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1w85

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(New page: 200px<br /> <applet load="1w85" size="450" color="white" frame="true" align="right" spinBox="true" caption="1w85, resolution 2.00&Aring;" /> '''THE CRYSTAL STRUCTU...)
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[[Image:1w85.gif|left|200px]]<br />
 
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<applet load="1w85" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1w85, resolution 2.00&Aring;" />
 
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'''THE CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE E1 BOUND TO THE PERIPHERAL SUBUNIT BINDING DOMAIN OF E2'''<br />
 
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==Overview==
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==The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2==
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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.
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<StructureSection load='1w85' size='340' side='right'caption='[[1w85]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</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>
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<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>
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<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>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/ODPA_GEOSE ODPA_GEOSE]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w8/1w85_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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>
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1W85 is a [[http://en.wikipedia.org/wiki/Protein_complex Protein complex]] structure of sequences from [[http://en.wikipedia.org/wiki/Bacillus_stearothermophilus Bacillus stearothermophilus]] with MG, K, TDP and PEG as [[http://en.wikipedia.org/wiki/ligands ligands]]. Active as [[http://en.wikipedia.org/wiki/ ]], with EC number [[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.1 1.2.4.1]]. Full crystallographic information is available from [[http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1W85 OCA]].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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]
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</div>
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[[Category: Bacillus stearothermophilus]]
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<div class="pdbe-citations 1w85" style="background-color:#fffaf0;"></div>
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[[Category: Protein complex]]
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[[Category: Frank, R.A.W.]]
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[[Category: Luisi, B.F.]]
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[[Category: Pei, X.Y.]]
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[[Category: Perham, R.N.]]
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[[Category: Pratap, J.V.]]
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[[Category: K]]
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[[Category: MG]]
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[[Category: PEG]]
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[[Category: TDP]]
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[[Category: acetyl transferase]]
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[[Category: dehydrogenase]]
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[[Category: dihydrolipoyl]]
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[[Category: multienzyme complex]]
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[[Category: oxidoreductase]]
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[[Category: pyruvate]]
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[[Category: transferase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Oct 29 21:23:27 2007''
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==See Also==
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*[[Dihydrolipoamide acetyltransferase 3D structures|Dihydrolipoamide acetyltransferase 3D structures]]
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*[[Pyruvate dehydrogenase 3D structures|Pyruvate dehydrogenase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Geobacillus stearothermophilus]]
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[[Category: Large Structures]]
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[[Category: Pyruvate Dehydrogenase Complex]]
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[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Frank RAW]]
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[[Category: Luisi BF]]
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[[Category: Pei XY]]
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[[Category: Perham RN]]
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[[Category: Pratap JV]]

Current revision

The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2

PDB ID 1w85

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