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| [[Image:2pp9.jpg|left|200px]]
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| {{Structure
| | ==Nitrate bound wild type oxidized AfNiR== |
| |PDB= 2pp9 |SIZE=350|CAPTION= <scene name='initialview01'>2pp9</scene>, resolution 1.80Å
| | <StructureSection load='2pp9' size='340' side='right'caption='[[2pp9]], [[Resolution|resolution]] 1.80Å' scene=''> |
| |SITE= <scene name='pdbsite=AC1:Cu1+Binding+Site+For+Residue+A+501'>AC1</scene>, <scene name='pdbsite=AC2:Cu+Binding+Site+For+Residue+A+502'>AC2</scene>, <scene name='pdbsite=AC3:Cu1+Binding+Site+For+Residue+B+501'>AC3</scene>, <scene name='pdbsite=AC4:Cu+Binding+Site+For+Residue+B+502'>AC4</scene>, <scene name='pdbsite=AC5:Cu1+Binding+Site+For+Residue+C+501'>AC5</scene>, <scene name='pdbsite=AC6:Cu+Binding+Site+For+Residue+C+502'>AC6</scene>, <scene name='pdbsite=AC7:No3+Binding+Site+For+Residue+A+503'>AC7</scene>, <scene name='pdbsite=AC8:No3+Binding+Site+For+Residue+B+503'>AC8</scene>, <scene name='pdbsite=AC9:No3+Binding+Site+For+Residue+C+503'>AC9</scene>, <scene name='pdbsite=BC1:Act+Binding+Site+For+Residue+B+2003'>BC1</scene>, <scene name='pdbsite=BC2:Act+Binding+Site+For+Residue+B+2004'>BC2</scene>, <scene name='pdbsite=BC3:Act+Binding+Site+For+Residue+B+2005'>BC3</scene>, <scene name='pdbsite=BC4:Act+Binding+Site+For+Residue+C+2006'>BC4</scene>, <scene name='pdbsite=BC5:Act+Binding+Site+For+Residue+C+2007'>BC5</scene>, <scene name='pdbsite=BC6:Act+Binding+Site+For+Residue+C+2008'>BC6</scene>, <scene name='pdbsite=BC7:Act+Binding+Site+For+Residue+C+2009'>BC7</scene>, <scene name='pdbsite=BC8:Act+Binding+Site+For+Residue+A+2010'>BC8</scene> and <scene name='pdbsite=BC9:Trs+Binding+Site+For+Residue+A+2001'>BC9</scene>
| | == Structural highlights == |
| |LIGAND= <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=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
| | <table><tr><td colspan='2'>[[2pp9]] 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=2PP9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PP9 FirstGlance]. <br> |
| |ACTIVITY= <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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| |GENE= nirK, nir ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=511 Alcaligenes faecalis])
| | <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=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam07732 Cu-oxidase_3], [http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=pfam00394 Cu-oxidase]</span>
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2pp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp9 OCA], [https://pdbe.org/2pp9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pp9 RCSB], [https://www.ebi.ac.uk/pdbsum/2pp9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pp9 ProSAT]</span></td></tr> |
| |RELATEDENTRY=[[1snr|1SNR]], [[1sjm|1SJM]], [[2fjs|2FJS]]
| | </table> |
| |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pp9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pp9 OCA], [http://www.ebi.ac.uk/pdbsum/2pp9 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pp9 RCSB]</span>
| | == Function == |
| }}
| | [https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA] |
| | == 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/2pp9_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/main_output.php?pdb_ID=2pp9 ConSurf]. |
| | <div style="clear:both"></div> |
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| '''Nitrate bound wild type oxidized AfNiR'''
| | ==See Also== |
| | | *[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]] |
| | | __TOC__ |
| ==Overview== | | </StructureSection> |
| 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.
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| ==About this Structure==
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| 2PP9 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=2PP9 OCA].
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| ==Reference==
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| 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]
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| [[Category: Alcaligenes faecalis]] | | [[Category: Alcaligenes faecalis]] |
| [[Category: Nitrite reductase (NO-forming)]] | | [[Category: Large Structures]] |
| [[Category: Single protein]]
| | [[Category: Murphy MEP]] |
| [[Category: Murphy, M E.P.]] | | [[Category: Tocheva EI]] |
| [[Category: Tocheva, E I.]] | |
| [[Category: bacteria]]
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| [[Category: copper]]
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| [[Category: denitrification]]
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| [[Category: nitrate]]
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| [[Category: nitrite reductase]]
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| [[Category: oxidoreductase]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:57:53 2008''
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