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| - | [[Image:2pp7.jpg|left|200px]] | |
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| - | {{Structure
| + | ==Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)== |
| - | |PDB= 2pp7 |SIZE=350|CAPTION= <scene name='initialview01'>2pp7</scene>, resolution 1.65Å
| + | <StructureSection load='2pp7' size='340' side='right'caption='[[2pp7]], [[Resolution|resolution]] 1.65Å' 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:Act+Binding+Site+For+Residue+A+503'>AC7</scene>, <scene name='pdbsite=AC8:Act+Binding+Site+For+Residue+B+503'>AC8</scene>, <scene name='pdbsite=AC9:Act+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+2007'>BC4</scene>, <scene name='pdbsite=BC5:Act+Binding+Site+For+Residue+C+2008'>BC5</scene>, <scene name='pdbsite=BC6:Act+Binding+Site+For+Residue+C+2009'>BC6</scene>, <scene name='pdbsite=BC7:Act+Binding+Site+For+Residue+A+2010'>BC7</scene>, <scene name='pdbsite=BC8:Act+Binding+Site+For+Residue+A+2011'>BC8</scene>, <scene name='pdbsite=BC9:Act+Binding+Site+For+Residue+B+2012'>BC9</scene>, <scene name='pdbsite=CC1:Act+Binding+Site+For+Residue+C+2013'>CC1</scene> and <scene name='pdbsite=CC2:Trs+Binding+Site+For+Residue+A+1'>CC2</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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
| + | <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> |
| - | |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]] 1.65Å</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=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=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> |
| - | |RELATEDENTRY=[[1snr|1SNR]], [[1sjm|1SJM]], [[2fjs|2FJS]]
| + | </table> |
| - | |RESOURCES=<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.ebi.ac.uk/pdbsum/2pp7 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2pp7 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/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/main_output.php?pdb_ID=2pp7 ConSurf]. |
| | + | <div style="clear:both"></div> |
| | | | |
| - | '''Crystal structure of anaerobically manipulated wild type oxidized AfNiR (acetate bound)'''
| + | ==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.
| + | |
| - | | + | |
| - | ==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].
| + | |
| - | | + | |
| - | ==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]
| + | |
| | [[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]]
| + | |
| - | [[Category: copper]]
| + | |
| - | [[Category: denitrification]]
| + | |
| - | [[Category: nitric oxide]]
| + | |
| - | [[Category: nitrite]]
| + | |
| - | [[Category: oxidoreductase]]
| + | |
| - | [[Category: reductase]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:57:50 2008''
| + | |
