7udp

From Proteopedia

(Difference between revisions)

Revision as of 07:17, 18 January 2023

Crystal structure of COQ8A-CA157 inhibitor complex in space group C2

Structural highlights

7udp is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

COQ8A_HUMAN Autosomal recessive ataxia due to ubiquinone deficiency. The disease is caused by variants affecting the gene represented in this entry.

Function

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).^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Small-molecule tools have enabled mechanistic investigations and therapeutic targeting of the protein kinase-like (PKL) superfamily. However, such tools are still lacking for many PKL members, including the highly conserved and disease-related UbiB family. Here, we sought to develop and characterize an inhibitor for the archetypal UbiB member COQ8, whose function is essential for coenzyme Q (CoQ) biosynthesis. Guided by crystallography, activity assays and cellular CoQ measurements, we repurposed the 4-anilinoquinoline scaffold to selectively inhibit human COQ8A in cells. Our chemical tool promises to lend mechanistic insights into the activities of these widespread and understudied proteins and to offer potential therapeutic strategies for human diseases connected to their dysfunction.

Small-molecule inhibition of the archetypal UbiB protein COQ8.,Murray NH, Asquith CRM, Fang Z, East MP, Ptak N, Smith RW, Vasta JD, Zimprich CA, Corona CR, Robers MB, Johnson GL, Bingman CA, Pagliarini DJ Nat Chem Biol. 2022 Oct 27. doi: 10.1038/s41589-022-01168-3. PMID:36302899^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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. Mitochondrial ADCK3 Employs an Atypical Protein Kinase-like Fold to Enable Coenzyme Q Biosynthesis. Mol Cell. 2015 Jan 8;57(1):83-94. doi: 10.1016/j.molcel.2014.11.002. Epub 2014, Dec 11. PMID:25498144 doi:http://dx.doi.org/10.1016/j.molcel.2014.11.002
↑ Stefely JA, Licitra F, Laredj L, Reidenbach AG, Kemmerer ZA, Grangeray A, Jaeg-Ehret T, Minogue CE, Ulbrich A, Hutchins PD, Wilkerson EM, Ruan Z, Aydin D, Hebert AS, Guo X, Freiberger EC, Reutenauer L, Jochem A, Chergova M, Johnson IE, Lohman DC, Rush MJ, Kwiecien NW, Singh PK, Schlagowski AI, Floyd BJ, Forsman U, Sindelar PJ, Westphall MS, Pierrel F, Zoll J, Dal Peraro M, Kannan N, Bingman CA, Coon JJ, Isope P, Puccio H, Pagliarini DJ. Cerebellar Ataxia and Coenzyme Q Deficiency through Loss of Unorthodox Kinase Activity. Mol Cell. 2016 Aug 18;63(4):608-20. doi: 10.1016/j.molcel.2016.06.030. Epub 2016 , Aug 4. PMID:27499294 doi:http://dx.doi.org/10.1016/j.molcel.2016.06.030
↑ Xie LX, Hsieh EJ, Watanabe S, Allan CM, Chen JY, Tran UC, Clarke CF. Expression of the human atypical kinase ADCK3 rescues coenzyme Q biosynthesis and phosphorylation of Coq polypeptides in yeast coq8 mutants. Biochim Biophys Acta. 2011 May;1811(5):348-60. doi: 10.1016/j.bbalip.2011.01.009., Epub 2011 Feb 4. PMID:21296186 doi:http://dx.doi.org/10.1016/j.bbalip.2011.01.009
↑ Wheeler B, Jia Z. Preparation and characterization of human ADCK3, a putative atypical kinase. Protein Expr Purif. 2015 Apr;108:13-17. doi: 10.1016/j.pep.2014.12.008. Epub 2014 , Dec 22. PMID:25540914 doi:http://dx.doi.org/10.1016/j.pep.2014.12.008
↑ Murray NH, Asquith CRM, Fang Z, East MP, Ptak N, Smith RW, Vasta JD, Zimprich CA, Corona CR, Robers MB, Johnson GL, Bingman CA, Pagliarini DJ. Small-molecule inhibition of the archetypal UbiB protein COQ8. Nat Chem Biol. 2022 Oct 27. doi: 10.1038/s41589-022-01168-3. PMID:36302899 doi:http://dx.doi.org/10.1038/s41589-022-01168-3

1 Structural highlights
2 Disease
3 Function
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7udp"

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7udp is ON HOLD
+==Crystal structure of COQ8A-CA157 inhibitor complex in space group C2==
+<StructureSection load='7udp' size='340' side='right'caption='[[7udp]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7udp]] 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=7UDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UDP FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MVS:4-[(3,4,5-trimethoxyphenyl)amino]quinoline-7-carbonitrile'>MVS</scene></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=7udp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7udp OCA], [https://pdbe.org/7udp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7udp RCSB], [https://www.ebi.ac.uk/pdbsum/7udp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7udp ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[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.
+== Function ==
+[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>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Small-molecule tools have enabled mechanistic investigations and therapeutic targeting of the protein kinase-like (PKL) superfamily. However, such tools are still lacking for many PKL members, including the highly conserved and disease-related UbiB family. Here, we sought to develop and characterize an inhibitor for the archetypal UbiB member COQ8, whose function is essential for coenzyme Q (CoQ) biosynthesis. Guided by crystallography, activity assays and cellular CoQ measurements, we repurposed the 4-anilinoquinoline scaffold to selectively inhibit human COQ8A in cells. Our chemical tool promises to lend mechanistic insights into the activities of these widespread and understudied proteins and to offer potential therapeutic strategies for human diseases connected to their dysfunction.
-Authors:
+Small-molecule inhibition of the archetypal UbiB protein COQ8.,Murray NH, Asquith CRM, Fang Z, East MP, Ptak N, Smith RW, Vasta JD, Zimprich CA, Corona CR, Robers MB, Johnson GL, Bingman CA, Pagliarini DJ Nat Chem Biol. 2022 Oct 27. doi: 10.1038/s41589-022-01168-3. PMID:36302899<ref>PMID:36302899</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7udp" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Bingman CA]]
+[[Category: Murray N]]
+[[Category: Pagliarini DJ]]
+[[Category: Smith RW]]

7udp

From Proteopedia

Revision as of 07:17, 18 January 2023

Crystal structure of COQ8A-CA157 inhibitor complex in space group C2

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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