3c5e: Difference between revisions

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-[[Image:3c5e.png|left|200px]]
-{{STRUCTURE_3c5e|  PDB=3c5e  |  SCENE=  }}
+==Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with ATP==
+<StructureSection load='3c5e' size='340' side='right'caption='[[3c5e]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3c5e]] is a 1 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=3C5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C5E 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]] 1.6&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</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=3c5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c5e OCA], [https://pdbe.org/3c5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c5e RCSB], [https://www.ebi.ac.uk/pdbsum/3c5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c5e ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ACS2A_HUMAN ACS2A_HUMAN] Has medium-chain fatty acid:CoA ligase activity with broad substrate specificity (in vitro). Acts on acids from C(4) to C(11) and on the corresponding 3-hydroxy- and 2,3- or 3,4-unsaturated acids (in vitro) (By similarity).
+== 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/c5/3c5e_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=3c5e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Acyl-CoA synthetases belong to the superfamily of adenylate-forming enzymes, and catalyze the two-step activation of fatty acids or carboxylate-containing xenobiotics. The carboxylate substrate first reacts with ATP to form an acyl-adenylate intermediate, which then reacts with CoA to produce an acyl-CoA ester. Here, we report the first crystal structure of a medium-chain acyl-CoA synthetase ACSM2A, in a series of substrate/product/cofactor complexes central to the catalytic mechanism. We observed a substantial rearrangement between the N- and C-terminal domains, driven purely by the identity of the bound ligand in the active site. Our structures allowed us to identify the presence or absence of the ATP pyrophosphates as the conformational switch, and elucidated new mechanistic details, including the role of invariant Lys557 and a divalent magnesium ion in coordinating the ATP pyrophosphates, as well as the involvement of a Gly-rich P-loop and the conserved Arg472-Glu365 salt bridge in the domain rearrangement.
-===Crystal structure of human acyl-CoA synthetase medium-chain family member 2A (L64P mutation) in complex with ATP===
+Structural snapshots for the conformation-dependent catalysis by human medium-chain acyl-coenzyme A synthetase ACSM2A.,Kochan G, Pilka ES, von Delft F, Oppermann U, Yue WW J Mol Biol. 2009 May 22;388(5):997-1008. Epub 2009 Apr 1. PMID:19345228<ref>PMID:19345228</ref>
-{{ABSTRACT_PUBMED_19345228}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3c5e" style="background-color:#fffaf0;"></div>
-[[3c5e]] is a 1 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=3C5E OCA].
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:019345228</ref><references group="xtra"/>
+</StructureSection>
-[[Category: Butyrate--CoA ligase]]
 [[Category: Homo sapiens]]
-[[Category: Arrowsmith, C H.]]
+[[Category: Large Structures]]
-[[Category: Bhatia, C.]]
+[[Category: Arrowsmith CH]]
-[[Category: Bountra, C.]]
+[[Category: Bhatia C]]
-[[Category: Delft, F Von.]]
+[[Category: Bountra C]]
-[[Category: Edwards, A M.]]
+[[Category: Edwards AM]]
-[[Category: Kochan, G T.]]
+[[Category: Kochan GT]]
-[[Category: Oppermann, U.]]
+[[Category: Oppermann U]]
-[[Category: Pilka, E S.]]
+[[Category: Pilka ES]]
-[[Category: SGC, Structural Genomics Consortium.]]
+[[Category: Weigelt J]]
-[[Category: Weigelt, J.]]
+[[Category: Von Delft F]]
-[[Category: Atp-binding]]
-[[Category: Fatty acid metabolism]]
-[[Category: Ligase]]
-[[Category: Lipid metabolism]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Middle-chain acyl-coa synthetase]]
-[[Category: Mitochondrion]]
-[[Category: Nucleotide-binding polymorphism]]
-[[Category: Sgc]]
-[[Category: Structural genomics consortium]]
-[[Category: Transit peptide]]
-[[Category: Xenobiotic/medium-chain fatty acid-coa ligase]]