1x7y: Difference between revisions

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-{{Seed}}
-[[Image:1x7y.png|left|200px]]
-<!--
+==Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase==
-The line below this paragraph, containing "STRUCTURE_1x7y", creates the "Structure Box" on the page.
+<StructureSection load='1x7y' size='340' side='right'caption='[[1x7y]], [[Resolution|resolution]] 1.57&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1x7y]] is a 2 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=1X7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1X7Y FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.57&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></td></tr>
-{{STRUCTURE_1x7y|  PDB=1x7y  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1x7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1x7y OCA], [https://pdbe.org/1x7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1x7y RCSB], [https://www.ebi.ac.uk/pdbsum/1x7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1x7y ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/ODBA_HUMAN ODBA_HUMAN] Defects in BCKDHA are a cause of maple syrup urine disease type IA (MSUD1A) [MIM:[https://omim.org/entry/248600 248600]. MSUD is an autosomal recessive disorder characterized by mental and physical retardation, feeding problems, and a maple syrup odor to the urine.<ref>PMID:2060625</ref> <ref>PMID:8037208</ref> <ref>PMID:2703538</ref> <ref>PMID:2241958</ref> <ref>PMID:1867199</ref> <ref>PMID:1885764</ref> <ref>PMID:8161368</ref> <ref>PMID:7883996</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/ODBA_HUMAN ODBA_HUMAN] The branched-chain alpha-keto dehydrogenase complex catalyzes the overall conversion of alpha-keto acids to acyl-CoA and CO(2). It contains multiple copies of three enzymatic components: branched-chain alpha-keto acid decarboxylase (E1), lipoamide acyltransferase (E2) and lipoamide dehydrogenase (E3).
+== 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/x7/1x7y_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=1x7y ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex (BCKDC) is a 4 MDa macromolecular machine comprising three catalytic components (E1b, E2b, and E3), a kinase, and a phosphatase. The BCKDC overall activity is tightly regulated by phosphorylation in response to hormonal and dietary stimuli. We report that phosphorylation of Ser292-alpha in the E1b active site channel results in an order-to-disorder transition of the conserved phosphorylation loop carrying the phosphoryl serine. The conformational change is triggered by steric clashes of the phosphoryl group with invariant His291-alpha that serves as an indispensable anchor for the phosphorylation loop through bound thiamin diphosphate. Phosphorylation of Ser292-alpha does not severely impede the E1b-dependent decarboxylation of alpha-ketoacids. However, the disordered loop conformation prevents phosphorylated E1b from binding the E2b lipoyl-bearing domain, which effectively shuts off the E1b-catalyzed reductive acylation reaction and therefore completely inactivates BCKDC. This mechanism provides a paradigm for regulation of mitochondrial alpha-ketoacid dehydrogenase complexes by phosphorylation.
-===Crystal structure of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase===
+Molecular mechanism for regulation of the human mitochondrial branched-chain alpha-ketoacid dehydrogenase complex by phosphorylation.,Wynn RM, Kato M, Machius M, Chuang JL, Li J, Tomchick DR, Chuang DT Structure. 2004 Dec;12(12):2185-96. PMID:15576032<ref>PMID:15576032</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1x7y" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_15576032}}, adds the Publication Abstract to the page
+*[[2-oxoisovalerate dehydrogenase 3D structures|2-oxoisovalerate dehydrogenase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 15576032 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_15576032}}
+__TOC__
+</StructureSection>
-==Disease==
-Known disease associated with this structure: Maple syrup urine disease, type Ia OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=608348 608348]], Maple syrup urine disease, type Ib OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=248611 248611]]
-==About this Structure==
-X7Y is a 2 chains structure of sequences 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=1X7Y OCA].
-==Reference==
-<ref group="xtra">PMID:15576032</ref><references group="xtra"/>
 [[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: Tomchick, D R.]]
+[[Category: Machius M]]
-[[Category: Wynn, R M.]]
+[[Category: Tomchick DR]]
-[[Category: Acylation]]
+[[Category: Wynn RM]]
-[[Category: Branched-chain]]
-[[Category: Flavoprotein]]
-[[Category: Multi-enzyme complex]]
-[[Category: Oxidative decarboxylation maple syrup urine disease]]
-[[Category: Oxidoreductase,ketoacid dehydrogenase]]
-[[Category: Phosphorylation]]
-[[Category: Thiamin diphosphate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 17:54:15 2009''