1w85: Difference between revisions

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-[[Image:1w85.gif|left|200px]]<br />
-<applet load="1w85" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1w85, resolution 2.00&Aring;" />
-'''THE CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE E1 BOUND TO THE PERIPHERAL SUBUNIT BINDING DOMAIN OF E2'''<br />
-==Overview==
+==The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2==
-Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic, enzymes. We present evidence that the ThDPs in the two active sites of the, E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex, communicate over a distance of 20 angstroms by reversibly shuttling a, proton through an acidic tunnel in the protein. This "proton wire" permits, the co-factors to serve reciprocally as general acid/base in catalysis and, to switch the conformation of crucial active-site peptide loops. This, synchronizes the progression of chemical events and can account for the, oligomeric organization, conformational asymmetry, and "ping-pong" kinetic, properties of E1 and other thiamine-dependent enzymes.
+<StructureSection load='1w85' size='340' side='right'caption='[[1w85]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1w85]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]. The September 2012 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Pyruvate Dehydrogenase Complex''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2012_9 10.2210/rcsb_pdb/mom_2012_9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1W85 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1W85 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&#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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</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=1w85 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1w85 OCA], [https://pdbe.org/1w85 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1w85 RCSB], [https://www.ebi.ac.uk/pdbsum/1w85 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1w85 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ODPA_GEOSE ODPA_GEOSE]
+== 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/w8/1w85_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=1w85 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Thiamine diphosphate (ThDP) is used as a cofactor in many key metabolic enzymes. We present evidence that the ThDPs in the two active sites of the E1 (EC 1.2.4.1) component of the pyruvate dehydrogenase complex communicate over a distance of 20 angstroms by reversibly shuttling a proton through an acidic tunnel in the protein. This "proton wire" permits the co-factors to serve reciprocally as general acid/base in catalysis and to switch the conformation of crucial active-site peptide loops. This synchronizes the progression of chemical events and can account for the oligomeric organization, conformational asymmetry, and "ping-pong" kinetic properties of E1 and other thiamine-dependent enzymes.
-==About this Structure==
+A molecular switch and proton wire synchronize the active sites in thiamine enzymes.,Frank RA, Titman CM, Pratap JV, Luisi BF, Perham RN Science. 2004 Oct 29;306(5697):872-6. PMID:15514159<ref>PMID:15514159</ref>
-W85 is a [[http://en.wikipedia.org/wiki/Protein_complex Protein complex]] structure of sequences from [[http://en.wikipedia.org/wiki/Geobacillus_stearothermophilus Geobacillus stearothermophilus]] with MG, K, TDP and PEG as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/Pyruvate_dehydrogenase_(acetyl-transferring) Pyruvate dehydrogenase (acetyl-transferring)]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1]]. Structure known Active Site: AC1. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1W85 OCA]].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-A molecular switch and proton wire synchronize the active sites in thiamine enzymes., Frank RA, Titman CM, Pratap JV, Luisi BF, Perham RN, Science. 2004 Oct 29;306(5697):872-6. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15514159 15514159]
+</div>
+<div class="pdbe-citations 1w85" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dihydrolipoamide acetyltransferase 3D structures|Dihydrolipoamide acetyltransferase 3D structures]]
+*[[Pyruvate dehydrogenase 3D structures|Pyruvate dehydrogenase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Geobacillus stearothermophilus]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Pyruvate dehydrogenase (acetyl-transferring)]]
+[[Category: Pyruvate Dehydrogenase Complex]]
-[[Category: Frank, R.A.W.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Luisi, B.F.]]
+[[Category: Frank RAW]]
-[[Category: Pei, X.Y.]]
+[[Category: Luisi BF]]
-[[Category: Perham, R.N.]]
+[[Category: Pei XY]]
-[[Category: Pratap, J.V.]]
+[[Category: Perham RN]]
-[[Category: K]]
+[[Category: Pratap JV]]
-[[Category: MG]]
-[[Category: PEG]]
-[[Category: TDP]]
-[[Category: acetyl transferase]]
-[[Category: dehydrogenase]]
-[[Category: dihydrolipoyl]]
-[[Category: multienzyme complex]]
-[[Category: oxidoreductase]]
-[[Category: pyruvate]]
-[[Category: transferase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Oct 30 13:58:53 2007''