2dws: Difference between revisions
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==Cu-containing nitrite reductase at pH 8.4 with bound nitrite== | ==Cu-containing nitrite reductase at pH 8.4 with bound nitrite== | ||
<StructureSection load='2dws' size='340' side='right' caption='[[2dws]], [[Resolution|resolution]] 1.85Å' scene=''> | <StructureSection load='2dws' size='340' side='right'caption='[[2dws]], [[Resolution|resolution]] 1.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [ | <table><tr><td colspan='2'>[[2dws]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DWS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DWS FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr> | </td></tr><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>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1zv2|1zv2]], [[2dwt|2dwt]], [[2dy2|2dy2]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1zv2|1zv2]], [[2dwt|2dwt]], [[2dy2|2dy2]]</div></td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nirK ([ | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">nirK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907])</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nitrite_reductase_(NO-forming) Nitrite reductase (NO-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.7.2.1 1.7.2.1] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2dws FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dws OCA], [https://pdbe.org/2dws PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dws RCSB], [https://www.ebi.ac.uk/pdbsum/2dws PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dws ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/2dws_consurf.spt"</scriptWhenChecked> | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/2dws_consurf.spt"</scriptWhenChecked> | ||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 2dws" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 2dws" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]] | |||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: Rhodococcus capsulatus molisch 1907]] | [[Category: Rhodococcus capsulatus molisch 1907]] | ||
[[Category: Large Structures]] | |||
[[Category: Jacobson, F]] | [[Category: Jacobson, F]] | ||
[[Category: Copper protein]] | [[Category: Copper protein]] | ||
Revision as of 14:39, 10 February 2021
Cu-containing nitrite reductase at pH 8.4 with bound nitriteCu-containing nitrite reductase at pH 8.4 with bound nitrite
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedMany properties of copper-containing nitrite reductase are pH-dependent, such as gene expression, enzyme activity, and substrate affinity. Here we use x-ray diffraction to investigate the structural basis for the pH dependence of activity and nitrite affinity by examining the type 2 copper site and its immediate surroundings in nitrite reductase from Rhodobacter sphaeroides 2.4.3. At active pH the geometry of the substrate-free oxidized type 2 copper site shows a near perfect tetrahedral geometry as defined by the positions of its ligands. At higher pH values the most favorable copper site geometry is altered toward a more distorted tetrahedral geometry whereby the solvent ligand adopts a position opposite to that of the His-131 ligand. This pH-dependent variation in type 2 copper site geometry is discussed in light of recent computational results. When co-crystallized with substrate, nitrite is seen to bind in a bidentate fashion with its two oxygen atoms ligating the type 2 copper, overlapping with the positions occupied by the solvent ligand in the high and low pH structures. Fourier transformation infrared spectroscopy is used to assign the pH dependence of the binding of nitrite to the active site, and EPR spectroscopy is used to characterize the pH dependence of the reduction potential of the type 2 copper site. Taken together, these spectroscopic and structural observations help to explain the pH dependence of nitrite reductase, highlighting the subtle relationship between copper site geometry, nitrite affinity, and enzyme activity. pH dependence of copper geometry, reduction potential, and nitrite affinity in nitrite reductase.,Jacobson F, Pistorius A, Farkas D, De Grip W, Hansson O, Sjolin L, Neutze R J Biol Chem. 2007 Mar 2;282(9):6347-55. Epub 2006 Dec 5. PMID:17148448[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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