1k03: Difference between revisions

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OCA

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 ==Crystal Structure of Old Yellow Enzyme Mutant Gln114Asn Complexed with Para-hydroxy Benzaldehyde==
-<StructureSection load='1k03' size='340' side='right' caption='[[1k03]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='1k03' size='340' side='right'caption='[[1k03]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1k03]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K03 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K03 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1k03]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K03 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K03 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>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.7&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1oya|1oya]], [[1oyb|1oyb]], [[1oyc|1oyc]], [[1k02|1k02]]</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>, <scene name='pdbligand=HBA:P-HYDROXYBENZALDEHYDE'>HBA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1k03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k03 OCA], [https://pdbe.org/1k03 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k03 RCSB], [https://www.ebi.ac.uk/pdbsum/1k03 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k03 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=1k03 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k03 OCA], [http://pdbe.org/1k03 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k03 RCSB], [http://www.ebi.ac.uk/pdbsum/1k03 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1k03 ProSAT]</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/k0/1k03_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k0/1k03_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 21: / Line 20: @@
 </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=1k03 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Glutamine 114 of OYE1 is a well conserved residue in the active site of the Old Yellow Enzyme family. It forms hydrogen bonds to the O2 and N3 of the flavoprotein prosthetic group, FMN. Glutamine 114 was mutated to asparagine, introducing an R-group that is one methylene group shorter. The resultant enzyme was characterized to determine the effect of the mutation on the mechanistic behavior of the enzyme, and the crystal structure was solved to determine the effect of the mutation on the structure of the protein. The Q114N mutation results in little change in the protein structure, moving the amide group of residue 114 out of H-bonding distance, allowing repositioning of the FMN prosthetic group to form new interactions that replace the lost H-bonds. The mutation decreases the ability to bind ligands, as all dissociation constants for substituted phenols are larger than for the wild type enzyme. The rate constant for the reductive half-reaction with beta-NADPH is slightly greater, whereas that for the oxidative half-reaction with 2-cyclohexenone is smaller than for the wild type enzyme. Oxidation with molecular oxygen is biphasic and involves formation and reaction with O(2), a phenomenon that is more pronounced with this mutation than with wild type enzyme. When superoxide dismutase is added to the reaction, we observe a single-phase reaction typical of the wild type enzyme. Turnover reactions using beta-NADPH with 2-cyclohexenone and molecular oxygen were studied to further characterize the mutant enzyme.
-The role of glutamine 114 in old yellow enzyme.,Brown BJ, Hyun JW, Duvvuri S, Karplus PA, Massey V J Biol Chem. 2002 Jan 18;277(3):2138-45. Epub 2001 Oct 19. PMID:11668181<ref>PMID:11668181</ref>
+==See Also==
+*[[NADPH dehydrogenase|NADPH dehydrogenase]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1k03" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: NADPH dehydrogenase]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Brown, B J]]
+[[Category: Brown BJ]]
-[[Category: Duvvuri, S D]]
+[[Category: Duvvuri SD]]
-[[Category: Hyun, J]]
+[[Category: Hyun J]]
-[[Category: Karplus, P A]]
+[[Category: Karplus PA]]
-[[Category: Massey, V]]
+[[Category: Massey V]]
-[[Category: Beta-alpha barrel]]
-[[Category: Oxidoreductase]]