View source for 8uct


==Crystal structure of TcPINK1 in complex with PRT==
<StructureSection load='8uct' size='340' side='right'caption='[[8uct]], [[Resolution|resolution]] 2.93&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8uct]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Tribolium_castaneum Tribolium castaneum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8UCT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8UCT FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.93&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3YT:2-{[(1R,2S)-2-AMINOCYCLOHEXYL]AMINO}-4-{[3-(2H-1,2,3-TRIAZOL-2-YL)PHENYL]AMINO}PYRIMIDINE-5-CARBOXAMIDE'>3YT</scene>, <scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=8uct FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8uct OCA], [https://pdbe.org/8uct PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8uct RCSB], [https://www.ebi.ac.uk/pdbsum/8uct PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8uct ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PINK1_TRICA PINK1_TRICA] Acts as a serine/threonine-protein kinase (PubMed:24751536, PubMed:25474007, PubMed:26116755, PubMed:26784449, PubMed:28980524, PubMed:29475881, PubMed:29991771, PubMed:32484300). Exhibits a substrate preference for proline at position P+1 and a general preference at several residues for basic residues such as arginine (PubMed:22645651). Also exhibits moderate preferences for a phosphotyrosine at position P-3 and a tryptophan at P-5 (PubMed:22645651). Critical to mitochondrial homeostasis it mediates several pathways that maintain mitochondrial health and function (By similarity). Protects against mitochondrial dysfunction during cellular stress by phosphorylating mitochondrial proteins such as park and likely Drp1, to coordinate mitochondrial quality control mechanisms that remove and replace dysfunctional mitochondrial components (PubMed:24751536, PubMed:25474007, PubMed:26116755, PubMed:28980524, PubMed:29991771, PubMed:32484300). Depending on the severity of mitochondrial damage and/or dysfunction, activity ranges from preventing apoptosis and stimulating mitochondrial biogenesis to regulating mitochondrial dynamics and eliminating severely damaged mitochondria via mitophagy (By similarity). Appears to be particularly important in maintaining the physiology and function of cells with high energy demands that are undergoing stress or altered metabolic environment, including spermatids, muscle cells and neurons such as the dopaminergic (DA) neurons (By similarity). Mediates the translocation and activation of park at the outer membrane (OMM) of dysfunctional/depolarized mitochondria (PubMed:25474007, PubMed:26116755). At the OMM of damaged mitochondria, phosphorylates pre-existing polyubiquitin chains, the Pink1-phosphorylated polyubiquitin then recruits park from the cytosol to the OMM where park is fully activated by phosphorylation at 'Ser-80' by Pink1 (PubMed:24751536, PubMed:25474007, PubMed:26116755, PubMed:29475881, PubMed:29991771). When cellular stress results in irreversible mitochondrial damage, functions with park to promote the clearance of dysfunctional and/or depolarized mitochondria by selective autophagy (mitophagy) (By similarity). The Pink1-park pathway also promotes fission and/or inhibits fusion of damaged mitochondria, by phosphorylating and thus promoting the park-dependent degradation of proteins involved in mitochondrial fusion/fission such as Marf, Opa1 and fzo (By similarity). This prevents the refusion of unhealthy mitochondria with the mitochondrial network or initiates mitochondrial fragmentation facilitating their later engulfment by autophagosomes (By similarity). Also likely to promote mitochondrial fission independently of park and Atg7-mediated mitophagy, via the phosphorylation and activation of Drp1 (PubMed:32484300). Regulates motility of damaged mitochondria by phosphorylating Miro which likely promotes its park-dependent degradation by the proteasome; in motor neurons, this inhibits mitochondrial intracellular anterograde transport along the axons which probably increases the chance of the mitochondria being eliminated in the soma (By similarity). The Pink1-park pathway is also involved in mitochondrial regeneration processes such as promoting mitochondrial biogenesis, activating localized mitochondrial repair, promoting selective turnover of mitochondrial proteins and initiating the mitochondrial import of endogenous proteins (By similarity). Involved in mitochondrial biogenesis by promoting the park-dependent ubiquitination of transcriptional repressor Paris which leads to its subsequent proteasomal degradation and allows activation of the transcription factor srl (By similarity). Functions with park to promote localized mitochondrial repair by activating the translation of specific nuclear-encoded mitochondrial RNAs (nc-mtRNAs) on the mitochondrial surface, including several key electron transport chain component nc-mtRNAs (By similarity). During oogenesis, phosphorylates and inactivates larp on the membrane of defective mitochondria, thus impairing local translation and mtDNA replication and consequently, reducing transmission of deleterious mtDNA mutations to the mature oocyte (By similarity). Phosphorylates the mitochondrial acyl-CoA dehydrogenase Mcad, and appears to be important for maintaining fatty acid and amino acid metabolism via a mechanism that is independent of it's role in maintaining production of ATP (By similarity).[UniProtKB:Q0KHV6]<ref>PMID:22645651</ref> <ref>PMID:24751536</ref> <ref>PMID:25474007</ref> <ref>PMID:26116755</ref> <ref>PMID:26784449</ref> <ref>PMID:28980524</ref> <ref>PMID:29475881</ref> <ref>PMID:29991771</ref> <ref>PMID:32484300</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Mutations in PINK1 and Parkin cause early-onset Parkinson's Disease (PD). PINK1 is a kinase which functions as a mitochondrial damage sensor and initiates mitochondrial quality control by accumulating on the damaged organelle. There, it phosphorylates ubiquitin, which in turn recruits and activates Parkin, an E3 ubiquitin ligase. Ubiquitylation of mitochondrial proteins leads to the autophagic degradation of the damaged organelle. Pharmacological modulation of PINK1 constitutes an appealing avenue to study its physiological function and develop therapeutics. In this study, we used a thermal shift assay with insect PINK1 to identify small molecules that inhibit ATP hydrolysis and ubiquitin phosphorylation. PRT062607, an SYK inhibitor, is the most potent inhibitor in our screen and inhibits both insect and human PINK1, with an IC(50) in the 0.5-3 microM range in HeLa cells and dopaminergic neurons. The crystal structures of insect PINK1 bound to PRT062607 or CYC116 reveal how the compounds interact with the ATP-binding pocket. PRT062607 notably engages with the catalytic aspartate and causes a destabilization of insert-2 at the autophosphorylation dimer interface. While PRT062607 is not selective for PINK1, it provides a scaffold for the development of more selective and potent inhibitors of PINK1 that could be used as chemical probes.

Identification and structural characterization of small molecule inhibitors of PINK1.,Rasool S, Shomali T, Truong L, Croteau N, Veyron S, Bustillos BA, Springer W, Fiesel FC, Trempe JF Sci Rep. 2024 Apr 2;14(1):7739. doi: 10.1038/s41598-024-58285-3. PMID:38565869<ref>PMID:38565869</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8uct" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Tribolium castaneum]]
[[Category: Rasool S]]
[[Category: Trempe JF]]
[[Category: Veyron S]]