3lcb: Difference between revisions

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 ==The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.==
-<StructureSection load='3lcb' size='340' side='right' caption='[[3lcb]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='3lcb' size='340' side='right'caption='[[3lcb]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3lcb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco57 Eco57] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. The September 2010 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Isocitrate Dehydrogenase''  by David Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2010_9 10.2210/rcsb_pdb/mom_2010_9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LCB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LCB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3lcb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] and [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. The September 2010 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Isocitrate Dehydrogenase''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2010_9 10.2210/rcsb_pdb/mom_2010_9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LCB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LCB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3eps|3eps]], [[3lc6|3lc6]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">aceK, ECH74115_5487 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57]), b1136, icd, icdA, icdE, icdh, JW1122 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3lcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lcb OCA], [https://pdbe.org/3lcb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lcb RCSB], [https://www.ebi.ac.uk/pdbsum/3lcb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lcb ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Isocitrate_dehydrogenase_(NADP(+)) Isocitrate dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.42 1.1.1.42] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3lcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lcb OCA], [http://pdbe.org/3lcb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lcb RCSB], [http://www.ebi.ac.uk/pdbsum/3lcb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lcb ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ACEK_ECO5E ACEK_ECO5E]] Bifunctional enzyme which can phosphorylate or dephosphorylate isocitrate dehydrogenase (IDH) on a specific serine residue. This is a regulatory mechanism which enables bacteria to bypass the Krebs cycle via the glyoxylate shunt in response to the source of carbon. When bacteria are grown on glucose, IDH is fully active and unphosphorylated, but when grown on acetate or ethanol, the activity of IDH declines drastically concomitant with its phosphorylation.
+[https://www.uniprot.org/uniprot/ACEK_ECO57 ACEK_ECO57] Bifunctional enzyme which can phosphorylate or dephosphorylate isocitrate dehydrogenase (IDH) on a specific serine residue. This is a regulatory mechanism which enables bacteria to bypass the Krebs cycle via the glyoxylate shunt in response to the source of carbon. When bacteria are grown on glucose, IDH is fully active and unphosphorylated, but when grown on acetate or ethanol, the activity of IDH declines drastically concomitant with its phosphorylation.
 == 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/lc/3lcb_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lc/3lcb_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 22: / Line 20: @@
 </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=3lcb ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-The Escherichia coli isocitrate dehydrogenase kinase/phosphatase (AceK) is a unique bifunctional enzyme that phosphorylates or dephosphorylates isocitrate dehydrogenase (ICDH) in response to environmental changes, resulting in the inactivation or, respectively, activation of ICDH. ICDH inactivation short-circuits the Krebs cycle by enabling the glyoxlate bypass. It was the discovery of AceK and ICDH that established the existence of protein phosphorylation regulation in prokaryotes. As a 65-kDa protein, AceK is significantly larger than typical eukaryotic protein kinases. Apart from the ATP-binding motif, AceK does not share sequence homology with any eukaryotic protein kinase or phosphatase. Most intriguingly, AceK possesses the two opposing activities of protein kinase and phosphatase within one protein, and specifically recognizes only intact ICDH. Additionally, AceK has strong ATPase activity. It has been shown that AceK kinase, phosphatase and ATPase activities reside at the same site, although the molecular basis of such multifunctionality and its regulation remains completely unknown. Here we report the structures of AceK and its complex with ICDH. The AceK structure reveals a eukaryotic protein-kinase-like domain containing ATP and a regulatory domain with a novel fold. As an AceK phosphatase activator and kinase inhibitor, AMP is found to bind in an allosteric site between the two AceK domains. An AMP-mediated conformational change exposes and shields ATP, acting as a switch between AceK kinase and phosphatase activities, and ICDH-binding induces further conformational change for AceK activation. The substrate recognition loop of AceK binds to the ICDH dimer, allowing higher-order substrate recognition and interaction, and inducing critical conformational change at the phosphorylation site of ICDH.
-Structure of the bifunctional isocitrate dehydrogenase kinase/phosphatase.,Zheng J, Jia Z Nature. 2010 Jun 17;465(7300):961-5. Epub 2010 May 26. PMID:20505668<ref>PMID:20505668</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3lcb" style="background-color:#fffaf0;"></div>
 ==See Also==
+*[[Isocitrate dehydrogenase 3D structures|Isocitrate dehydrogenase 3D structures]]
 *[[Isocitrate dehydrogenase kinase/phosphatase|Isocitrate dehydrogenase kinase/phosphatase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Eco57]]
+[[Category: Escherichia coli K-12]]
-[[Category: Ecoli]]
+[[Category: Escherichia coli O157:H7]]
 [[Category: Isocitrate Dehydrogenase]]
+[[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Jia, Z]]
+[[Category: Jia Z]]
-[[Category: Zheng, J]]
+[[Category: Zheng J]]
-[[Category: Glyoxylate bypass]]
-[[Category: Hydrolase]]
-[[Category: Hydrolaseprotein phosphatase]]
-[[Category: Isocitrate]]
-[[Category: Kinase phosphatase]]
-[[Category: Transferase]]
-[[Category: Tricarboxylic acid cycle]]