2ppc - Revision history

OCA at 09:11, 21 February 2024

2024-02-21T09:11:16Z

←Older revision		Revision as of 09:11, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2ppc' size='340' side='right'caption='[[2ppc]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='2ppc' size='340' side='right'caption='[[2ppc]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ppc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Alcfa Alcfa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PPC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ppc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PPC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 1.58Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1snr\|1snr]], [[1sjm\|1sjm]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [https://pdbe.org/2ppc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [https://www.ebi.ac.uk/pdbsum/2ppc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ppc 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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [https://pdbe.org/2ppc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [https://www.ebi.ac.uk/pdbsum/2ppc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ppc ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA]
	== 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=2ppc 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=2ppc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Nitrite reductase (NiR) is an enzyme that uses type 1 and type 2 copper sites to reduce nitrite to nitric oxide during bacterial denitrification. A copper-nitrosyl intermediate is a proposed, yet poorly characterized feature of the NiR catalytic cycle. This intermediate is formally described as Cu(I)-NO+ and is proposed to be formed at the type 2 copper site after nitrite binding and electron transfer from the type 1 copper site. In this study, copper-nitrosyl complexes were formed by prolonged exposure of exogenous NO to crystals of wild-type and two variant forms of NiR from Alcaligenes faecalis (AfNiR), and the structures were determined to 1.8 A or better resolution. Exposing oxidized wild-type crystals to NO results in the reverse reaction and formation of nitrite that remains bound at the active site. In a type 1 copper site mutant (H145A) that is incapable of electron transfer to the type 2 site, the reverse reaction is not observed. Instead, in both oxidized and reduced H145A crystals, NO is observed bound in a side-on manner to the type 2 copper. In AfNiR, Asp98 forms hydrogen bonds to both substrate and product bound to the type 2 Cu. In the D98N variant, NO is bound side-on but is more disordered when observed for the wild-type enzyme. The solution EPR spectra of the crystallographically characterized NiR-NO complexes indicate the presence of an oxidized type 2 copper site and thus are interpreted as resulting from stable copper-nitrosyls and formally assigned as Cu(II)-NO-. A reaction scheme in which a second NO molecule is oxidized to nitrite can account for the formation of a Cu(II)-NO- species after exposure of the oxidized H145A variant to NO gas.
-
-	Stable copper-nitrosyl formation by nitrite reductase in either oxidation state.,Tocheva EI, Rosell FI, Mauk AG, Murphy ME Biochemistry. 2007 Oct 30;46(43):12366-74. Epub 2007 Oct 9. PMID:17924665<ref>PMID:17924665</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2ppc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]		*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alcfa~~]]	+	[[Category: Alcaligenes faecalis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Murphy~~, M E.P~~]]	+	[[Category: Murphy MEP]]
-	[[Category: Tocheva~~, E I]]~~	+	[[Category: Tocheva EI]]
-	~~[[Category: Denitrification]]~~	+
-	~~[[Category: Nitric oxide]]~~	+
-	~~[[Category: Nitrite]]~~	+
-	~~[[Category: Nitrite reductase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 15:29, 17 June 2021

2021-06-17T15:29:35Z

←Older revision		Revision as of 15:29, 17 June 2021
Line 1:		Line 1:

	==Oxidized wild type AfNiR exposed to NO (nitrite bound)==		==Oxidized wild type AfNiR exposed to NO (nitrite bound)==
-	<StructureSection load='2ppc' size='340' side='right' caption='[[2ppc]], [[Resolution\|resolution]] 1.58Å' scene=''>	+	<StructureSection load='2ppc' size='340' side='right'caption='[[2ppc]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ppc]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PPC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ppc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PPC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1snr\|1snr]], [[1sjm\|1sjm]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1snr\|1snr]], [[1sjm\|1sjm]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [~~http~~://pdbe.org/2ppc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ppc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ppc 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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [https://pdbe.org/2ppc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [https://www.ebi.ac.uk/pdbsum/2ppc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ppc ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Nitrite reductase\|Nitrite reductase]]	+	*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Alcfa]]		[[Category: Alcfa]]
		+	[[Category: Large Structures]]
	[[Category: Murphy, M E.P]]		[[Category: Murphy, M E.P]]
	[[Category: Tocheva, E I]]		[[Category: Tocheva, E I]]

OCA at 08:17, 29 August 2018

2018-08-29T08:17:50Z

←Older revision		Revision as of 08:17, 29 August 2018
Line 1:		Line 1:
		+
	==Oxidized wild type AfNiR exposed to NO (nitrite bound)==		==Oxidized wild type AfNiR exposed to NO (nitrite bound)==
	<StructureSection load='2ppc' size='340' side='right' caption='[[2ppc]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='2ppc' size='340' side='right' caption='[[2ppc]], [[Resolution\|resolution]] 1.58Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [http://pdbe.org/2ppc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [http://www.ebi.ac.uk/pdbsum/2ppc 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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [http://pdbe.org/2ppc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [http://www.ebi.ac.uk/pdbsum/2ppc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ppc ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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/pp/2ppc_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pp/2ppc_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>
Line 30:		Line 31:

	==See Also==		==See Also==
-	*[[~~Nitric~~ reductase\|~~Nitric~~ reductase]]	+	*[[Nitrite reductase\|Nitrite reductase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 05:48, 10 February 2016

2016-02-10T05:48:39Z

←Older revision		Revision as of 05:48, 10 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ppc ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:57, 11 September 2015

2015-09-11T05:57:48Z

←Older revision		Revision as of 05:57, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2ppc' size='340' side='right' caption='[[2ppc]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='2ppc' size='340' side='right' caption='[[2ppc]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2ppc]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Alcaligenes_faecalis Alcaligenes faecalis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PPC FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2ppc]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcfa Alcfa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PPC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1snr\|1snr]], [[1sjm\|1sjm]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1snr\|1snr]], [[1sjm\|1sjm]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ~~Alcaligenes faecalis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 ALCFA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [http://www.ebi.ac.uk/pdbsum/2ppc 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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [http://pdbe.org/2ppc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [http://www.ebi.ac.uk/pdbsum/2ppc PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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 2ppc" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Alcaligenes faecalis~~]]	+	[[Category: Alcfa]]
	[[Category: Murphy, M E.P]]		[[Category: Murphy, M E.P]]
	[[Category: Tocheva, E I]]		[[Category: Tocheva, E I]]

OCA at 16:13, 19 January 2015

2015-01-19T16:13:08Z

←Older revision		Revision as of 16:13, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ppc]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ppc]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PPC FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1snr\|1snr]], [[1sjm\|1sjm]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1snr\|1snr]], [[1sjm\|1sjm]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [http://www.ebi.ac.uk/pdbsum/2ppc 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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [http://www.ebi.ac.uk/pdbsum/2ppc PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
-	[[Category: Murphy, M E.P.]]	+	[[Category: Murphy, M E.P]]
-	[[Category: Tocheva, E I.]]	+	[[Category: Tocheva, E I]]
	[[Category: Denitrification]]		[[Category: Denitrification]]
	[[Category: Nitric oxide]]		[[Category: Nitric oxide]]

OCA at 04:03, 3 October 2014

2014-10-03T04:03:52Z

←Older revision		Revision as of 04:03, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_2ppc\| PDB=2ppc \| SCENE= }}~~	+	==Oxidized wild type AfNiR exposed to NO (nitrite bound)==
-	===Oxidized wild type AfNiR exposed to NO (nitrite bound)===	+	<StructureSection load='2ppc' size='340' side='right' caption='[[2ppc]], [[Resolution\|resolution]] 1.58Å' scene=''>
-	~~{{ABSTRACT_PUBMED_17924665}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2ppc]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PPC FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1snr\|1snr]], [[1sjm\|1sjm]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [http://www.ebi.ac.uk/pdbsum/2ppc 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/pp/2ppc_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 ==
		+	Nitrite reductase (NiR) is an enzyme that uses type 1 and type 2 copper sites to reduce nitrite to nitric oxide during bacterial denitrification. A copper-nitrosyl intermediate is a proposed, yet poorly characterized feature of the NiR catalytic cycle. This intermediate is formally described as Cu(I)-NO+ and is proposed to be formed at the type 2 copper site after nitrite binding and electron transfer from the type 1 copper site. In this study, copper-nitrosyl complexes were formed by prolonged exposure of exogenous NO to crystals of wild-type and two variant forms of NiR from Alcaligenes faecalis (AfNiR), and the structures were determined to 1.8 A or better resolution. Exposing oxidized wild-type crystals to NO results in the reverse reaction and formation of nitrite that remains bound at the active site. In a type 1 copper site mutant (H145A) that is incapable of electron transfer to the type 2 site, the reverse reaction is not observed. Instead, in both oxidized and reduced H145A crystals, NO is observed bound in a side-on manner to the type 2 copper. In AfNiR, Asp98 forms hydrogen bonds to both substrate and product bound to the type 2 Cu. In the D98N variant, NO is bound side-on but is more disordered when observed for the wild-type enzyme. The solution EPR spectra of the crystallographically characterized NiR-NO complexes indicate the presence of an oxidized type 2 copper site and thus are interpreted as resulting from stable copper-nitrosyls and formally assigned as Cu(II)-NO-. A reaction scheme in which a second NO molecule is oxidized to nitrite can account for the formation of a Cu(II)-NO- species after exposure of the oxidized H145A variant to NO gas.

-	~~==About this Structure==~~	+	Stable copper-nitrosyl formation by nitrite reductase in either oxidation state.,Tocheva EI, Rosell FI, Mauk AG, Murphy ME Biochemistry. 2007 Oct 30;46(43):12366-74. Epub 2007 Oct 9. PMID:17924665<ref>PMID:17924665</ref>
-	~~[[2ppc]] is a 3 chain structure with sequence from [http~~:~~//en~~.~~wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id=2PPC OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

	==See Also==		==See Also==
	*[[Nitric reductase\|Nitric reductase]]		*[[Nitric reductase\|Nitric reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:017924665</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
	[[Category: Murphy, M E.P.]]		[[Category: Murphy, M E.P.]]

OCA at 08:39, 21 August 2013

2013-08-21T08:39:06Z

←Older revision		Revision as of 08:39, 21 August 2013
Line 1:		Line 1:
-	[[Image:2ppc.png\|left\|200px]]
-
	{{STRUCTURE_2ppc\| PDB=2ppc \| SCENE= }}		{{STRUCTURE_2ppc\| PDB=2ppc \| SCENE= }}
-
	===Oxidized wild type AfNiR exposed to NO (nitrite bound)===		===Oxidized wild type AfNiR exposed to NO (nitrite bound)===
-
	{{ABSTRACT_PUBMED_17924665}}		{{ABSTRACT_PUBMED_17924665}}

Line 14:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:017924665</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017924665</ref><references group="xtra"/><references/>
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
	[[Category: Murphy, M E.P.]]		[[Category: Murphy, M E.P.]]

OCA at 16:32, 20 October 2012

2012-10-20T16:32:33Z

←Older revision		Revision as of 16:32, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2ppc]] is a 3 chain structure ~~of [[Nitric reductase]]~~ with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA].	+	[[2ppc]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPC OCA].

	==See Also==		==See Also==

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

2012-07-26T22:01:06Z

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

←Older revision

Revision as of 22:01, 26 July 2012