6jbd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:37, 27 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='6jbd' size='340' side='right'caption='[[6jbd]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='6jbd' size='340' side='right'caption='[[6jbd]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6jbd]] 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=6JBD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JBD FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6jbd]] 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=6JBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JBD FirstGlance]. <br>
-
</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.5&#8491;</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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=6jbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbd OCA], [https://pdbe.org/6jbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jbd RCSB], [https://www.ebi.ac.uk/pdbsum/6jbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbd 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=6jbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jbd OCA], [http://pdbe.org/6jbd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jbd RCSB], [http://www.ebi.ac.uk/pdbsum/6jbd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jbd 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;">
+
-
== 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<ref>PMID:31697438</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 6jbd" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
Line 25: Line 15:
</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]]
+

Current revision

Phosphotransferase-ATP complex related to CoA biosynthesis pathway

PDB ID 6jbd

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6jbd"
Personal tools