2pp7 - Revision history

OCA at 09:11, 21 February 2024

2024-02-21T09:11:12Z

← Older revision		Revision as of 09:11, 21 February 2024
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	<StructureSection load='2pp7' size='340' side='right'caption='[[2pp7]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2pp7' size='340' side='right'caption='[[2pp7]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pp7]] 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=2PP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PP7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pp7]] 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=2PP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PP7 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=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]] 1.65Å</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]], [[2fjs\|2fjs]]</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=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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [https://pdbe.org/2pp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [https://www.ebi.ac.uk/pdbsum/2pp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pp7 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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [https://pdbe.org/2pp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [https://www.ebi.ac.uk/pdbsum/2pp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pp7 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]]
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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=2pp7 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=2pp7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The interaction of copper-containing dissimilatory nitrite reductase from Alcaligenes faecalis S-6 ( AfNiR) with each of five small molecules was studied using crystallography and steady-state kinetics. Structural studies revealed that each small molecule interacted with the oxidized catalytic type 2 copper of AfNiR. Three small molecules (formate, acetate and nitrate) mimic the substrate by having at least two oxygen atoms for bidentate coordination to the type 2 copper atom. These three anions bound to the copper ion in the same asymmetric, bidentate manner as nitrite. Consistent with their weak inhibition of the enzyme ( K i >50 mM), the Cu-O distances in these AfNiR-inhibitor complexes were approximately 0.15 A longer than that observed in the AfNiR-nitrite complex. The binding mode of each inhibitor is determined in part by steric interactions with the side chain of active site residue Ile257. Moreover, the side chain of Asp98, a conserved residue that hydrogen bonds to type 2 copper-bound nitrite and nitric oxide, was either disordered or pointed away from the inhibitors. Acetate and formate inhibited AfNiR in a mixed fashion, consistent with the occurrence of second acetate binding site in the AfNiR-acetate complex that occludes access to the type 2 copper. A fourth small molecule, nitrous oxide, bound to the oxidized metal in a side-on fashion reminiscent of nitric oxide to the reduced copper. Nevertheless, nitrous oxide bound at a farther distance from the metal. The fifth small molecule, azide, inhibited the reduction of nitrite by AfNiR most strongly ( K ic = 2.0 +/- 0.1 mM). This ligand bound to the type 2 copper center end-on with a Cu-N c distance of approximately 2 A, and was the only inhibitor to form a hydrogen bond with Asp98. Overall, the data substantiate the roles of Asp98 and Ile257 in discriminating substrate from other small anions.

	Conserved Active Site Residues Limit Inhibition of a Copper-Containing Nitrite Reductase by Small Molecules.,Tocheva EI, Eltis LD, Murphy ME Biochemistry. 2008 Mar 22;. PMID:18358002<ref>PMID:18358002</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2pp7" 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: Bacteria]]~~
	~~[[Category: Denitrification]]~~
	~~[[Category: Nitric oxide]]~~
	~~[[Category: Nitrite]]~~
	~~[[Category: Oxidoreductase]]~~
	~~[[Category: Reductase~~]]

OCA at 15:29, 17 June 2021

2021-06-17T15:29:29Z

← Older revision		Revision as of 15:29, 17 June 2021
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	==Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)==		==Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)==
	<StructureSection load='2pp7' size='340' side='right' caption='[[2pp7]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2pp7' size='340' side='right'caption='[[2pp7]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pp7]] 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=2PP7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2PP7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pp7]] 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=2PP7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PP7 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=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=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]], [[2fjs\|2fjs]]</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]], [[2fjs\|2fjs]]</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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [~~http~~://pdbe.org/2pp7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2pp7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2pp7 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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [https://pdbe.org/2pp7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [https://www.ebi.ac.uk/pdbsum/2pp7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pp7 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
	*[[Nitrite reductase\|Nitrite reductase]]		*[[Nitrite reductase 3D structures\|Nitrite reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</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 08:32, 29 August 2018

2018-08-29T08:32:59Z

← Older revision		Revision as of 08:32, 29 August 2018
Line 1:		Line 1:

	==Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)==		==Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)==
	<StructureSection load='2pp7' size='340' side='right' caption='[[2pp7]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2pp7' size='340' side='right' caption='[[2pp7]], [[Resolution\|resolution]] 1.65Å' scene=''>
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	<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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [http://pdbe.org/2pp7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [http://www.ebi.ac.uk/pdbsum/2pp7 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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [http://pdbe.org/2pp7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [http://www.ebi.ac.uk/pdbsum/2pp7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2pp7 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/2pp7_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pp/2pp7_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>
	</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=2pp7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 31:

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

OCA at 15:15, 11 September 2015

2015-09-11T15:15:48Z

← Older revision		Revision as of 15:15, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2pp7' size='340' side='right' caption='[[2pp7]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='2pp7' size='340' side='right' caption='[[2pp7]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pp7]] 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=2PP7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PP7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pp7]] 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=2PP7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PP7 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=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=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]], [[2fjs\|2fjs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1snr\|1snr]], [[1sjm\|1sjm]], [[2fjs\|2fjs]]</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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [http://www.ebi.ac.uk/pdbsum/2pp7 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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [http://pdbe.org/2pp7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [http://www.ebi.ac.uk/pdbsum/2pp7 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 2pp7" 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 16:39, 19 January 2015

2015-01-19T16:39:23Z

← Older revision		Revision as of 16:39, 19 January 2015
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2pp7]] 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=2PP7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PP7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2pp7]] 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=2PP7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PP7 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=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=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]], [[2fjs\|2fjs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1snr\|1snr]], [[1sjm\|1sjm]], [[2fjs\|2fjs]]</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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [http://www.ebi.ac.uk/pdbsum/2pp7 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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [http://www.ebi.ac.uk/pdbsum/2pp7 PDBsum]</span></td></tr>
	<table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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: Bacteria]]		[[Category: Bacteria]]
	[[Category: Denitrification]]		[[Category: Denitrification]]

OCA at 08:40, 29 September 2014

2014-09-29T08:40:34Z

← Older revision		Revision as of 08:40, 29 September 2014
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	[[Image:~~2pp7~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)==
			<StructureSection load='2pp7' size='340' side='right' caption='[[2pp7]], [[Resolution\|resolution]] 1.65Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2pp7]] 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=2PP7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PP7 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=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]], [[2fjs\|2fjs]]</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=2pp7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pp7 RCSB], [http://www.ebi.ac.uk/pdbsum/2pp7 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/2pp7_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 ==
			The interaction of copper-containing dissimilatory nitrite reductase from Alcaligenes faecalis S-6 ( AfNiR) with each of five small molecules was studied using crystallography and steady-state kinetics. Structural studies revealed that each small molecule interacted with the oxidized catalytic type 2 copper of AfNiR. Three small molecules (formate, acetate and nitrate) mimic the substrate by having at least two oxygen atoms for bidentate coordination to the type 2 copper atom. These three anions bound to the copper ion in the same asymmetric, bidentate manner as nitrite. Consistent with their weak inhibition of the enzyme ( K i >50 mM), the Cu-O distances in these AfNiR-inhibitor complexes were approximately 0.15 A longer than that observed in the AfNiR-nitrite complex. The binding mode of each inhibitor is determined in part by steric interactions with the side chain of active site residue Ile257. Moreover, the side chain of Asp98, a conserved residue that hydrogen bonds to type 2 copper-bound nitrite and nitric oxide, was either disordered or pointed away from the inhibitors. Acetate and formate inhibited AfNiR in a mixed fashion, consistent with the occurrence of second acetate binding site in the AfNiR-acetate complex that occludes access to the type 2 copper. A fourth small molecule, nitrous oxide, bound to the oxidized metal in a side-on fashion reminiscent of nitric oxide to the reduced copper. Nevertheless, nitrous oxide bound at a farther distance from the metal. The fifth small molecule, azide, inhibited the reduction of nitrite by AfNiR most strongly ( K ic = 2.0 +/- 0.1 mM). This ligand bound to the type 2 copper center end-on with a Cu-N c distance of approximately 2 A, and was the only inhibitor to form a hydrogen bond with Asp98. Overall, the data substantiate the roles of Asp98 and Ile257 in discriminating substrate from other small anions.

	~~{{STRUCTURE_2pp7\| PDB=2pp7 \| SCENE= }}~~		Conserved Active Site Residues Limit Inhibition of a Copper-Containing Nitrite Reductase by Small Molecules.,Tocheva EI, Eltis LD, Murphy ME Biochemistry. 2008 Mar 22;. PMID:18358002<ref>PMID:18358002</ref>

	~~===Crystal structure~~ of ~~anaerobically manipulated wild type oxidized AfNiR (acetate bound)===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18358002}}~~

	~~==About this Structure==~~
	~~[[2pp7]] 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=2PP7 OCA].~~

	==See Also==		==See Also==
	*[[Nitric reductase\|Nitric reductase]]		*[[Nitric reductase\|Nitric reductase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:018358002<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
	[[Category: Murphy, M E.P.]]		[[Category: Murphy, M E.P.]]

OCA at 19:52, 20 October 2012

2012-10-20T19:52:04Z

← Older revision		Revision as of 19:52, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[2pp7]] 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=2PP7 OCA].		[[2pp7]] 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=2PP7 OCA].

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

OCA: Protected "2pp7" [edit=sysop:move=sysop]

2012-07-27T08:43:43Z

Protected "2pp7" [edit=sysop:move=sysop]

← Older revision	Revision as of 08:43, 27 July 2012
(No difference)

OCA at 08:43, 27 July 2012

2012-07-27T08:43:40Z

← Older revision		Revision as of 08:43, 27 July 2012
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	~~{{Seed}}~~
	[[Image:2pp7.png\|left\|200px]]		[[Image:2pp7.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2pp7", 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_2pp7\| PDB=2pp7 \| SCENE= }}		{{STRUCTURE_2pp7\| PDB=2pp7 \| SCENE= }}

	===Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)===		===Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18358002}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18358002 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18358002}}		{{ABSTRACT_PUBMED_18358002}}

	==About this Structure==		==About this Structure==
	~~2PP7~~ is a 3 ~~chains~~ structure of ~~sequences~~ 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=2PP7 OCA].		[[2pp7]] 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=2PP7 OCA].

			==See Also==
			*[[Nitric reductase\|Nitric reductase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18358002~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018358002</ref><references group="xtra"/>
	[[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: Bacteria]]		[[Category: Bacteria]]
	~~[[Category: Copper]]~~
	[[Category: Denitrification]]		[[Category: Denitrification]]
	[[Category: Nitric oxide]]		[[Category: Nitric oxide]]
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	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Reductase]]		[[Category: Reductase]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:50:40 2009''~~

OCA at 23:50, 17 February 2009

2009-02-17T23:50:42Z

← Older revision		Revision as of 23:50, 17 February 2009
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	==About this Structure==		==About this Structure==
	2PP7 is a ~~[[Single protein]]~~ structure of ~~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=2PP7 OCA].		2PP7 is a 3 chains structure of sequences 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=2PP7 OCA].

	==Reference==		==Reference==
	~~Conserved Active Site Residues Limit Inhibition of a Copper-Containing Nitrite Reductase by Small Molecules., Tocheva EI, Eltis LD, Murphy ME, Biochemistry. 2008 Mar 22;.~~ PMID:~~[http://www.ncbi.nlm.nih.gov~~/~~pubmed~~/~~18358002 18358002]~~		<ref group="xtra">PMID:18358002</ref><references group="xtra"/>
	[[Category: Alcaligenes faecalis]]		[[Category: Alcaligenes faecalis]]
	~~[[Category: Single protein]]~~
	[[Category: Murphy, M E.P.]]		[[Category: Murphy, M E.P.]]
	[[Category: Tocheva, E I.]]		[[Category: Tocheva, E I.]]
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	[[Category: Reductase]]		[[Category: Reductase]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 08~~:43:~~43 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:50:40 2009''