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Parkin binds the Rpn10 subunit of 26S proteasomes through its ubiquitin-like domain

Department of Structural Biology and Biomolecular Engineering, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.
EMBO Reports (Impact Factor: 7.86). 04/2003; 4(3):301-6. DOI: 10.1038/sj.embor.embor764
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ABSTRACT Parkin, a product of the causative gene of autosomal-recessive juvenile parkinsonism (AR-JP), is a RING-type E3 ubiquitin ligase and has an amino-terminal ubiquitin-like (Ubl) domain. Although a single mutation that causes an Arg to Pro substitution at position 42 of the Ubl domain (the Arg 42 mutation) has been identified in AR-JP patients, the function of this domain is not clear. In this study, we determined the three-dimensional structure of the Ubl domain of parkin by NMR, in particular by extensive use of backbone (15)N-(1)H residual dipolar-coupling data. Inspection of chemical-shift-perturbation data showed that the parkin Ubl domain binds the Rpn10 subunit of 26S proteasomes via the region of parkin that includes position 42. Our findings suggest that the Arg 42 mutation induces a conformational change in the Rpn10-binding site of Ubl, resulting in impaired proteasomal binding of parkin, which could be the cause of AR-JP.

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    • "A number of substrates of Parkin have been proposed, but how most of them are recruited to Parkin is unknown. The prime suspect for that function is the Ubl domain, a protein-protein interaction domain that has been shown to bind ubiquitin-interacting motifs (UIM) (Sakata et al., 2003; Fallon et al., 2006), SH3 domains (Trempe et al., 2009) as well as its own C-terminus (Chaugule et al., 2011). A comparison of affinity constants shows that binding to the SH3 domain of endophilin-A and C-terminal of Parkin is in the 1–10 µM range (Trempe et al., 2009; Chaugule et al., 2011), whereas binding to UIMs is >100 µM (Safadi and Shaw, 2010). "
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    ABSTRACT: Autosomal recessive forms of Parkinson's disease are caused by mutations in three genes: Parkin, PINK1, and DJ-1. These genes encode for proteins with distinct enzymatic activities that may work together to confer neuroprotection. Parkin is an E3 ubiquitin ligase that has been shown to ubiquitinate substrates and to trigger proteasome-dependent degradation or autophagy, two crucial homeostatic processes in neurons. PINK1 is a mitochondrial protein kinase whose activity is required for Parkin-dependent mitophagy, a process that has been linked to neurodegeneration. Finally, DJ-1 is a protein homologous to a broad class of bacterial enzymes that may function as a sensor and modulator of reactive oxygen species, which have been implicated in neurodegenerative diseases. Here, we review the literature on the structure and biochemical functions of these three proteins.
    Frontiers in Neurology 04/2013; 4:38. DOI:10.3389/fneur.2013.00038
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    • "The C-terminal of Parkin holds two RING domains, common to several E3 ligases, associated with an 'in-between'-RING (Morett and Bork 1999; Ardley et al. 2001). The RING domains are cysteine-rich zinc fingers responsible for the recognition of substrate and transfer of monoubiquitin from their attachment with E2 enzymes to substrate while the Ubl domain (residues 1–75) binds to the Rpn10 subunit of the 26S proteasome (Sakata et al. 2003). Parkin may act as a neuro-protective agent by contributing to the clearance of a-synuclein and b-amyloid, thus attenuating their toxicity. "
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    ABSTRACT: The study of neurodegenerative disorders has had a major impact on our understanding of more fundamental mechanisms underlying neurobiology. Breakthroughs in the genetics of Alzheimer's (AD) and Parkinson's diseases (PD) has resulted in new knowledge in the areas of axonal transport, energy metabolism, protein trafficking/clearance and synaptic physiology. The major neurodegenerative diseases have in common a regional or network pathology associated with abnormal protein accumulation(s) and various degrees of motor or cognitive decline. In AD, β-amyloids are deposited in extracellular diffuse and compacted plaques as well as intracellularly. There is a major contribution to the disease by the co-existence of an intraneuronal tauopathy. Additionally, PD-like Lewy Bodies (LBs) bearing aggregated α-synuclein is present in 40-60% of all AD cases, especially involving amygdala. Amyloid deposits can be degraded or cleared by several mechanisms, including immune-mediated and transcytosis across the blood-brain barrier. Another avenue for disposal involves the lysosome pathway via autophagy. Enzymatic pathways include insulin degradative enzyme and neprilysin. Finally, the co-operative actions of C-terminus Hsp70 interacting protein (CHIP) and Parkin, components of a multiprotein E3 ubiquitin ligase complex, may be a portal to proteasome-mediated degradation. Mutations in the Parkin gene are the most common genetic link to autosomal recessive Parkinson's disease. Parkin catalyzes the post-translational modification of proteins with polyubiquitin, targeting them to the 26S proteasome. Parkin reduces intracellular Aβ(1-42) peptide levels, counteracts its effects on cell death, and reverses its effect to inhibit the proteasome. Additionally, Parkin has intrinsic cytoprotective activity to promote proteasome function and defend against oxidative stress to mitochondria. Parkin and CHIP are also active in amyloid clearance and cytoprotection in vivo. Parkin has cross-functionality in additional neurodegenerative diseases, for instance, to eliminate polyglutamine-expanded proteins, reducing their aggregation and toxicity and reinstate proteasome function. The dual actions of CHIP (molecular co-chaperone and E3 ligase) and Parkin (as E3-ubiquitin ligase and anti-oxidant) may also play a role in suppressing inflammatory reactions in animal models of neurodegeneration. In this review, we focus on the significance of CHIP and Parkin as inducers of amyloid clearance, as cytoprotectants and in the suppression of reactive inflammation. A case is made for more effort to explore whether neurodegeneration associated with proteinopathies can be arrested at early stages by promoting their mutual action.
    Journal of Neurochemistry 11/2011; 120(3):350-70. DOI:10.1111/j.1471-4159.2011.07588.x · 4.24 Impact Factor
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    • "It also contains an N-terminal UblD, which has been demonstrated to interact with multiple proteins in distinct pathways: an interaction with ubiquitin-interacting motifs (UIMs) in Eps15, allowing Parkin-mediated Eps15 ubiquitination, has implicated it in EGF receptor trafficking and PI3K-Akt signalling (Fallon et al, 2006); it further binds SH3 domains from endocytic BAR proteins such as endophilin-A, thus linking Parkin to synaptic ubiquitination (Trempe et al, 2009). Parkin was likewise reported to bind the proteasome subunit S5a/ Rpn10 via the UblD (Sakata et al, 2003), and to activate the 26S proteasome by enhancing interaction between its 19S components (Um et al, 2010). Parkin is also linked to mitochondrial quality control (Narendra et al, 2008), and the UblD promotes Parkin recruitment to, and subsequent mitophagy of, depolarized mitochondria (Narendra et al, 2010). "
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    ABSTRACT: Mutations in the E3 ubiquitin ligase Parkin are linked to Autosomal Recessive Juvenile Parkinsonism, including a cluster of pathogenic mutations in exon 2 that gives rise to Parkin's N-terminal ubiquitin-like domain (UblD). A study in this issue of The EMBO Journal reveals a new role for this domain, showing that the UblD engages in an intramolecular interaction with Parkin's C-terminal region to restrict autoubiquitination. Loss of this autoinhibitory mechanism in pathogenic variants renders Parkin constitutively active. Moreover, other proteins that bind to Parkin's UblD can also relieve autoinhibition, suggesting control by substrate-mediated activation.
    The EMBO Journal 07/2011; 30(14):2757-8. DOI:10.1038/emboj.2011.223 · 10.75 Impact Factor
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