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3wdk

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Current revision (08:44, 20 March 2024) (edit) (undo)
 
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<StructureSection load='3wdk' size='340' side='right'caption='[[3wdk]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='3wdk' size='340' side='right'caption='[[3wdk]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3wdk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_kodakaraensis_(strain_kod1) Pyrococcus kodakaraensis (strain kod1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WDK FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3wdk]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WDK FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=PTJ:5-O-[(S)-HYDROXY{[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]OXY}PHOSPHORYL]ADENOSINE'>PTJ</scene></td></tr>
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</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>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wdl|3wdl]], [[3wdm|3wdm]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=PTJ:5-O-[(S)-HYDROXY{[(2R)-2-HYDROXY-3,3-DIMETHYL-4-(PHOSPHONOOXY)BUTANOYL]OXY}PHOSPHORYL]ADENOSINE'>PTJ</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK1686 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/4-phosphopantoate--beta-alanine_ligase 4-phosphopantoate--beta-alanine ligase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.2.36 6.3.2.36] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3wdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdk OCA], [https://pdbe.org/3wdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wdk RCSB], [https://www.ebi.ac.uk/pdbsum/3wdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wdk ProSAT]</span></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=3wdk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wdk OCA], [https://pdbe.org/3wdk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wdk RCSB], [https://www.ebi.ac.uk/pdbsum/3wdk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wdk ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/PPS_THEKO PPS_THEKO]] Catalyzes the conversion of (R)-4-phosphopantoate and beta-alanine to 4'-phosphopantothenate in the CoA biosynthesis pathway. Cannot use (R)-pantoate as substrate and thus does not display pantothenate synthetase (PS) activity.
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[https://www.uniprot.org/uniprot/PPS_THEKO PPS_THEKO] Catalyzes the conversion of (R)-4-phosphopantoate and beta-alanine to 4'-phosphopantothenate in the CoA biosynthesis pathway. Cannot use (R)-pantoate as substrate and thus does not display pantothenate synthetase (PS) activity.
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Bacteria/eukaryotes share a common pathway for coenzyme A biosynthesis which involves two enzymes to convert pantoate to 4'-phosphopantothenate. These two enzymes are absent in almost all archaea. Recently, it was reported that two novel enzymes, pantoate kinase (PoK) and phosphopantothenate synthetase (PPS), are responsible for this conversion in archaea. Here, we report the crystal structure of PPS from the hyperthermophilic archaeon, Thermococcus kodakarensis and its complexes with substrates, ATP, and ATP and 4-phosphopantoate (PPo). PPS forms an asymmetric homodimer, in which two monomers composing a dimer, deviated from the exact 2-fold symmetry, displaying 4 degrees -13 degrees distortion. The structural features are consistent with the mutagenesis data and the results of biochemical experiments previously reported. Based on these structures, we discuss the catalytic mechanism by which PPS produces phosphopantoyl adenylate (PPA), which is thought to be a reaction intermediate. (c) Proteins 2014;. (c) 2014 Wiley Periodicals, Inc.
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Crystal Structure of Phosphopantothenate Synthetase from Thermococcus k odakarensis.,Kishimoto A, Kita A, Ishibashi T, Tomita H, Yokooji Y, Imanaka T, Atomi H, Miki K Proteins. 2014 Mar 17. doi: 10.1002/prot.24546. PMID:24638914<ref>PMID:24638914</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3wdk" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: 4-phosphopantoate--beta-alanine ligase]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Atomi, H]]
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[[Category: Thermococcus kodakarensis KOD1]]
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[[Category: Imanaka, T]]
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[[Category: Atomi H]]
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[[Category: Ishibashi, T]]
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[[Category: Imanaka T]]
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[[Category: Kishimoto, A]]
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[[Category: Ishibashi T]]
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[[Category: Kita, A]]
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[[Category: Kishimoto A]]
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[[Category: Miki, K]]
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[[Category: Kita A]]
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[[Category: Tomita, H]]
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[[Category: Miki K]]
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[[Category: Yokooji, Y]]
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[[Category: Tomita H]]
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[[Category: Ligase]]
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[[Category: Yokooji Y]]

Current revision

Crystal structure of 4-phosphopantoate-beta-alanine ligase complexed with reaction intermediate

PDB ID 3wdk

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