1k02: Difference between revisions

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-[[Image:1k02.jpg|left|200px]]<br /><applet load="1k02" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1k02, resolution 2.7&Aring;" />
-'''Crystal Structure of Old Yellow Enzyme Mutant Gln114Asn'''<br />
-==Overview==
+==Crystal Structure of Old Yellow Enzyme Mutant Gln114Asn==
-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.
+<StructureSection load='1k02' size='340' side='right'caption='[[1k02]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1k02]] 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=1K02 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1K02 FirstGlance]. <br>
+</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='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=MG:MAGNESIUM+ION'>MG</scene></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=1k02 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k02 OCA], [https://pdbe.org/1k02 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1k02 RCSB], [https://www.ebi.ac.uk/pdbsum/1k02 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1k02 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[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/k0/1k02_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=1k02 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-K02 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=FMN:'>FMN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K02 OCA].
+*[[NADPH dehydrogenase|NADPH dehydrogenase]]
+__TOC__
-==Reference==
+</StructureSection>
-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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11668181 11668181]
+[[Category: Large Structures]]
-[[Category: NADPH dehydrogenase]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Brown BJ]]
-[[Category: Brown, B J.]]
+[[Category: Duvvuri SD]]
-[[Category: Duvvuri, S D.]]
+[[Category: Hyun J]]
-[[Category: Hyun, J.]]
+[[Category: Karplus PA]]
-[[Category: Karplus, P A.]]
+[[Category: Massey V]]
-[[Category: Massey, V.]]
-[[Category: FMN]]
-[[Category: MG]]
-[[Category: beta-alpha barrels]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:28:40 2008''