3bf1: Difference between revisions

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 ==Type III pantothenate kinase from Thermotoga maritima complexed with pantothenate and ADP==
-<StructureSection load='3bf1' size='340' side='right' caption='[[3bf1]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='3bf1' size='340' side='right'caption='[[3bf1]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3bf1]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BF1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3BF1 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3bf1]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BF1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BF1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=PAU:PANTOTHENOIC+ACID'>PAU</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]] 2.3&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3bex|3bex]], [[3bf3|3bf3]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=PAU:PANTOTHENOIC+ACID'>PAU</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">coaX ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</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=3bf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bf1 OCA], [https://pdbe.org/3bf1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bf1 RCSB], [https://www.ebi.ac.uk/pdbsum/3bf1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bf1 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/Pantothenate_kinase Pantothenate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.33 2.7.1.33] </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=3bf1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bf1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3bf1 RCSB], [http://www.ebi.ac.uk/pdbsum/3bf1 PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/COAX_THEMA COAX_THEMA]] Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis.<ref>PMID:16855243</ref>
+[https://www.uniprot.org/uniprot/COAX_THEMA COAX_THEMA] Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis.<ref>PMID:16855243</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/bf/3bf1_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bf/3bf1_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3bf1 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Pantothenate kinase (PanK) catalyzes the first step of the universal five-step coenzyme A (CoA) biosynthetic pathway. The recently characterized type III PanK (PanK-III, encoded by the coaX gene) is distinct in sequence, structure and enzymatic properties from both the long-known bacterial type I PanK (PanK-I, exemplified by the Escherichia coli CoaA protein) and the predominantly eukaryotic type II PanK (PanK-II). PanK-III enzymes have an unusually high Km for ATP, are resistant to feedback inhibition by CoA, and are unable to utilize the N-alkylpantothenamide family of pantothenate analogues as alternative substrates, thus making type III PanK ineffective in generating CoA analogues as antimetabolites in vivo. Previously, we reported the crystal structure of the PanK-III from Thermotoga maritima and identified it as a member of the "acetate and sugar kinase/heat shock protein 70/actin" (ASKHA) superfamily. Here we report the crystal structures of the same PanK-III in complex with one of its substrates (pantothenate), its product (phosphopantothenate) as well as a ternary complex structure of PanK-III with pantothenate and ADP. These results are combined with isothermal titration calorimetry experiments to present a detailed structural and thermodynamic characterization of the interactions between PanK-III and its substrates ATP and pantothenate. Comparison of substrate binding and catalytic sites of PanK-III with that of eukaryotic PanK-II revealed drastic differences in the binding modes for both ATP and pantothenate substrates, and suggests that these differences may be exploited in the development of new inhibitors specifically targeting PanK-III.
-Structural basis for substrate binding and the catalytic mechanism of type III pantothenate kinase.,Yang K, Strauss E, Huerta C, Zhang H Biochemistry. 2008 Feb 5;47(5):1369-80. Epub 2008 Jan 11. PMID:18186650<ref>PMID:18186650</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
-*[[Pantothenate kinase|Pantothenate kinase]]
+*[[Pantothenate kinase 3D structures|Pantothenate kinase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Pantothenate kinase]]
+[[Category: Large Structures]]
 [[Category: Thermotoga maritima]]
-[[Category: Huerta, C]]
+[[Category: Huerta C]]
-[[Category: Strauss, E]]
+[[Category: Strauss E]]
-[[Category: Yang, K]]
+[[Category: Yang K]]
-[[Category: Zhang, H]]
+[[Category: Zhang H]]
-[[Category: Actin-like fold]]
-[[Category: Atp-binding]]
-[[Category: Coenzyme a biosynthesis]]
-[[Category: Kinase]]
-[[Category: Metal-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: Potassium]]
-[[Category: Transferase]]