4ped

From Proteopedia

(Difference between revisions)

Revision as of 12:56, 1 February 2023

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

Structural highlights

4ped 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

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.

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^[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
↑ 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

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/4ped"

@@ Line 3: / Line 3: @@
 <StructureSection load='4ped' size='340' side='right'caption='[[4ped]], [[Resolution|resolution]] 1.64&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ped]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PED FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><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>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=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>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ADCK3, CABC1, PP265 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ped FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ped OCA], [http://pdbe.org/4ped PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ped RCSB], [http://www.ebi.ac.uk/pdbsum/4ped PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ped ProSAT]</span></td></tr>
 </table>
 == Disease ==
-[[http://www.uniprot.org/uniprot/ADCK3_HUMAN ADCK3_HUMAN]] Autosomal recessive ataxia due to ubiquinone deficiency. The disease is caused by mutations affecting the gene represented in this entry.
+[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 ==
-[[http://www.uniprot.org/uniprot/ADCK3_HUMAN ADCK3_HUMAN]] Putative protein kinase involved in the biosynthesis of coenzyme Q since it is able to rescue partially coenzyme Q6 biosynthesis of yeast COQ8 mutants. May be a chaperone-like protein essential for the proper conformation and functioning of protein complexes in the respiratory chain.<ref>PMID:21296186</ref>
+[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 ==
@@ Line 26: / Line 24: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Barber, G E]]
+[[Category: Barber GE]]
-[[Category: Bingman, C A]]
+[[Category: Bingman CA]]
-[[Category: Coon, J J]]
+[[Category: Coon JJ]]
-[[Category: Floyd, B J]]
+[[Category: Floyd BJ]]
-[[Category: Jochem, A]]
+[[Category: Jochem A]]
-[[Category: Johnson, I E]]
+[[Category: Johnson IE]]
-[[Category: Joshi, S]]
+[[Category: Joshi S]]
-[[Category: Kannan, N]]
+[[Category: Kannan N]]
-[[Category: Lee, D]]
+[[Category: Lee D]]
-[[Category: Li, S]]
+[[Category: Li S]]
-[[Category: MPP, Mitochondrial Protein Partnership]]
+[[Category: Oruganty O]]
-[[Category: Oruganty, O]]
+[[Category: Pagliarini DJ]]
-[[Category: Pagliarini, D J]]
+[[Category: Reidenbach AG]]
-[[Category: Reidenbach, A G]]
+[[Category: Saunders JM]]
-[[Category: Saunders, J M]]
+[[Category: Smith R]]
-[[Category: Smith, R]]
+[[Category: Stefely JA]]
-[[Category: Stefely, J A]]
+[[Category: Ulbrich A]]
-[[Category: Ulbrich, A]]
+[[Category: Wrobel RL]]
-[[Category: Wrobel, R L]]
-[[Category: Coenzyme q biosynthesis]]
-[[Category: Membrane associated]]
-[[Category: Mitochondrial]]
-[[Category: Mitochondrial protein partnership]]
-[[Category: Mpp]]
-[[Category: Protein kinase-like]]
-[[Category: Psi-biology]]
-[[Category: Structural genomic]]
-[[Category: Transferase]]

4ped

From Proteopedia

Revision as of 12:56, 1 February 2023

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

Structural highlights

Disease

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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