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2ppe

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[[Image:2ppe.jpg|left|200px]]<br /><applet load="2ppe" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2ppe, resolution 1.75&Aring;" />
 
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'''Reduced H145A mutant of AfNiR exposed to NO'''<br />
 
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==Overview==
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==Reduced H145A mutant of AfNiR exposed to NO==
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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.
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<StructureSection load='2ppe' size='340' side='right'caption='[[2ppe]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2ppe]] 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=2PPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PPE FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
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<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=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ppe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppe OCA], [https://pdbe.org/2ppe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ppe RCSB], [https://www.ebi.ac.uk/pdbsum/2ppe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ppe ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NIR_ALCFA NIR_ALCFA]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pp/2ppe_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=2ppe ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2PPE is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis] with <scene name='pdbligand=CU1:'>CU1</scene>, <scene name='pdbligand=CU:'>CU</scene>, <scene name='pdbligand=ACT:'>ACT</scene>, <scene name='pdbligand=NO:'>NO</scene> and <scene name='pdbligand=TRS:'>TRS</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PPE OCA].
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*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17924665 17924665]
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[[Category: Alcaligenes faecalis]]
[[Category: Alcaligenes faecalis]]
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[[Category: Nitrite reductase (NO-forming)]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Murphy MEP]]
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[[Category: Murphy, M E.P.]]
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[[Category: Tocheva EI]]
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[[Category: Tocheva, E I.]]
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[[Category: ACT]]
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[[Category: CU]]
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[[Category: CU1]]
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[[Category: NO]]
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[[Category: TRS]]
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[[Category: bacteria]]
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[[Category: copper containing nitrite reductase]]
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[[Category: denitrification]]
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[[Category: h145a]]
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[[Category: nitric oxide]]
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[[Category: oxidoreductase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:31:52 2008''
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Current revision

Reduced H145A mutant of AfNiR exposed to NO

PDB ID 2ppe

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