3exh: Difference between revisions

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-[[Image:3exh.png|left|200px]]
-{{STRUCTURE_3exh|  PDB=3exh  |  SCENE=  }}
+==Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex==
+<StructureSection load='3exh' size='340' side='right'caption='[[3exh]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3exh]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EXH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EXH 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]] 2.444&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</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=3exh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3exh OCA], [https://pdbe.org/3exh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3exh RCSB], [https://www.ebi.ac.uk/pdbsum/3exh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3exh ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/ODPA_HUMAN ODPA_HUMAN] Defects in PDHA1 are a cause of pyruvate dehydrogenase E1-alpha deficiency (PDHAD) [MIM:[https://omim.org/entry/312170 312170]. An enzymatic defect causing primary lactic acidosis in children. It is associated with a broad clinical spectrum ranging from fatal lactic acidosis in the newborn to chronic neurologic dysfunction with structural abnormalities in the central nervous system without systemic acidosis.<ref>PMID:1338114</ref> <ref>PMID:1909401</ref> <ref>PMID:1551669</ref> <ref>PMID:1293379</ref> <ref>PMID:8504306</ref> <ref>PMID:8032855</ref> <ref>PMID:7545958</ref> <ref>PMID:7967473</ref> <ref>PMID:7887409</ref> <ref>PMID:7573035</ref> <ref>PMID:7757088</ref> <ref>PMID:8664900</ref> <ref>PMID:8844217</ref> <ref>PMID:9671272</ref>   Defects in PDHA1 are the cause of X-linked Leigh syndrome (X-LS) [MIM:[https://omim.org/entry/308930 308930]. X-LS is an early-onset progressive neurodegenerative disorder with a characteristic neuropathology consisting of focal, bilateral lesions in one or more areas of the central nervous system, including the brainstem, thalamus, basal ganglia, cerebellum, and spinal cord. The lesions are areas of demyelination, gliosis, necrosis, spongiosis, or capillary proliferation. Clinical symptoms depend on which areas of the central nervous system are involved. The most common underlying cause is a defect in oxidative phosphorylation. LS may be a feature of a deficiency of any of the mitochondrial respiratory chain complexes.<ref>PMID:1909401</ref> <ref>PMID:7887409</ref> <ref>PMID:8498846</ref> <ref>PMID:8199595</ref> <ref>PMID:9266390</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/ODPA_HUMAN ODPA_HUMAN] The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2), and thereby links the glycolytic pathway to the tricarboxylic cycle.<ref>PMID:7782287</ref> <ref>PMID:19081061</ref>
+== 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/ex/3exh_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3exh ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We report the crystal structures of the phosporylated pyruvate dehydrogenase (E1p) component of the human pyruvate dehydrogenase complex (PDC). The complete phosphorylation at Ser264-alpha (site 1) of a variant E1p protein was achieved using robust pyruvate dehydrogenase kinase 4 free of the PDC core. We show that unlike its unmodified counterpart, the presence of a phosphoryl group at Ser264-alpha prevents the cofactor thiamine diphosphate-induced ordering of the two loops carrying the three phosphorylation sites. The disordering of these phosphorylation loops is caused by a previously unrecognized steric clash between the phosphoryl group at site 1 and a nearby Ser266-alpha, which nullifies a hydrogen-bonding network essential for maintaining the loop conformations. The disordered phosphorylation loops impede the binding of lipoyl domains of the PDC core to E1p, negating the reductive acetylation step. This results in the disruption of the substrate channeling in the PDC, leading to the inactivation of this catalytic machine.
-===Crystal structure of the pyruvate dehydrogenase (E1p) component of human pyruvate dehydrogenase complex===
+Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops.,Kato M, Wynn RM, Chuang JL, Tso SC, Machius M, Li J, Chuang DT Structure. 2008 Dec 10;16(12):1849-59. PMID:19081061<ref>PMID:19081061</ref>
-{{ABSTRACT_PUBMED_19081061}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3exh" style="background-color:#fffaf0;"></div>
-[[3exh]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EXH OCA].
 ==See Also==
-*[[Pyruvate dehydrogenase|Pyruvate dehydrogenase]]
+*[[Pyruvate dehydrogenase 3D structures|Pyruvate dehydrogenase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019081061</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Chuang, D T.]]
+[[Category: Large Structures]]
-[[Category: Chuang, J L.]]
+[[Category: Chuang DT]]
-[[Category: Kato, M.]]
+[[Category: Chuang JL]]
-[[Category: Li, J.]]
+[[Category: Kato M]]
-[[Category: Machius, M.]]
+[[Category: Li J]]
-[[Category: Tso, S C.]]
+[[Category: Machius M]]
-[[Category: Wynn, R M.]]
+[[Category: Tso S-C]]
-[[Category: Alternative splicing]]
+[[Category: Wynn RM]]
-[[Category: Disease mutation]]
-[[Category: Glycolysis]]
-[[Category: Heterotetramer]]
-[[Category: Leigh syndrome]]
-[[Category: Mitochondrion]]
-[[Category: Oxidoreductase]]
-[[Category: Phosphoprotein]]
-[[Category: Polymorphism]]
-[[Category: Pyruvate]]
-[[Category: Thiamine diphosphate-dependent enzyme]]
-[[Category: Thiamine pyrophosphate]]
-[[Category: Transit peptide]]