2nrd: Difference between revisions

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-[[Image:2nrd.gif|left|200px]]
- {{Structure
+==THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED==
-|PDB= 2nrd |SIZE=350|CAPTION= <scene name='initialview01'>2nrd</scene>, resolution 2.1&Aring;
+<StructureSection load='2nrd' size='340' side='right'caption='[[2nrd]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CU:COPPER (II) ION'>CU</scene>
+<table><tr><td colspan='2'>[[2nrd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1nrd 1nrd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NRD FirstGlance]. <br>
-|ACTIVITY= [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]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</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=2nrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nrd OCA], [https://pdbe.org/2nrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nrd RCSB], [https://www.ebi.ac.uk/pdbsum/2nrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nrd ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NIR_ACHCY NIR_ACHCY]
+== 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/nr/2nrd_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=2nrd ConSurf].
+<div style="clear:both"></div>
-'''THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED'''
+==See Also==
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-High resolution x-ray crystallographic structures of nitrite reductase from Achromobacter cycloclastes, undertaken in order to understand the pH optimum of the reaction with nitrite, show that at pH 5.0, 5.4, 6.0, 6.2, and 6.8, no significant changes occur, other than in the occupancy of the type II copper at the active site. An extensive network of hydrogen bonds, both within and between subunits of the trimer, maintains the rigidity of the protein structure. A water occupies a site approximately 1.5 A from the site of the type II copper in the structure of the type II copper-depleted structure (at pH 5.4), again with no other significant changes in structure. In nitrite-soaked crystals, nitrite binds via its oxygens to the type II copper and replaces the water normally bound to the type II copper. The active-site cavity of the protein is distinctly hydrophobic on one side and hydrophilic on the other, providing a possible path for diffusion of the product NO. Asp-98 exhibits thermal parameter values higher than its surroundings, suggesting a role in shuttling the two protons necessary for the overall reaction. The strong structural homology with cupredoxins is described.
-==About this Structure==
-NRD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Achromobacter_cycloclastes Achromobacter cycloclastes]. This structure supersedes the now removed PDB entry 1NRD. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NRD OCA].
-==Reference==
-The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted., Adman ET, Godden JW, Turley S, J Biol Chem. 1995 Nov 17;270(46):27458-74. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7499203 7499203]
 [[Category: Achromobacter cycloclastes]]
-[[Category: Nitrite reductase (NO-forming)]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Adman ET]]
-[[Category: Adman, E T.]]
+[[Category: Godden JW]]
-[[Category: Godden, J W.]]
+[[Category: Turley S]]
-[[Category: Turley, S.]]
-[[Category: CU]]
-[[Category: oxidoreductase (nitric oxide(a))]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:50:05 2008''