2ppc: Difference between revisions

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OCA

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-[[Image:2ppc.jpg|left|200px]]
- {{Structure
+==Oxidized wild type AfNiR exposed to NO (nitrite bound)==
-|PDB= 2ppc |SIZE=350|CAPTION= <scene name='initialview01'>2ppc</scene>, resolution 1.58&Aring;
+<StructureSection load='2ppc' size='340' side='right'caption='[[2ppc]], [[Resolution|resolution]] 1.58&Aring;' 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:No2+Binding+Site+For+Residue+A+503'>AC7</scene>, <scene name='pdbsite=AC8:No2+Binding+Site+For+Residue+B+503'>AC8</scene>, <scene name='pdbsite=AC9:Act+Binding+Site+For+Residue+B+504'>AC9</scene>, <scene name='pdbsite=BC1:No2+Binding+Site+For+Residue+C+503'>BC1</scene>, <scene name='pdbsite=BC2:Act+Binding+Site+For+Residue+C+504'>BC2</scene>, <scene name='pdbsite=BC3:Act+Binding+Site+For+Residue+B+1503'>BC3</scene>, <scene name='pdbsite=BC4:Act+Binding+Site+For+Residue+B+1504'>BC4</scene>, <scene name='pdbsite=BC5:Act+Binding+Site+For+Residue+B+1505'>BC5</scene>, <scene name='pdbsite=BC6:Act+Binding+Site+For+Residue+B+1506'>BC6</scene>, <scene name='pdbsite=BC7:Act+Binding+Site+For+Residue+C+1507'>BC7</scene>, <scene name='pdbsite=BC8:Act+Binding+Site+For+Residue+C+1508'>BC8</scene>, <scene name='pdbsite=BC9:Act+Binding+Site+For+Residue+C+1509'>BC9</scene>, <scene name='pdbsite=CC1:Act+Binding+Site+For+Residue+A+1510'>CC1</scene> and <scene name='pdbsite=CC2:Trs+Binding+Site+For+Residue+A+1501'>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=NO2:NITRITE+ION'>NO2</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>
+<table><tr><td colspan='2'>[[2ppc]] 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=2PPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PPC 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]] 1.58&#8491;</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=NO2:NITRITE+ION'>NO2</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=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [https://pdbe.org/2ppc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ppc RCSB], [https://www.ebi.ac.uk/pdbsum/2ppc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ppc ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1snr|1SNR]], [[1sjm|1SJM]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ppc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ppc OCA], [http://www.ebi.ac.uk/pdbsum/2ppc PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2ppc 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/2ppc_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=2ppc ConSurf].
+<div style="clear:both"></div>
-'''Oxidized wild type AfNiR exposed to NO (nitrite bound)'''
+==See Also==
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-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.
-==About this Structure==
-PPC 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=2PPC OCA].
-==Reference==
-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://www.ncbi.nlm.nih.gov/pubmed/17924665 17924665]
 [[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: copper]]
-[[Category: denitrification]]
-[[Category: nitric oxide]]
-[[Category: nitrite]]
-[[Category: nitrite reductase]]
-[[Category: oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr  2 11:57:56 2008''