2vk4: Difference between revisions

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[2vk4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_lactis Kluyveromyces lactis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2g1i 2g1i]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VK4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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]] 1.95&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2g1i|2g1i]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pyruvate_decarboxylase Pyruvate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.1 4.1.1.1] </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=2vk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vk4 OCA], [https://pdbe.org/2vk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vk4 RCSB], [https://www.ebi.ac.uk/pdbsum/2vk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vk4 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/PDC1_KLULA PDC1_KLULA]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 19: / 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=2vk4 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis has been determined to 2.26 A resolution. Like other yeast enzymes, Kluyveromyces lactis pyruvate decarboxylase is subject to allosteric substrate activation. Binding of substrate at a regulatory site induces catalytic activity. This process is accompanied by conformational changes and subunit rearrangements. In the nonactivated form of the corresponding enzyme from Saccharomyces cerevisiae, all active sites are solvent accessible due to the high flexibility of loop regions 106-113 and 292-301. The binding of the activator pyruvamide arrests these loops. Consequently, two of four active sites become closed. In Kluyveromyces lactis pyruvate decarboxylase, this half-side closed tetramer is present even without any activator. However, one of the loops (residues 105-113), which are flexible in nonactivated Saccharomyces cerevisiae pyruvate decarboxylase, remains flexible. Even though the tetramer assemblies of both enzyme species are different in the absence of activating agents, their substrate activation kinetics are similar. This implies an equilibrium between the open and the half-side closed state of yeast pyruvate decarboxylase tetramers. The completely open enzyme state is favoured for Saccharomyces cerevisiae pyruvate decarboxylase, whereas the half-side closed form is predominant for Kluyveromyces lactis pyruvate decarboxylase. Consequently, the structuring of the flexible loop region 105-113 seems to be the crucial step during the substrate activation process of Kluyveromyces lactis pyruvate decarboxylase.
-The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis. Implications for the substrate activation mechanism of this enzyme.,Kutter S, Wille G, Relle S, Weiss MS, Hubner G, Konig S FEBS J. 2006 Sep;273(18):4199-209. PMID:16939618<ref>PMID:16939618</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2vk4" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Pyruvate decarboxylase|Pyruvate decarboxylase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Kluyveromyces lactis]]
 [[Category: Large Structures]]
-[[Category: Pyruvate decarboxylase]]
+[[Category: Konig S]]
-[[Category: Konig, S]]
+[[Category: Kutter S]]
-[[Category: Kutter, S]]
+[[Category: Relle S]]
-[[Category: Relle, S]]
+[[Category: Weiss MS]]
-[[Category: Weiss, M S]]
+[[Category: Wille G]]
-[[Category: Wille, G]]
-[[Category: Asymmetric active site]]
-[[Category: Decarboxylase]]
-[[Category: Dimer of dimer]]
-[[Category: Flavoprotein]]
-[[Category: Lyase]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Substrate activation]]
-[[Category: Tdp]]
-[[Category: Thiamine diphosphate]]
-[[Category: Thiamine pyrophosphate]]
-[[Category: Tpp]]