2ozl

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{{STRUCTURE_2ozl| PDB=2ozl | SCENE= }}
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==Human pyruvate dehydrogenase S264E variant==
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===Human pyruvate dehydrogenase S264E variant===
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<StructureSection load='2ozl' size='340' side='right' caption='[[2ozl]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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{{ABSTRACT_PUBMED_17474719}}
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2ozl]] is a 4 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=2OZL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OZL FirstGlance]. <br>
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</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene><br>
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<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDHA1, PHE1A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), PDHB, PHE1B ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
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<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
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<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ozl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ozl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ozl RCSB], [http://www.ebi.ac.uk/pdbsum/2ozl PDBsum]</span></td></tr>
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<table>
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== Disease ==
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[[http://www.uniprot.org/uniprot/ODPA_HUMAN ODPA_HUMAN]] Defects in PDHA1 are a cause of pyruvate dehydrogenase E1-alpha deficiency (PDHAD) [MIM:[http://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:[http://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> [[http://www.uniprot.org/uniprot/ODPB_HUMAN ODPB_HUMAN]] Defects in PDHB are the cause of pyruvate dehydrogenase E1-beta deficiency (PDHBD) [MIM:[http://omim.org/entry/614111 614111]]. 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:15138885</ref>
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== Function ==
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[[http://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> [[http://www.uniprot.org/uniprot/ODPB_HUMAN ODPB_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:17474719</ref> <ref>PMID:19081061</ref>
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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/oz/2ozl_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/chain_selection.php?pdb_ID=2ata 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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At the junction of glycolysis and the Krebs cycle in cellular metabolism, the pyruvate dehydrogenase multienzyme complex (PDHc) catalyzes the oxidative decarboxylation of pyruvate to acetyl-CoA. In mammals, PDHc is tightly regulated by phosphorylation-dephosphorylation of three serine residues in the thiamin-dependent pyruvate dehydrogenase (E1) component. In vivo, inactivation of human PDHc correlates mostly with phosphorylation of serine 264, which is located at the entrance of the substrate channel leading to the active site of E1. Despite intense investigations, the molecular mechanism of this inactivation has remained enigmatic. Here, a detailed analysis of microscopic steps of catalysis in human wild-type PDHc-E1 and pseudophosphorylation variant Ser264Glu elucidates how phosphorylation of Ser264 affects catalysis. Whereas the intrinsic reactivity of the active site in catalysis of pyruvate decarboxylation remains nearly unaltered, the preceding binding of substrate to the enzyme's active site via the substrate channel and the subsequent reductive acetylation of the E2 component are severely slowed in the phosphorylation variant. The structure of pseudophosphorylation variant Ser264Glu determined by X-ray crystallography reveals no differences in the three-dimensional architecture of the phosphorylation loop or of the active site, when compared to those of the wild-type enzyme. However, the channel leading to the active site is partially obstructed by the side chain of residue 264 in the variant. By analogy, a similar obstruction of the substrate channel can be anticipated to result from a phosphorylation of Ser264. The kinetic and thermodynamic results in conjunction with the structure of Ser264Glu suggest that phosphorylation blocks access to the active site by imposing a steric and electrostatic barrier for substrate binding and active site coupling with the E2 component. As a Ser264Gln variant, which carries no charge at position 264, is also selectively deficient in pyruvate binding and reductive acetylation of E2, we conclude that mostly steric effects account for inhibition of PDHc by phosphorylation.
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==Disease==
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Phosphorylation of serine 264 impedes active site accessibility in the E1 component of the human pyruvate dehydrogenase multienzyme complex.,Seifert F, Ciszak E, Korotchkina L, Golbik R, Spinka M, Dominiak P, Sidhu S, Brauer J, Patel MS, Tittmann K Biochemistry. 2007 May 29;46(21):6277-87. Epub 2007 May 3. PMID:17474719<ref>PMID:17474719</ref>
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[[http://www.uniprot.org/uniprot/ODPA_HUMAN ODPA_HUMAN]] Defects in PDHA1 are a cause of pyruvate dehydrogenase E1-alpha deficiency (PDHAD) [MIM:[http://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:[http://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> [[http://www.uniprot.org/uniprot/ODPB_HUMAN ODPB_HUMAN]] Defects in PDHB are the cause of pyruvate dehydrogenase E1-beta deficiency (PDHBD) [MIM:[http://omim.org/entry/614111 614111]]. 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:15138885</ref>
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==Function==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[http://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> [[http://www.uniprot.org/uniprot/ODPB_HUMAN ODPB_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:17474719</ref><ref>PMID:19081061</ref>
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</div>
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==About this Structure==
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[[2ozl]] is a 4 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=2OZL OCA].
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==See Also==
==See Also==
*[[Pyruvate dehydrogenase|Pyruvate dehydrogenase]]
*[[Pyruvate dehydrogenase|Pyruvate dehydrogenase]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:017474719</ref><references group="xtra"/><references/>
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Ciszak, E M.]]
[[Category: Ciszak, E M.]]

Revision as of 18:51, 30 September 2014

Human pyruvate dehydrogenase S264E variant

2ozl, resolution 1.90Å

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