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  • 1
    Publication Date: 2014-05-03
    Description: PINK1 (PTEN induced putative kinase 1) and PARKIN (also known as PARK2) have been identified as the causal genes responsible for hereditary recessive early-onset Parkinsonism. PINK1 is a Ser/Thr kinase that specifically accumulates on depolarized mitochondria, whereas parkin is an E3 ubiquitin ligase that catalyses ubiquitin transfer to mitochondrial substrates. PINK1 acts as an upstream factor for parkin and is essential both for the activation of latent E3 parkin activity and for recruiting parkin onto depolarized mitochondria. Recently, mechanistic insights into mitochondrial quality control mediated by PINK1 and parkin have been revealed, and PINK1-dependent phosphorylation of parkin has been reported. However, the requirement of PINK1 for parkin activation was not bypassed by phosphomimetic parkin mutation, and how PINK1 accelerates the E3 activity of parkin on damaged mitochondria is still obscure. Here we report that ubiquitin is the genuine substrate of PINK1. PINK1 phosphorylated ubiquitin at Ser 65 both in vitro and in cells, and a Ser 65 phosphopeptide derived from endogenous ubiquitin was only detected in cells in the presence of PINK1 and following a decrease in mitochondrial membrane potential. Unexpectedly, phosphomimetic ubiquitin bypassed PINK1-dependent activation of a phosphomimetic parkin mutant in cells. Furthermore, phosphomimetic ubiquitin accelerates discharge of the thioester conjugate formed by UBCH7 (also known as UBE2L3) and ubiquitin (UBCH7 approximately ubiquitin) in the presence of parkin in vitro, indicating that it acts allosterically. The phosphorylation-dependent interaction between ubiquitin and parkin suggests that phosphorylated ubiquitin unlocks autoinhibition of the catalytic cysteine. Our results show that PINK1-dependent phosphorylation of both parkin and ubiquitin is sufficient for full activation of parkin E3 activity. These findings demonstrate that phosphorylated ubiquitin is a parkin activator.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koyano, Fumika -- Okatsu, Kei -- Kosako, Hidetaka -- Tamura, Yasushi -- Go, Etsu -- Kimura, Mayumi -- Kimura, Yoko -- Tsuchiya, Hikaru -- Yoshihara, Hidehito -- Hirokawa, Takatsugu -- Endo, Toshiya -- Fon, Edward A -- Trempe, Jean-Francois -- Saeki, Yasushi -- Tanaka, Keiji -- Matsuda, Noriyuki -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2014 Jun 5;510(7503):162-6. doi: 10.1038/nature13392. Epub 2014 Jun 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan [2] Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan. ; Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, The University of Tokushima, Tokushima 770-8503, Japan. ; Research Center for Materials Science, Nagoya University, Nagoya, Aichi 464-8602, Japan. ; Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan. ; 1] Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan [2] Graduate School of Agriculture, Shizuoka University, 836 Ohya, Shizuoka 422-8529, Japan. ; Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan. ; 1] JST-CREST/Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan [2] JST-CREST/Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-motoyama, Kita-ku, Kyoto 603-8555, Japan. ; McGill Parkinson Program, Department of Neurology and Neurosurgery, Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec H3A 2B4, Canada. ; Department of Pharmacology & Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada. ; 1] Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan [2] Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science, Setagaya-ku, Tokyo 156-8506, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24784582" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Enzyme Activation ; Fibroblasts ; HeLa Cells ; Humans ; Membrane Potential, Mitochondrial ; Mice ; Mitochondria/metabolism ; Mutation/genetics ; Parkinson Disease ; Phosphorylation ; Phosphoserine/metabolism ; Protein Kinases/*metabolism ; Ubiquitin/chemistry/*metabolism ; Ubiquitin-Protein Ligases/genetics/*metabolism ; Ubiquitination
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2016-05-10
    Description: Author(s): Mandar Patil, Tomohiro Harada, Ken-ichi Nakao, Pankaj S. Joshi, and Masashi Kimura The origin of the ultrahigh-energy particles we receive on Earth from outer space such as EeV cosmic rays and PeV neutrinos remains an enigma. All mechanisms known to us currently make use of electromagnetic interaction to accelerate charged particles. In this paper, we propose a mechanism exclusive… [Phys. Rev. D 93, 104015] Published Mon May 09, 2016
    Keywords: General Relativity and Gravitation
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 3
    Publication Date: 2015-06-09
    Description: Author(s): Gregory Gabadadze, Rampei Kimura, and David Pirtskhalava The Vainshtein mechanism suppresses the fifth force at astrophysical distances, while enabling it to compete with gravity at cosmological scales. Typically, Vainshtein solutions exhibit superluminal perturbations. However, a restricted class of solutions with special boundary conditions was shown to... [Phys. Rev. D 91, 124024] Published Mon Jun 08, 2015
    Keywords: General Relativity and Gravitation
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 4
    Publication Date: 2016-01-22
    Description: Author(s): Hideki Ishihara, Masashi Kimura, and Ken Matsuno We construct time-dependent charged black string solutions in five-dimensional Einstein-Maxwell theory. In the far region, the spacetime approaches a five-dimensional Kasner universe with an expanding three-dimensional space and a shrinking extra dimension. Near the event horizon, the spacetime is a… [Phys. Rev. D 93, 024037] Published Thu Jan 21, 2016
    Keywords: General Relativity and Gravitation
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 5
    Publication Date: 2014-01-14
    Description: Author(s): Naoki Tsukamoto, Masashi Kimura, and Tomohiro Harada We study high energy particle collisions around higher dimensional black holes. It is shown that the center of mass energy can be arbitrarily large in the vicinity of the event horizon like the Bañados, Silk and West (BSW) process in four dimensions if the following two conditions are satisfied: (i)... [Phys. Rev. D 89, 024020] Published Mon Jan 13, 2014
    Keywords: General Relativity and Gravitation
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 6
    Publication Date: 2014-10-04
    Description: Author(s): Yuki Kanou, Hideki Ishihara, Masashi Kimura, Ken Matsuno, and Takamitsu Tatsuoka We examine an exact solution which represents a charged black hole in a Kaluza-Klein universe in the five-dimensional Einstein-Maxwell theory. The spacetime approaches to the five-dimensional Kasner solution that describes a universe with the expanding three-dimensional space and the shrinking extra... [Phys. Rev. D 90, 084004] Published Fri Oct 03, 2014
    Keywords: General Relativity and Gravitation
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 7
    Publication Date: 2014-12-04
    Description: Author(s): Ryo Shiose, Masashi Kimura, and Takeshi Chiba We study the motion of a charged particle around a weakly magnetized rotating black hole. We classify the fate of a charged particle kicked out from the innermost stable circular orbit. We find that the final fate of the charged particle depends mostly on the energy of the particle and the radius of... [Phys. Rev. D 90, 124016] Published Wed Dec 03, 2014
    Keywords: General Relativity and Gravitation
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 8
    Publication Date: 2014-12-30
    Description: Author(s): Ken-ichi Nakao, Masashi Kimura, Tomohiro Harada, Mandar Patil, and Pankaj S. Joshi The angular momentum of the Kerr singularity should not be larger than a threshold value so that it is enclosed by an event horizon: The Kerr singularity with the angular momentum exceeding the threshold value is naked. This fact suggests that if the cosmic censorship exists in our Universe, an over... [Phys. Rev. D 90, 124079] Published Mon Dec 29, 2014
    Keywords: General Relativity and Gravitation
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
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  • 9
    Publication Date: 2014-07-11
    Description: Author(s): Gregory Gabadadze, Rampei Kimura, and David Pirtskhalava Quasidilaton massive gravity is an extension of massive general relativity to a theory with additional scale invariance and approximate internal Galilean symmetry. The theory has a novel self-accelerated solution with the metric indistinguishable (in the decoupling limit) from the de Sitter space, i... [Phys. Rev. D 90, 024029] Published Thu Jul 10, 2014
    Keywords: General Relativity and Gravitation
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  • 10
    Publication Date: 2011-07-12
    Description: In eukaryotes, accurate chromosome segregation during mitosis and meiosis is coordinated by kinetochores, which are unique chromosomal sites for microtubule attachment. Centromeres specify the kinetochore formation sites on individual chromosomes, and are epigenetically marked by the assembly of nucleosomes containing the centromere-specific histone H3 variant, CENP-A. Although the underlying mechanism is unclear, centromere inheritance is probably dictated by the architecture of the centromeric nucleosome. Here we report the crystal structure of the human centromeric nucleosome containing CENP-A and its cognate alpha-satellite DNA derivative (147 base pairs). In the human CENP-A nucleosome, the DNA is wrapped around the histone octamer, consisting of two each of histones H2A, H2B, H4 and CENP-A, in a left-handed orientation. However, unlike the canonical H3 nucleosome, only the central 121 base pairs of the DNA are visible. The thirteen base pairs from both ends of the DNA are invisible in the crystal structure, and the alphaN helix of CENP-A is shorter than that of H3, which is known to be important for the orientation of the DNA ends in the canonical H3 nucleosome. A structural comparison of the CENP-A and H3 nucleosomes revealed that CENP-A contains two extra amino acid residues (Arg 80 and Gly 81) in the loop 1 region, which is completely exposed to the solvent. Mutations of the CENP-A loop 1 residues reduced CENP-A retention at the centromeres in human cells. Therefore, the CENP-A loop 1 may function in stabilizing the centromeric chromatin containing CENP-A, possibly by providing a binding site for trans-acting factors. The structure provides the first atomic-resolution picture of the centromere-specific nucleosome.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tachiwana, Hiroaki -- Kagawa, Wataru -- Shiga, Tatsuya -- Osakabe, Akihisa -- Miya, Yuta -- Saito, Kengo -- Hayashi-Takanaka, Yoko -- Oda, Takashi -- Sato, Mamoru -- Park, Sam-Yong -- Kimura, Hiroshi -- Kurumizaka, Hitoshi -- England -- Nature. 2011 Jul 10;476(7359):232-5. doi: 10.1038/nature10258.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21743476" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Autoantigens/*chemistry/metabolism ; Base Sequence ; Chromosomal Proteins, Non-Histone/*chemistry/metabolism ; Crystallography, X-Ray ; DNA/*chemistry/genetics/metabolism ; Histones/*chemistry/metabolism ; Humans ; Models, Molecular ; Molecular Conformation ; Molecular Sequence Data ; Nucleosomes/*chemistry/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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