1w85: Difference between revisions
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< | ==The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2== | ||
<StructureSection load='1w85' size='340' side='right'caption='[[1w85]], [[Resolution|resolution]] 2.00Å' scene=''> | |||
You may | == 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]] 2Å</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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</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: Geobacillus stearothermophilus]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Pyruvate Dehydrogenase Complex]] | ||
[[Category: | [[Category: RCSB PDB Molecule of the Month]] | ||
[[Category: | [[Category: Frank RAW]] | ||
[[Category: | [[Category: Luisi BF]] | ||
[[Category: | [[Category: Pei XY]] | ||
[[Category: | [[Category: Perham RN]] | ||
[[Category: | [[Category: Pratap JV]] | ||
Latest revision as of 16:20, 13 December 2023
The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2The crystal structure of pyruvate dehydrogenase E1 bound to the peripheral subunit binding domain of E2
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThiamine 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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