PRKN (arkin RBR E3 ubiquitin protein ligase )
2015-12-01 Valentina La Cognata  , Sebastiano Cavallaro   AffiliationFunctional Genomics Unit - Institute of Neurogical Sciences - Italian National Research Council - Catania- Italy. [email protected]; [email protected]
Identity

Abstract
PARK2 (also known as Parkin RBR E3 ubiquitin protein ligase) is one of the largest genes in our genome. It undergoes an extensive alternative splicing both at transcript and protein level, producing multiple transcript variants and distinct protein isoforms. The precise function of PARK2 is still not clear; however, the encoded protein is a component of a multiprotein E3 ubiquitin ligase complex that mediates the targeting of substrates for proteasomal degradation. Mutations in this gene cause Parkinson disease and autosomal recessive juvenile Parkinson disease. Further molecular defects have been linked to other human malignancies. Here, we review some major data on PARK2, concerning the genetic structure, the transcription regulation, the encoded protein and functions, and its implication in human diseases.
DNA/RNA


Description
Transcription
Gene | #mRNA | Acc.Num. | Transcript Length |
PARK2 | 1. | NM_004562.2 | 4073 bp |
2. | AF381282.1 | 1157 bp | |
3. | AF381284.1 | 1158 bp | |
4. | BC022014.2 | 1575 bp | |
5. | NM_013987.2 | 3989 bp | |
6. | NM_013988.2 | 3626 bp | |
7. | AK294684.1 | 1115 bp | |
8. | GU345837.1 | 1298 bp | |
9. | GU345838.1 | 1340 bp | |
10. | GU345840.1 | 1313 bp | |
11. | GU357501.1 | 936 bp | |
12. | GU357502.1 | 873 bp | |
13. | GU361466.1 | 1279 bp | |
14. | GU361467.1 | 1229 bp | |
15. | GU361468.1 | 1010 bp | |
16. | GU361469.1 | 1559 bp | |
17. | GU361470.1 | 1561 bp | |
18. | GU361471.1 | 634 bp | |
19. | KC357594.1 | 454 bp | |
20. | KC357595.1 | 1627 bp | |
21. | KC774171.1 | 1282 bp |
Pseudogene
Proteins

Description
Domain | Start | Stop | E-value |
UBQ | 1 | 72 | 2.95e-16 |
IBR | 313 | 377 | 4.49e-14 |
IBR | 401 | 457 | 0.142 |

Expression

Localisation

Function

Homology
Mutations

Germinal
Somatic
Mutation Type | Mutant samples |
Substitution nonsense | 6 |
Substitution missense | 105 |
Substitution synonymous | 52 |
Insertion inframe | 0 |
Insertion frameshift | 2 |
Deletion inframe | 0 |
Deletion frameshift | 4 |
Complex | 1 |
Other | 0 |
Epigenetics
Implicated in
An interesting transcriptional target of parkin is p53. Viotti et al. were able to demonstrate that parkin levels inversely correlate to brain tumour grade and p53 levels in oligodendrogliomas, mixed gliomas and glioblastomas, and established that p53 controls parkin promoter transactivation, mRNA and protein levels (Viotti et al., 2014).
Breakpoints

Note
Article Bibliography
| Pubmed ID | Last Year | Title | Authors |
|---|---|---|---|
| 16287063 | 2006 | Abnormal methylation of the common PARK2 and PACRG promoter is associated with downregulation of gene expression in acute lymphoblastic leukemia and chronic myeloid leukemia. | Agirre X et al |
| 23052943 | 2013 | Linkage disequilibrium pattern and age-at-diagnosis are critical for replicating genetic associations across ethnic groups in leprosy. | Alter A et al |
| 25833766 | 2015 | Genomic instability in the PARK2 locus is associated with Parkinson's disease. | Ambroziak W et al |
| 22166450 | 2012 | Autosomal recessive parkinsonism. | Bonifati V et al |
| 21296869 | 2011 | Broad activation of the ubiquitin-proteasome system by Parkin is critical for mitophagy. | Chan NC et al |
| 11590439 | 2001 | Parkin ubiquitinates the alpha-synuclein-interacting protein, synphilin-1: implications for Lewy-body formation in Parkinson disease. | Chung KK et al |
| 22951446 | 2012 | Parkinsonism due to mutations in PINK1, parkin, and DJ-1 and oxidative stress and mitochondrial pathways. | Cookson MR et al |
| 11029628 | 2000 | Regional and cellular expression of the parkin gene in the rat cerebral cortex. | D'Agata V et al |
| 14614460 | 2003 | Alterations in the common fragile site gene Parkin in ovarian and other cancers. | Denison SR et al |
| 24793136 | 2014 | Pan-cancer genetic analysis identifies PARK2 as a master regulator of G1/S cyclins. | Gong Y et al |
| 10737637 | 2000 | Cloning of rat parkin cDNA and distribution of parkin in rat brain. | Gu WJ et al |
| 17314283 | 2007 | Parkin mediates neuroprotection through activation of IkappaB kinase/nuclear factor-kappaB signaling. | Henn IH et al |
| 10599851 | 1999 | Identification and distribution of Parkin in rat brain. | Horowitz JM et al |
| 11675120 | 2001 | Differential expression and tissue distribution of parkin isoforms during mouse development. | Huynh DP et al |
| 19585504 | 2009 | Attenuation of proteolysis-mediated cyclin E regulation by alternatively spliced Parkin in human colorectal cancers. | Ikeuchi K et al |
| 12150907 | 2002 | CHIP is associated with Parkin, a gene responsible for familial Parkinson's disease, and enhances its ubiquitin ligase activity. | Imai Y et al |
| 22302706 | 2012 | Contribution of germline mutations to PARK2 gene inactivation in lung adenocarcinoma. | Iwakawa R et al |
| 22448035 | 2012 | PINK1- and Parkin-mediated mitophagy at a glance. | Jin SM et al |
| 19501131 | 2009 | Evidence for the presence of full-length PARK2 mRNA and Parkin protein in human blood. | Kasap M et al |
| 9560156 | 1998 | Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. | Kitada T et al |
| 10824074 | 2000 | Association between early-onset Parkinson's disease and mutations in the parkin gene. | Lücking CB et al |
| 24955028 | 2014 | Increasing the Coding Potential of Genomes Through Alternative Splicing: The Case of PARK2 Gene. | La Cognata V et al |
| 16227987 | 2005 | Dopamine covalently modifies and functionally inactivates parkin. | LaVoie MJ et al |
| 25877876 | 2015 | Genomic and Functional Analysis of the E3 Ligase PARK2 in Glioma. | Lin DC et al |
| 22954671 | 2013 | Diminished parkin solubility and co-localization with intraneuronal amyloid-β are associated with autophagic defects in Alzheimer's disease. | Lonskaya I et al |
| 25378326 | 2015 | Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics. | Louis A et al |
| 26238155 | 2015 | Expression profile of parkin isoforms in human gliomas. | Maugeri G et al |
| 14737177 | 2004 | Susceptibility to leprosy is associated with PARK2 and PACRG. | Mira MT et al |
| 19029340 | 2008 | Parkin is recruited selectively to impaired mitochondria and promotes their autophagy. | Narendra D et al |
| 20506312 | 2010 | Genetic etiology of Parkinson disease associated with mutations in the SNCA, PARK2, PINK1, PARK7, and LRRK2 genes: a mutation update. | Nuytemans K et al |
| 12730996 | 2003 | Parkin mutations and susceptibility alleles in late-onset Parkinson's disease. | Oliveira SA et al |
| 12972409 | 2003 | Novel monoclonal antibodies demonstrate biochemical variation of brain parkin with age. | Pawlyk AC et al |
| 20696900 | 2010 | PARK2 deletions occur frequently in sporadic colorectal cancer and accelerate adenoma development in Apc mutant mice. | Poulogiannis G et al |
| 12716939 | 2003 | Parkin binds to alpha/beta tubulin and increases their ubiquitination and degradation. | Ren Y et al |
| 16517603 | 2006 | Parkin protects against mitochondrial toxins and beta-amyloid accumulation in skeletal muscle cells. | Rosen KM et al |
| 12000718 | 2002 | Parkin localizes to the Lewy bodies of Parkinson disease and dementia with Lewy bodies. | Schlossmacher MG et al |
| 25136611 | 2014 | Alternative splicing generates different parkin protein isoforms: evidences in human, rat, and mouse brain. | Scuderi S et al |
| 10888878 | 2000 | Familial Parkinson disease gene product, parkin, is a ubiquitin-protein ligase. | Shimura H et al |
| 11431533 | 2001 | Ubiquitination of a new form of alpha-synuclein by parkin from human brain: implications for Parkinson's disease. | Shimura H et al |
| 12628165 | 2003 | Parkin is a component of an SCF-like ubiquitin ligase complex and protects postmitotic neurons from kainate excitotoxicity. | Staropoli JF et al |
| 11122330 | 2000 | Parkin expression in the adult mouse brain. | Stichel CC et al |
| 23392669 | 2013 | ATF4 protects against neuronal death in cellular Parkinson's disease models by maintaining levels of parkin. | Sun X et al |
| 20630868 | 2010 | Parkin enhances the expression of cyclin-dependent kinase 6 and negatively regulates the proliferation of breast cancer cells. | Tay SP et al |
| 19946270 | 2010 | Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies. | Veeriah S et al |
| 23644658 | 2014 | Glioma tumor grade correlates with parkin depletion in mutant p53-linked tumors and results from loss of function of p53 transcriptional activity. | Viotti J et al |
| 12547187 | 2003 | Identification of a novel gene linked to parkin via a bi-directional promoter. | West AB et al |
| 25640678 | 2015 | A recurrent mutation in PARK2 is associated with familial lung cancer. | Xiong D et al |
| 24297497 | 2014 | An emerging role of PARK2 in cancer. | Xu L et al |
| 15557340 | 2005 | Parkin phosphorylation and modulation of its E3 ubiquitin ligase activity. | Yamamoto A et al |
| 22431710 | 2012 | Parkin pathway activation mitigates glioma cell proliferation and predicts patient survival. | Yeo CW et al |
| 21454557 | 2011 | Parkin mediates proteasome-dependent protein degradation and rupture of the outer mitochondrial membrane. | Yoshii SR et al |
| 11078524 | 2000 | Parkin functions as an E2-dependent ubiquitin- protein ligase and promotes the degradation of the synaptic vesicle-associated protein, CDCrel-1. | Zhang Y et al |
Other Information
Locus ID:
NCBI: 5071
MIM: 602544
HGNC: 8607
Ensembl: ENSG00000185345
Variants:
dbSNP: 5071
ClinVar: 5071
TCGA: ENSG00000185345
COSMIC: PRKN
RNA/Proteins
Pathways
Protein levels (Protein atlas)
References
| Pubmed ID | Year | Title | Citations |
|---|---|---|---|
| 37532837 | 2024 | MiR-181c-5p Regulates Lung Adenocarcinoma Progression via Targeting PRKN. | 1 |
| 37658959 | 2024 | Pregnancy, fertile life factors, and associated clinical course in PRKN early-onset Parkinson's disease. | 0 |
| 37915257 | 2024 | Association between copy number variations in parkin (PRKN) and schizophrenia and autism spectrum disorder: A case-control study. | 1 |
| 38357851 | 2024 | Parkin mRNA Expression Levels in Peripheral Blood Mononuclear Cells in Parkin-Related Parkinson's Disease. | 0 |
| 38424181 | 2024 | Parkin inhibits proliferation and migration of bladder cancer via ubiquitinating Catalase. | 0 |
| 38683365 | 2024 | Interplay between α-synuclein and parkin genes: Insights of Parkinson's disease. | 0 |
| 38710055 | 2024 | PINK1/Park2-Mediated Mitophagy Relieve Non-Alcoholic Fatty Liver Disease. | 0 |
| 37532837 | 2024 | MiR-181c-5p Regulates Lung Adenocarcinoma Progression via Targeting PRKN. | 1 |
| 37658959 | 2024 | Pregnancy, fertile life factors, and associated clinical course in PRKN early-onset Parkinson's disease. | 0 |
| 37915257 | 2024 | Association between copy number variations in parkin (PRKN) and schizophrenia and autism spectrum disorder: A case-control study. | 1 |
| 38357851 | 2024 | Parkin mRNA Expression Levels in Peripheral Blood Mononuclear Cells in Parkin-Related Parkinson's Disease. | 0 |
| 38424181 | 2024 | Parkin inhibits proliferation and migration of bladder cancer via ubiquitinating Catalase. | 0 |
| 38683365 | 2024 | Interplay between α-synuclein and parkin genes: Insights of Parkinson's disease. | 0 |
| 38710055 | 2024 | PINK1/Park2-Mediated Mitophagy Relieve Non-Alcoholic Fatty Liver Disease. | 0 |
| 36282767 | 2023 | PINK1-PRKN mediated mitophagy: differences between in vitro and in vivo models. | 14 |
Citation
Valentina La Cognata ; Sebastiano Cavallaro
PRKN (arkin RBR E3 ubiquitin protein ligase )
Atlas Genet Cytogenet Oncol Haematol. 2015-12-01
Online version: http://atlasgeneticsoncology.org/gene/46408/prkn-(arkin-rbr-e3-ubiquitin-protein-ligase-)
