2bcp: Difference between revisions

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-[[Image:2bcp.jpg|left|200px]]
-<!--
+==Structural Analysis of Streptococcus pyogenes NADH oxidase: C44S Nox with Azide==
-The line below this paragraph, containing "STRUCTURE_2bcp", creates the "Structure Box" on the page.
+<StructureSection load='2bcp' size='340' side='right'caption='[[2bcp]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2bcp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pyogenes Streptococcus pyogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BCP FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-{{STRUCTURE_2bcp|  PDB=2bcp  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2bcp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bcp OCA], [https://pdbe.org/2bcp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bcp RCSB], [https://www.ebi.ac.uk/pdbsum/2bcp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bcp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NAOX_STRP6 NAOX_STRP6] Catalyzes the four-electron reduction of molecular oxygen to water.[UniProtKB:P37061]
+== 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/bc/2bcp_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=2bcp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+In probing the oxygen reactivity of an Enterococcus faecalis NADH oxidase (Nox; O2 --&gt; 2H2O) C42S mutant lacking the Cys42-sulfenic acid (Cys42-SOH) redox center, we provided direct evidence of a C(4a)-peroxyflavin intermediate in the oxidative half-reaction and also described a conformational or chemical change that is rate-limiting for full reoxidation of the homodimer. In this work, the Nox from Streptococcus pyogenes (SpyNox) has been expressed and crystallized, and the overoxidized wild-type [Cys44-SOH --&gt; Cys44-sulfinic acid (Cys44-SO2H)] and C44S mutant enzyme structures have been refined at 2.0 and 2.15 A, respectively. We show that azide binds to the two-electron reduced wild-type (EH2) enzyme and to the mutant enzyme in solution, but with a significantly higher affinity for the mutant protein. The spectral course of the titration with the SpyNox EH2 form clearly indicates progressive displacement of the Cys44-S(-) --&gt; FAD charge-transfer interaction. An azide soak with C44S Nox crystals led to the structure of the complex, as refined at 2.10 A. The active-site N3(-) ligand is proximal to the Ser44 and His11 side chains, and a significant shift in the Ser44 side chain also appears. This provides an attractive explanation for the azide-induced loss of charge-transfer absorbance seen with the wild-type EH2 form and also permits accommodation of a C(4a)-peroxyflavin structural model. The conformation of Ser44 and the associated helical element, and the resulting steric accommodation, appear to be linked to the conformational change described in the E. faecalis C42S Nox oxidative half-reaction.
-'''Structural Analysis of Streptococcus pyogenes NADH oxidase: C44S Nox with Azide'''
+Structural Analysis of Streptococcus pyogenes NADH Oxidase: Conformational Dynamics Involved in Formation of the C(4a)-Peroxyflavin Intermediate.,Wallen JR, Mallett TC, Okuno T, Parsonage D, Sakai H, Tsukihara T, Claiborne A Biochemistry. 2015 Nov 17;54(45):6815-29. doi: 10.1021/acs.biochem.5b00676. Epub , 2015 Nov 6. PMID:26506002<ref>PMID:26506002</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-==About this Structure==
+</div>
-BCP is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_pyogenes Streptococcus pyogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BCP OCA].
+<div class="pdbe-citations 2bcp" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptococcus pyogenes]]
-[[Category: Boles, W H.]]
+[[Category: Boles WH]]
-[[Category: Mallett, T C.]]
+[[Category: Mallett TC]]
-[[Category: Azide]]
-[[Category: Conformational dynamic]]
-[[Category: Crystallography]]
-[[Category: Cysteine oxidation]]
-[[Category: Flavoprotein]]
-[[Category: Nadh oxidase]]
-[[Category: Pyridine nucleotide disulfide oxidoreductase]]
-[[Category: Sulfinic acid]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 20:07:02 2008''