1oyc: Difference between revisions

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 ==OLD YELLOW ENZYME AT 2 ANGSTROMS RESOLUTION: OVERALL STRUCTURE, LIGAND BINDING AND COMPARISON WITH RELATED FLAVOPROTEINS==
-<StructureSection load='1oyc' size='340' side='right' caption='[[1oyc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='1oyc' size='340' side='right'caption='[[1oyc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1oyc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lager_yeast Lager yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OYC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1OYC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1oyc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_pastorianus Saccharomyces pastorianus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OYC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OYC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
+</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&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">OYE1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=27292 Lager yeast])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/NADPH_dehydrogenase NADPH dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.6.99.1 1.6.99.1] </span></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=1oyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oyc OCA], [https://pdbe.org/1oyc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1oyc RCSB], [https://www.ebi.ac.uk/pdbsum/1oyc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1oyc ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1oyc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1oyc OCA], [http://pdbe.org/1oyc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1oyc RCSB], [http://www.ebi.ac.uk/pdbsum/1oyc PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/OYE1_SACPS OYE1_SACPS]] Oxidizes beta-NADH, beta-NADPH, and alpha-NADPH.
+[https://www.uniprot.org/uniprot/OYE1_SACPS OYE1_SACPS] Oxidizes beta-NADH, beta-NADPH, and alpha-NADPH.
 == 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/oy/1oyc_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oy/1oyc_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1oyc ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-BACKGROUND: Old yellow enzyme (OYE) was the first flavoenzyme purified, but its function is still unknown. Nevertheless, the NADPH oxidase activity, the flavin mononucleotide environment and the ligand-binding properties of OYE have been extensively studied by biochemical and spectroscopic approaches. Full interpretation of these data requires structural information. RESULTS: The crystal structures of oxidized and reduced OYE at 2 A resolution reveal an alpha/beta-barrel topology clearly related to trimethylamine dehydrogenase. Complexes of OYE with p-hydroxybenzaldehyde, beta-estradiol, and an NADPH analog show all three binding at a common site, stacked on the flavin. The putative NADPH binding mode is novel as it involves primary recognition of the nicotinamide mononucleotide portion. CONCLUSIONS: This work shows that the striking spectral changes seen upon phenol binding are due to close physical association of the flavin and phenolate. It also identifies the structural class of OYE and suggests that if NADPH is its true substrate, then OYE has adopted NADPH dependence during evolution.
-Old yellow enzyme at 2 A resolution: overall structure, ligand binding, and comparison with related flavoproteins.,Fox KM, Karplus PA Structure. 1994 Nov 15;2(11):1089-105. PMID:7881908<ref>PMID:7881908</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1oyc" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[NADPH dehydrogenase|NADPH dehydrogenase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Lager yeast]]
+[[Category: Large Structures]]
-[[Category: NADPH dehydrogenase]]
+[[Category: Saccharomyces pastorianus]]
-[[Category: Fox, K M]]
+[[Category: Fox KM]]
-[[Category: Karplus, P A]]
+[[Category: Karplus PA]]