4ped

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(New page: '''Unreleased structure''' The entry 4ped is ON HOLD Authors: Stefely, J.A., Reidenbach, A.G., Ulbrich, A., Oruganty, O., Floyd, B.J., Jochem, A., Saunders, J.M., Johnson, I.E., Wrobel,...)
Current revision (00:42, 28 December 2023) (edit) (undo)
 
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'''Unreleased structure'''
 
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The entry 4ped is ON HOLD
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==Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthes==
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<StructureSection load='4ped' size='340' side='right'caption='[[4ped]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4ped]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PED FirstGlance]. <br>
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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]] 1.64&#8491;</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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=4ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ped OCA], [https://pdbe.org/4ped PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ped RCSB], [https://www.ebi.ac.uk/pdbsum/4ped PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ped ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/COQ8A_HUMAN COQ8A_HUMAN] Autosomal recessive ataxia due to ubiquinone deficiency. The disease is caused by variants affecting the gene represented in this entry.
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== Function ==
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[https://www.uniprot.org/uniprot/COQ8A_HUMAN COQ8A_HUMAN] Atypical kinase involved in the biosynthesis of coenzyme Q, also named ubiquinone, an essential lipid-soluble electron transporter for aerobic cellular respiration (PubMed:25498144, PubMed:21296186, PubMed:25540914, PubMed:27499294). Its substrate specificity is unclear: does not show any protein kinase activity (PubMed:25498144, PubMed:27499294). Probably acts as a small molecule kinase, possibly a lipid kinase that phosphorylates a prenyl lipid in the ubiquinone biosynthesis pathway, as suggested by its ability to bind coenzyme Q lipid intermediates (PubMed:25498144, PubMed:27499294). Shows an unusual selectivity for binding ADP over ATP (PubMed:25498144).<ref>PMID:25498144</ref> <ref>PMID:27499294</ref> <ref>PMID:21296186</ref> <ref>PMID:25540914</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The ancient UbiB protein kinase-like family is involved in isoprenoid lipid biosynthesis and is implicated in human diseases, but demonstration of UbiB kinase activity has remained elusive for unknown reasons. Here, we quantitatively define UbiB-specific sequence motifs and reveal their positions within the crystal structure of a UbiB protein, ADCK3. We find that multiple UbiB-specific features are poised to inhibit protein kinase activity, including an N-terminal domain that occupies the typical substrate binding pocket and a unique A-rich loop that limits ATP binding by establishing an unusual selectivity for ADP. A single alanine-to-glycine mutation of this loop flips this coenzyme selectivity and enables autophosphorylation but inhibits coenzyme Q biosynthesis in vivo, demonstrating functional relevance for this unique feature. Our work provides mechanistic insight into UbiB enzyme activity and establishes a molecular foundation for further investigation of how UbiB family proteins affect diseases and diverse biological pathways.
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Authors: Stefely, J.A., Reidenbach, A.G., Ulbrich, A., Oruganty, O., Floyd, B.J., Jochem, A., Saunders, J.M., Johnson, I.E., Wrobel, R.L., Barber, G.E., Lee, D., Li, S., Kannan, N., Coon, J.J., Bingman, C.A., Pagliarini, D.J., Mitochondrial Protein Partnership (MPP)
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Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis.,Stefely JA, Reidenbach AG, Ulbrich A, Oruganty K, Floyd BJ, Jochem A, Saunders JM, Johnson IE, Minogue CE, Wrobel RL, Barber GE, Lee D, Li S, Kannan N, Coon JJ, Bingman CA, Pagliarini DJ Mol Cell. 2015 Jan 8;57(1):83-94. doi: 10.1016/j.molcel.2014.11.002. Epub 2014, Dec 11. PMID:25498144<ref>PMID:25498144</ref>
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Description: Structure of mitochondrial ADCK3 defines an ancient protein kinase-like fold
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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 4ped" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Barber GE]]
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[[Category: Bingman CA]]
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[[Category: Coon JJ]]
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[[Category: Floyd BJ]]
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[[Category: Jochem A]]
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[[Category: Johnson IE]]
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[[Category: Joshi S]]
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[[Category: Kannan N]]
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[[Category: Lee D]]
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[[Category: Li S]]
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[[Category: Oruganty O]]
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[[Category: Pagliarini DJ]]
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[[Category: Reidenbach AG]]
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[[Category: Saunders JM]]
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[[Category: Smith R]]
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[[Category: Stefely JA]]
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[[Category: Ulbrich A]]
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[[Category: Wrobel RL]]

Current revision

Mitochondrial ADCK3 employs an atypical protein kinase-like fold to enable coenzyme Q biosynthes

PDB ID 4ped

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