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New page: left|200px<br /><applet load="2ppf" size="350" color="white" frame="true" align="right" spinBox="true" caption="2ppf, resolution 1.65Å" /> '''Reduced mutant D98N ...
 
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[[Image:2ppf.jpg|left|200px]]<br /><applet load="2ppf" size="350" color="white" frame="true" align="right" spinBox="true"
caption="2ppf, resolution 1.65&Aring;" />
'''Reduced mutant D98N of AfNiR exposed to nitric oxide'''<br />


==Overview==
==Reduced mutant D98N of AfNiR exposed to nitric oxide==
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.
<StructureSection load='2ppf' size='340' side='right'caption='[[2ppf]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ppf]] 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=2PPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PPF FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.65&#8491;</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=NO:NITRIC+OXIDE'>NO</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></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=2ppf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppf OCA], [https://pdbe.org/2ppf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ppf RCSB], [https://www.ebi.ac.uk/pdbsum/2ppf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ppf ProSAT]</span></td></tr>
</table>
== 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/2ppf_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=2ppf ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
2PPF 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=2PPF OCA].
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
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]
[[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: ACT]]
[[Category: CU]]
[[Category: CU1]]
[[Category: NO]]
[[Category: TRS]]
[[Category: bacteria]]
[[Category: copper]]
[[Category: d98n]]
[[Category: denitrification]]
[[Category: nitric oxide]]
[[Category: nitrite reductase]]
[[Category: oxidoreductase]]
 
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Retrieved from "https://proteopedia.org/2ppf"