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| | <StructureSection load='6jbc' size='340' side='right'caption='[[6jbc]], [[Resolution|resolution]] 2.70Å' scene=''> | | <StructureSection load='6jbc' size='340' side='right'caption='[[6jbc]], [[Resolution|resolution]] 2.70Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6jbc]] is a 1 chain structure with sequence from [http://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=6JBC OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JBC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6jbc]] is a 1 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=6JBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JBC FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</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]] 2.7Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TK2141 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69014 Pyrococcus kodakaraensis (strain KOD1)])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PPV:PYROPHOSPHATE'>PPV</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pantoate_kinase Pantoate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.169 2.7.1.169] </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=6jbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbc OCA], [https://pdbe.org/6jbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jbc RCSB], [https://www.ebi.ac.uk/pdbsum/6jbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbc ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbc OCA], [http://pdbe.org/6jbc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jbc RCSB], [http://www.ebi.ac.uk/pdbsum/6jbc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbc ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/POK_THEKO POK_THEKO]] Phosphorylates (R)-pantoate to form (R)-4-phosphopantoate in the CoA biosynthesis pathway (PubMed:19666462, PubMed:22865846). Displays broad nucleotide specificity and utilizes ATP, GTP, UTP, and CTP with comparable catalytic efficiencies (PubMed:22865846).<ref>PMID:19666462</ref> <ref>PMID:22865846</ref> | + | [https://www.uniprot.org/uniprot/POK_THEKO POK_THEKO] Phosphorylates (R)-pantoate to form (R)-4-phosphopantoate in the CoA biosynthesis pathway (PubMed:19666462, PubMed:22865846). Displays broad nucleotide specificity and utilizes ATP, GTP, UTP, and CTP with comparable catalytic efficiencies (PubMed:22865846).<ref>PMID:19666462</ref> <ref>PMID:22865846</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pantoate kinase]] | + | [[Category: Thermococcus kodakarensis KOD1]] |
| - | [[Category: Atomi, H]] | + | [[Category: Atomi H]] |
| - | [[Category: Imanaka, T]] | + | [[Category: Imanaka T]] |
| - | [[Category: Kishimoto, A]] | + | [[Category: Kishimoto A]] |
| - | [[Category: Kita, A]] | + | [[Category: Kita A]] |
| - | [[Category: Miki, K]] | + | [[Category: Miki K]] |
| - | [[Category: Shimosaka, T]] | + | [[Category: Shimosaka T]] |
| - | [[Category: Tomita, H]] | + | [[Category: Tomita H]] |
| - | [[Category: Yokooji, Y]] | + | [[Category: Yokooji Y]] |
| - | [[Category: Coa biosynthesis]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
6jbc is a 1 chain structure with sequence from Thermococcus kodakarensis KOD1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.7Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
POK_THEKO Phosphorylates (R)-pantoate to form (R)-4-phosphopantoate in the CoA biosynthesis pathway (PubMed:19666462, PubMed:22865846). Displays broad nucleotide specificity and utilizes ATP, GTP, UTP, and CTP with comparable catalytic efficiencies (PubMed:22865846).[1] [2]
Publication Abstract from PubMed
The coenzyme A biosynthesis pathways in most archaea involve two unique enzymes, pantoate kinase and phosphopantothenate synthetase, to convert pantoate to 4'-phosphopantothenate. Here, we report the first crystal structure of pantoate kinase from the hyperthermophilic archaeon, Thermococcus kodakarensis and its complex with ATP and a magnesium ion. The electron density for the adenosine moiety of ATP was very weak, which most likely relates to its broad nucleotide specificity. Based on the structure of the active site that contains a glycerol molecule, the pantoate binding site and the roles of the highly conserved residues are suggested.
Crystal structure of pantoate kinase from Thermococcus kodakarensis.,Kita A, Kishimoto A, Shimosaka T, Tomita H, Yokooji Y, Imanaka T, Atomi H, Miki K Proteins. 2020 May;88(5):718-724. doi: 10.1002/prot.25852. Epub 2019 Nov 20. PMID:31697438[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yokooji Y, Tomita H, Atomi H, Imanaka T. Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the Archaea. J Biol Chem. 2009 Oct 9;284(41):28137-45. doi: 10.1074/jbc.M109.009696. Epub 2009, Aug 7. PMID:19666462 doi:http://dx.doi.org/10.1074/jbc.M109.009696
- ↑ Tomita H, Yokooji Y, Ishibashi T, Imanaka T, Atomi H. Biochemical characterization of pantoate kinase, a novel enzyme necessary for coenzyme A biosynthesis in the Archaea. J Bacteriol. 2012 Oct;194(19):5434-43. doi: 10.1128/JB.06624-11. Epub 2012 Aug 3. PMID:22865846 doi:http://dx.doi.org/10.1128/JB.06624-11
- ↑ Kita A, Kishimoto A, Shimosaka T, Tomita H, Yokooji Y, Imanaka T, Atomi H, Miki K. Crystal structure of pantoate kinase from Thermococcus kodakarensis. Proteins. 2020 May;88(5):718-724. doi: 10.1002/prot.25852. Epub 2019 Nov 20. PMID:31697438 doi:http://dx.doi.org/10.1002/prot.25852
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