Ito, K.]]
	[[Category: Azoreductase]]		[[Category: Azoreductase]]
Line 34:		Line 33:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 19~~:37:~~50 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:26:40 2009''

OCA at 16:38, 27 July 2008

OCA — Sun, 27 Jul 2008 16:38:00 GMT

←Older revision		Revision as of 16:38, 27 July 2008
Line 1:		Line 1:
-	[[Image:2z9d.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2z9d.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2z9d\| PDB=2z9d \| SCENE= }}		{{STRUCTURE_2z9d\| PDB=2z9d \| SCENE= }}

-	~~'''~~The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals~~'''~~	+	===The crystal structure of AzoR (azoreductase) from Escherichia coli: Oxidized AzoR in orthorhombic crystals===


-	~~==Overview==~~	+	<!--
-	~~AzoR is an FMN~~-~~dependent NADH~~-~~azoreductase isolated from Escherichia coli as a protein responsible for~~ the degradation of azo compounds. We previously reported the crystal structure of the enzyme in the oxidized form. In the present study, different structures of AzoR were determined under several conditions to obtain clues to the reaction mechanism of the enzyme. AzoR in its reduced form revealed a twisted butterfly bend of the isoalloxazine ring of the FMN cofactor and a rearrangement of solvent molecules. The crystal structure of oxidized AzoR in a different space group and the structure of the enzyme in complex with the inhibitor dicoumarol were also determined. These structures indicate that the formation of a hydrophobic part around the isoalloxazine ring is important for substrate binding and an electrostatic interaction between Arg-59 and the carboxyl group of the azo compound causes a substrate preference for methyl red over p-methyl red. The substitution of Arg-59 with Ala enhanced the V(~~max) value for p-methyl red 27-fold with a 3~~.~~8-fold increase of the K(m) value~~. ~~This result indicates that Arg-59 decides the substrate specificity of AzoR. The V(max~~) ~~value for the p-methyl red reduction of the R59A mutant~~ is ~~comparable with that for~~ the ~~methyl red reduction of the wild-type enzyme, whereas the activity toward methyl red was retained~~. ~~These findings indicate the expansion of AzoR substrate specificity by a single amino acid substitution. Furthermore, we built an authentic model of the AzoR~~-~~methyl red complex based on the results of the study.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_18337254}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18337254 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18337254}}

	==About this Structure==		==About this Structure==
Line 29:		Line 33:
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jun 4 10~~:00:26 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 19:37:50 2008''