1as6: Difference between revisions

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-[[Image:1as6.jpg|left|200px]]
- {{Structure
+==STRUCTURE OF NITRITE BOUND TO OXIDIZED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE==
-|PDB= 1as6 |SIZE=350|CAPTION= <scene name='initialview01'>1as6</scene>, resolution 1.8&Aring;
+<StructureSection load='1as6' size='340' side='right'caption='[[1as6]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
-|SITE= <scene name='pdbsite=CU1:Cu+Site'>CU1</scene>, <scene name='pdbsite=CU2:Cu+Site'>CU2</scene>, <scene name='pdbsite=CU3:Cu+Site'>CU3</scene>, <scene name='pdbsite=CU4:Cu+Site'>CU4</scene>, <scene name='pdbsite=CU5:Cu+Site'>CU5</scene> and <scene name='pdbsite=CU6:Cu+Site'>CU6</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene>
+<table><tr><td colspan='2'>[[1as6]] 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=1AS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AS6 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]] 1.8&#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>, <scene name='pdbligand=NO2:NITRITE+ION'>NO2</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1as6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1as6 OCA], [https://pdbe.org/1as6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1as6 RCSB], [https://www.ebi.ac.uk/pdbsum/1as6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1as6 ProSAT]</span></td></tr>
-|RELATEDENTRY=
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1as6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1as6 OCA], [http://www.ebi.ac.uk/pdbsum/1as6 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1as6 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/as/1as6_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=1as6 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structures of oxidized, reduced, nitrite-soaked oxidized and nitrite-soaked reduced nitrite reductase from Alcaligenes faecalis have been determined at 1.8-2.0 A resolution using data collected at -160 degrees C. The active site at cryogenic temperature, as at room temperature, contains a tetrahedral type II copper site liganded by three histidines and a water molecule. The solvent site is empty when crystals are reduced with ascorbate. A fully occupied oxygen-coordinate nitrite occupies the solvent site in crystals soaked in nitrite. Ascorbate-reduced crystals soaked in a glycerol-methanol solution and nitrite at -40 degrees C remain colorless at -160 degrees C but turn amber-brown when warmed, suggesting that NO is released. Nitrite is found at one-half occupancy. Five new solvent sites in the oxidized nitrite bound form exhibit defined but different occupancies in the other three forms. These results support a previously proposed mechanism by which nitrite is bound primarily by a single oxygen atom that is protonable, and after reduction and cleavage of that N-O bond, NO is released leaving the oxygen atom bound to the Cu site as hydroxide or water.
-'''STRUCTURE OF NITRITE BOUND TO OXIDIZED ALCALIGENES FAECALIS NITRITE REDUCTASE AT CRYO TEMPERATURE'''
+Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications.,Murphy ME, Turley S, Adman ET J Biol Chem. 1997 Nov 7;272(45):28455-60. PMID:9353305<ref>PMID:9353305</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1as6" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The structures of oxidized, reduced, nitrite-soaked oxidized and nitrite-soaked reduced nitrite reductase from Alcaligenes faecalis have been determined at 1.8-2.0 A resolution using data collected at -160 degrees C. The active site at cryogenic temperature, as at room temperature, contains a tetrahedral type II copper site liganded by three histidines and a water molecule. The solvent site is empty when crystals are reduced with ascorbate. A fully occupied oxygen-coordinate nitrite occupies the solvent site in crystals soaked in nitrite. Ascorbate-reduced crystals soaked in a glycerol-methanol solution and nitrite at -40 degrees C remain colorless at -160 degrees C but turn amber-brown when warmed, suggesting that NO is released. Nitrite is found at one-half occupancy. Five new solvent sites in the oxidized nitrite bound form exhibit defined but different occupancies in the other three forms. These results support a previously proposed mechanism by which nitrite is bound primarily by a single oxygen atom that is protonable, and after reduction and cleavage of that N-O bond, NO is released leaving the oxygen atom bound to the Cu site as hydroxide or water.
+*[[Nitrite reductase 3D structures|Nitrite reductase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-AS6 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=1AS6 OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Structure of nitrite bound to copper-containing nitrite reductase from Alcaligenes faecalis. Mechanistic implications., Murphy ME, Turley S, Adman ET, J Biol Chem. 1997 Nov 7;272(45):28455-60. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9353305 9353305]
 [[Category: Alcaligenes faecalis]]
-[[Category: Nitrite reductase (NO-forming)]]
+[[Category: Large Structures]]
-[[Category: Single protein]]
+[[Category: Adman ET]]
-[[Category: Adman, E T.]]
+[[Category: Murphy MEP]]
-[[Category: Murphy, M E.P.]]
+[[Category: Turley S]]
-[[Category: Turley, S.]]
-[[Category: copper]]
-[[Category: denitrification]]
-[[Category: nitrite]]
-[[Category: oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:46:34 2008''