3dva: Difference between revisions

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-{{Seed}}
-[[Image:3dva.jpg|left|200px]]
-<!--
+==Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex==
-The line below this paragraph, containing "STRUCTURE_3dva", creates the "Structure Box" on the page.
+<StructureSection load='3dva' size='340' side='right'caption='[[3dva]], [[Resolution|resolution]] 2.35&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'>[[3dva]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DVA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DVA 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]] 2.35&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPW:2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL+TRIHYDROGEN+DIPHOSPHATE'>TPW</scene></td></tr>
-{{STRUCTURE_3dva|  PDB=3dva  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dva FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dva OCA], [https://pdbe.org/3dva PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dva RCSB], [https://www.ebi.ac.uk/pdbsum/3dva PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dva ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ODPB_GEOSE ODPB_GEOSE] The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).
+== 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/dv/3dva_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=3dva ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The pyruvate dehydrogenase multienzyme assembly (PDH) generates acetyl coenzyme A and reducing equivalents from pyruvate in a multiple-step process that is a nexus of central metabolism. We report crystal structures of the Geobacillus stearothermophilus PDH E1p subunit with ligands that mimic the prereaction complex and the postdecarboxylation product. The structures implicate residues that help to orient substrates, nurture intermediates, and organize surface loops so that they can engage a mobile lipoyl domain that receives the acetyl group and shuttles it to the next active site. The structural and enzymatic data suggest that H128beta performs a dual role: first, as electrostatic catalyst of the reaction of pyruvate with the thiamine cofactor; and second, as a proton donor in the second reaction of acetyl group with the lipoate. We also identify I206alpha as a key residue in mediating the conformation of active-site loops. We propose that a simple conformational flip of the H271alpha side chain assists transfer of the acetyl group from thiamine cofactor to lipoyl domain in synchrony with reduction of the dithiolane ring.
-===Snapshots of catalysis in the E1 subunit of the pyruvate dehydrogenase multi-enzyme complex===
+Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex.,Pei XY, Titman CM, Frank RA, Leeper FJ, Luisi BF Structure. 2008 Dec 12;16(12):1860-72. PMID:19081062<ref>PMID:19081062</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3dva" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_19081062}}, adds the Publication Abstract to the page
+*[[Dihydrolipoamide acetyltransferase 3D structures|Dihydrolipoamide acetyltransferase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 19081062 is the PubMed ID number.
+*[[Pyruvate dehydrogenase 3D structures|Pyruvate dehydrogenase 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_19081062}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-DVA is a 10 chains structure of sequences from [http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DVA OCA].
-==Reference==
-Snapshots of catalysis in the e1 subunit of the pyruvate dehydrogenase multienzyme complex., Pei XY, Titman CM, Frank RA, Leeper FJ, Luisi BF, Structure. 2008 Dec 12;16(12):1860-72. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/19081062 19081062]
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Frank, R A.W.]]
+[[Category: Large Structures]]
-[[Category: Leeper, F J.]]
+[[Category: Frank RAW]]
-[[Category: Luisi, B F.]]
+[[Category: Leeper FJ]]
-[[Category: Pei, X Y.]]
+[[Category: Luisi BF]]
-[[Category: Titman, C M.]]
+[[Category: Pei XY]]
-[[Category: Acetyl transferase]]
+[[Category: Titman CM]]
-[[Category: Acyltransferase]]
-[[Category: Dehydrogenase]]
-[[Category: Dihydrolipoyl]]
-[[Category: Glycolysis]]
-[[Category: Multienzyme complex]]
-[[Category: Oxidoreductase]]
-[[Category: Oxidoreductase/transferase complex]]
-[[Category: Phosphoprotein]]
-[[Category: Pyruvate]]
-[[Category: Thiamine pyrophosphate]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 14 13:32:56 2009''