34 results on '"Sakurako Goto-Ito"'
Search Results
2. Structural insights into modulation and selectivity of transsynaptic neurexin–LRRTM interaction
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Atsushi Yamagata, Sakurako Goto-Ito, Yusuke Sato, Tomoko Shiroshima, Asami Maeda, Masahiko Watanabe, Takashi Saitoh, Katsumi Maenaka, Tohru Terada, Tomoyuki Yoshida, Takeshi Uemura, and Shuya Fukai
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Science - Abstract
Leucine-rich repeat transmembrane neuronal proteins (LRRTMs) function as postsynaptic organizers that induce excitatory synapses. Here authors solve the crystal structure of LRRTM2 in complex with its ligand Nrxn1β and shed light on how selective binding of ligands to LRRTM1/2 is achieved.
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- 2018
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3. Structural basis of epilepsy-related ligand–receptor complex LGI1–ADAM22
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Atsushi Yamagata, Yuri Miyazaki, Norihiko Yokoi, Hideki Shigematsu, Yusuke Sato, Sakurako Goto-Ito, Asami Maeda, Teppei Goto, Makoto Sanbo, Masumi Hirabayashi, Mikako Shirouzu, Yuko Fukata, Masaki Fukata, and Shuya Fukai
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Science - Abstract
LGI1 is an epilepsy-related gene that encodes a secreted neuronal protein. Here the authors present the crystal structure of LGI1 bound to its receptor ADAM22, which provides structural insights into epilepsy-causing LGI1 mutations and might facilitate the development of novel anti-epilepsy drugs.
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- 2018
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4. Structural basis of trans-synaptic interactions between PTPδ and SALMs for inducing synapse formation
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Sakurako Goto-Ito, Atsushi Yamagata, Yusuke Sato, Takeshi Uemura, Tomoko Shiroshima, Asami Maeda, Ayako Imai, Hisashi Mori, Tomoyuki Yoshida, and Shuya Fukai
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Science - Abstract
Synaptic organizers are cell adhesion molecules that facilitate synapse formation through trans-synaptic interactions. Here the authors give molecular insights into synaptic differentiation by determining the structures of the synaptic adhesion-like molecules SALM2 and SALM5 bound to the presynaptic organizer PTPδ.
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- 2018
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5. Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168
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Tomio S. Takahashi, Yoshihiro Hirade, Aya Toma, Yusuke Sato, Atsushi Yamagata, Sakurako Goto-Ito, Akiko Tomita, Shinichiro Nakada, and Shuya Fukai
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Science - Abstract
E3 ubiquitin ligase RNF168 is important for the repair of DNA double-strand breaks and recognizes ubiquitylated targets through two Ub-dependent DSB recruitment modules UDM1 and UDM2. Here the authors combine crystallography, cell biology and biochemical experiments to reveal how UDM1 and UDM2 interact with polyubiquitin chains.
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- 2018
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6. Structural basis for ubiquitin recognition by ubiquitin-binding zinc finger of FAAP20.
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Aya Toma, Tomio S Takahashi, Yusuke Sato, Atsushi Yamagata, Sakurako Goto-Ito, Shinichiro Nakada, Atsuhiko Fukuto, Yasunori Horikoshi, Satoshi Tashiro, and Shuya Fukai
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Medicine ,Science - Abstract
Several ubiquitin-binding zinc fingers (UBZs) have been reported to preferentially bind K63-linked ubiquitin chains. In particular, the UBZ domain of FAAP20 (FAAP20-UBZ), a member of the Fanconi anemia core complex, seems to recognize K63-linked ubiquitin chains, in order to recruit the complex to DNA interstrand crosslinks and mediate DNA repair. By contrast, it is reported that the attachment of a single ubiquitin to Rev1, a translesion DNA polymerase, increases binding of Rev1 to FAAP20. To clarify the specificity of FAAP20-UBZ, we determined the crystal structure of FAAP20-UBZ in complex with K63-linked diubiquitin at 1.9 Å resolution. In this structure, FAAP20-UBZ interacts only with one of the two ubiquitin moieties. Consistently, binding assays using surface plasmon resonance spectrometry showed that FAAP20-UBZ binds ubiquitin and M1-, K48- and K63-linked diubiquitin chains with similar affinities. Residues in the vicinity of Ala168 within the α-helix and the C-terminal Trp180 interact with the canonical Ile44-centered hydrophobic patch of ubiquitin. Asp164 within the α-helix and the C-terminal loop mediate a hydrogen bond network, which reinforces ubiquitin-binding of FAAP20-UBZ. Mutations of the ubiquitin-interacting residues disrupted binding to ubiquitin in vitro and abolished the accumulation of FAAP20 to DNA damage sites in vivo. Finally, structural comparison among FAAP20-UBZ, WRNIP1-UBZ and RAD18-UBZ revealed distinct modes of ubiquitin binding. UBZ family proteins could be divided into at least three classes, according to their ubiquitin-binding modes.
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- 2015
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7. A <scp>SNARE</scp> geranylgeranyltransferase essential for the organization of the Golgi apparatus
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Jinglei Cheng, Ryutaro Shirakawa, Shonosuke Wakayama, Hiroshi Masumoto, Sakurako Goto-Ito, Haremaru Kubo, Duc Anh Trinh, Yusuke Sato, Hisanori Horiuchi, Toyoshi Fujimoto, Shuya Fukai, Kota Goto, Atsushi Yamagata, and Natsumi Sakata
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Male ,Prenyltransferase ,Protein Prenylation ,Golgi Apparatus ,Biology ,Membrane Fusion ,General Biochemistry, Genetics and Molecular Biology ,R-SNARE Proteins ,03 medical and health sciences ,symbols.namesake ,0302 clinical medicine ,Prenylation ,Animals ,Humans ,News & Views ,Rats, Wistar ,Molecular Biology ,030304 developmental biology ,SNARE complex assembly ,G alpha subunit ,0303 health sciences ,Alkyl and Aryl Transferases ,General Immunology and Microbiology ,General Neuroscience ,Articles ,Golgi apparatus ,Dimethylallyltranstransferase ,Rats ,Cell biology ,Protein Transport ,Biotinylation ,symbols ,Protein prenylation ,Protein Multimerization ,Signal transduction ,SNARE Proteins ,030217 neurology & neurosurgery ,Protein Binding - Abstract
Protein prenylation is essential for many cellular processes including signal transduction, cytoskeletal reorganization, and membrane trafficking. Here, we identify a novel type of protein prenyltransferase, which we named geranylgeranyltransferase type-III (GGTase-III). GGTase-III consists of prenyltransferase alpha subunit repeat containing 1 (PTAR1) and the β subunit of RabGGTase. Using a biotinylated geranylgeranyl analogue, we identified the Golgi SNARE protein Ykt6 as a substrate of GGTase-III. GGTase-III transfers a geranylgeranyl group to mono-farnesylated Ykt6, generating doubly prenylated Ykt6. The crystal structure of GGTase-III in complex with Ykt6 provides structural basis for Ykt6 double prenylation. In GGTase-III-deficient cells, Ykt6 remained in a singly prenylated form, and the Golgi SNARE complex assembly was severely impaired. Consequently, the Golgi apparatus was structurally disorganized, and intra-Golgi protein trafficking was delayed. Our findings reveal a fourth type of protein prenyltransferase that generates geranylgeranyl-farnesyl Ykt6. Double prenylation of Ykt6 is essential for the structural and functional organization of the Golgi apparatus.
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- 2020
8. Structural insights into modulation and selectivity of transsynaptic neurexin–LRRTM interaction
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Shuya Fukai, Atsushi Yamagata, Takeshi Uemura, Katsumi Maenaka, Takashi Saitoh, Sakurako Goto-Ito, Asami Maeda, Masahiko Watanabe, Tomoko Shiroshima, Tomoyuki Yoshida, Tohru Terada, and Yusuke Sato
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0301 basic medicine ,Cell Adhesion Molecules, Neuronal ,Science ,Neurexin ,General Physics and Astronomy ,Nerve Tissue Proteins ,LRRTM1 ,Plasma protein binding ,Article ,General Biochemistry, Genetics and Molecular Biology ,Mice ,03 medical and health sciences ,0302 clinical medicine ,Postsynaptic potential ,Animals ,Humans ,Amino Acid Sequence ,lcsh:Science ,Neural Cell Adhesion Molecules ,Multidisciplinary ,Chemistry ,Calcium-Binding Proteins ,Alternative splicing ,HEK 293 cells ,Membrane Proteins ,General Chemistry ,Transmembrane protein ,Cell biology ,HEK293 Cells ,030104 developmental biology ,Synapses ,Excitatory postsynaptic potential ,Mutant Proteins ,lcsh:Q ,030217 neurology & neurosurgery ,Protein Binding - Abstract
Leucine-rich repeat transmembrane neuronal proteins (LRRTMs) function as postsynaptic organizers that induce excitatory synapses. Neurexins (Nrxns) and heparan sulfate proteoglycans have been identified as presynaptic ligands for LRRTMs. Specifically, LRRTM1 and LRRTM2 bind to the Nrxn splice variant lacking an insert at the splice site 4 (S4). Here, we report the crystal structure of the Nrxn1β–LRRTM2 complex at 3.4 Å resolution. The Nrxn1β–LRRTM2 interface involves Ca2+-mediated interactions and overlaps with the Nrxn–neuroligin interface. Together with structure-based mutational analyses at the molecular and cellular levels, the present structural analysis unveils the mechanism of selective binding between Nrxn and LRRTM1/2 and its modulation by the S4 insertion of Nrxn., Leucine-rich repeat transmembrane neuronal proteins (LRRTMs) function as postsynaptic organizers that induce excitatory synapses. Here authors solve the crystal structure of LRRTM2 in complex with its ligand Nrxn1β and shed light on how selective binding of ligands to LRRTM1/2 is achieved.
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- 2018
9. Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30
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Yasushi Saeki, Keiji Tanaka, Minoru Ishikawa, Sakurako Goto-Ito, Noriyuki Matsuda, Atsushi Yamagata, Yusuke Sato, Koji Yamano, Shuya Fukai, Kei Okatsu, Ai Kaiho, and Yuichi Hashimoto
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Models, Molecular ,0301 basic medicine ,Protein Conformation ,DNA Mutational Analysis ,Crystallography, X-Ray ,Cleavage (embryo) ,Parkin ,Deubiquitinating enzyme ,03 medical and health sciences ,Protein structure ,Ubiquitin ,Structural Biology ,Catalytic triad ,Animals ,Polyubiquitin ,Molecular Biology ,Zebrafish ,chemistry.chemical_classification ,DNA ligase ,biology ,Chemistry ,Cell biology ,030104 developmental biology ,Mutagenesis ,biology.protein ,Ubiquitin-Specific Proteases ,Deubiquitination - Abstract
Parkin ubiquitin (Ub) ligase (also known as PARK2) ubiquitinates damaged mitochondria for their clearance and quality control. USP30 deubiquitinase opposes parkin-mediated Ub-chain formation on mitochondria by preferentially cleaving Lys6-linked Ub chains. Here, we report the crystal structure of zebrafish USP30 in complex with a Lys6-linked diubiquitin (diUb or Ub2) at 1.87-A resolution. The distal Ub-recognition mechanism of USP30 is similar to those of other USP family members, whereas Phe4 and Thr12 of the proximal Ub are recognized by a USP30-specific surface. Structure-based mutagenesis showed that the interface with the proximal Ub is critical for the specific cleavage of Lys6-linked Ub chains, together with the noncanonical catalytic triad composed of Cys-His-Ser. The structural findings presented here reveal a mechanism for Lys6-linkage-specific deubiquitination.
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- 2017
10. Structural basis of ubiquitin recognition by the winged-helix domain of Cockayne syndrome group B protein
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Masafumi Saijo, Atsushi Yamagata, Yusuke Sato, Tomio S. Takahashi, Sakurako Goto-Ito, and Shuya Fukai
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musculoskeletal diseases ,0303 health sciences ,congenital, hereditary, and neonatal diseases and abnormalities ,biology ,DNA repair ,T-cell receptor ,Helicase ,nutritional and metabolic diseases ,Winged Helix ,medicine.disease ,Sciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire ,Cockayne syndrome ,Cell biology ,03 medical and health sciences ,0302 clinical medicine ,Ubiquitin ,Structural Biology ,Genetics ,biology.protein ,Mutation testing ,medicine ,ERCC6 ,030217 neurology & neurosurgery ,030304 developmental biology - Abstract
Cockayne syndrome group B (CSB, also known as ERCC6) protein is involved in many DNA repair processes and essential for transcription-coupled repair (TCR). The central region of CSB has the helicase motif, whereas the C-terminal region contains important regulatory elements for repair of UV- and oxidative stress-induced damages and double-strand breaks (DSBs). A previous study suggested that a small part (∼30 residues) within this region was responsible for binding to ubiquitin (Ub). Here, we show that the Ub-binding of CSB requires a larger part of CSB, which was previously identified as a winged-helix domain (WHD) and is involved in the recruitment of CSB to DSBs. We also present the crystal structure of CSB WHD in complex with Ub. CSB WHD folds as a single globular domain, defining a class of Ub-binding domains (UBDs) different from 23 UBD classes identified so far. The second α-helix and C-terminal extremity of CSB WHD interact with Ub. Together with structure-guided mutational analysis, we identified the residues critical for the binding to Ub. CSB mutants defective in the Ub binding reduced repair of UV-induced damage. This study supports the notion that DSB repair and TCR may be associated with the Ub-binding of CSB.
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- 2019
11. Structural insights into ubiquitin phosphorylation by PINK1
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Yutaka Ito, Noriyuki Matsuda, Kei Okatsu, Yusuke Sato, Atsushi Yamagata, Toshihiko Oka, Masaki Mishima, Lumi Negishi, Keiji Tanaka, Koji Yamano, Shuya Fukai, Akiko Takahashi, and Sakurako Goto-Ito
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0301 basic medicine ,Protein Conformation ,Ubiquitin-Protein Ligases ,Protein domain ,lcsh:Medicine ,Crystallography, X-Ray ,Parkin ,Article ,03 medical and health sciences ,Protein structure ,Adenosine Triphosphate ,Ubiquitin ,Parkinsonian Disorders ,Protein Domains ,Humans ,Phosphorylation ,lcsh:Science ,Protein kinase C ,chemistry.chemical_classification ,DNA ligase ,Multidisciplinary ,biology ,lcsh:R ,Cell biology ,030104 developmental biology ,Protein kinase domain ,chemistry ,Mutation ,biology.protein ,lcsh:Q ,Protein Kinases ,Protein Binding - Abstract
Mutations of PTEN-induced putative kinase 1 (PINK1) and the E3 ubiquitin (Ub) ligase parkin can cause familial parkinsonism. These two proteins are essential for ubiquitylation of damaged mitochondria and subsequent degradation. PINK1 phosphorylates Ser65 of Ub and the Ub-like (UBL) domain of parkin to allosterically relieve the autoinhibition of parkin. To understand the structural mechanism of the Ub/UBL-specific phosphorylation by PINK1, we determined the crystal structure of Tribolium castaneum PINK1 kinase domain (TcPINK1) in complex with a nonhydrolyzable ATP analogue at 2.5 Å resolution. TcPINK1 consists of the N- and C-terminal lobes with the PINK1-specific extension. The ATP analogue is bound in the cleft between the N- and C-terminal lobes. The adenine ring of the ATP analogue is bound to a hydrophobic pocket, whereas the triphosphate group of the ATP analogue and two coordinated Mg ions interact with the catalytic hydrophilic residues. Comparison with protein kinases A and C (PKA and PKC, respectively) unveils a putative Ub/UBL-binding groove, which is wider than the peptide-binding groove of PKA or PKC to accommodate the globular head of Ub or UBL. Further crosslinking analyses suggested a PINK1-interacting surface of Ub. Structure-guided mutational analyses support the findings from the present structural analysis of PINK1.
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- 2018
12. Structural basis of epilepsy-related ligand–receptor complex LGI1–ADAM22
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Sakurako Goto-Ito, Masumi Hirabayashi, Hideki Shigematsu, Atsushi Yamagata, Norihiko Yokoi, Makoto Sanbo, Yuri Miyazaki, Yusuke Sato, Asami Maeda, Teppei Goto, Shuya Fukai, Mikako Shirouzu, Masaki Fukata, and Yuko Fukata
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0301 basic medicine ,Receptor complex ,Protein Conformation ,Science ,Protein domain ,General Physics and Astronomy ,Nerve Tissue Proteins ,Plasma protein binding ,medicine.disease_cause ,Synaptic Transmission ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Protein structure ,Protein Domains ,medicine ,Animals ,Humans ,lcsh:Science ,Neurons ,Mutation ,Brain Diseases ,Multidisciplinary ,Epilepsy ,Chemistry ,ADAM22 ,HEK 293 cells ,Cell Membrane ,Cryoelectron Microscopy ,Intracellular Signaling Peptides and Proteins ,Brain ,Proteins ,General Chemistry ,Ligand (biochemistry) ,Cell biology ,ADAM Proteins ,Disease Models, Animal ,030104 developmental biology ,HEK293 Cells ,Synapses ,lcsh:Q ,Dimerization ,030217 neurology & neurosurgery ,Protein Binding - Abstract
Epilepsy is a common brain disorder throughout history. Epilepsy-related ligand–receptor complex, LGI1–ADAM22, regulates synaptic transmission and has emerged as a determinant of brain excitability, as their mutations and acquired LGI1 autoantibodies cause epileptic disorders in human. Here, we report the crystal structure of human LGI1–ADAM22 complex, revealing a 2:2 heterotetrameric assembly. The hydrophobic pocket of the C-terminal epitempin-repeat (EPTP) domain of LGI1 binds to the metalloprotease-like domain of ADAM22. The N-terminal leucine-rich repeat and EPTP domains of LGI1 mediate the intermolecular LGI1–LGI1 interaction. A pathogenic R474Q mutation of LGI1, which does not exceptionally affect either the secretion or the ADAM22 binding, is located in the LGI1–LGI1 interface and disrupts the higher-order assembly of the LGI1–ADAM22 complex in vitro and in a mouse model for familial epilepsy. These studies support the notion that the LGI1–ADAM22 complex functions as the trans-synaptic machinery for precise synaptic transmission., LGI1 is an epilepsy-related gene that encodes a secreted neuronal protein. Here the authors present the crystal structure of LGI1 bound to its receptor ADAM22, which provides structural insights into epilepsy-causing LGI1 mutations and might facilitate the development of novel anti-epilepsy drugs.
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- 2018
13. Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168
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Sakurako Goto-Ito, Akiko Tomita, Yoshihiro Hirade, Tomio S. Takahashi, Shuya Fukai, Aya Toma, Yusuke Sato, Atsushi Yamagata, and Shinichiro Nakada
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0301 basic medicine ,Models, Molecular ,Protein Folding ,DNA damage ,Science ,Ubiquitin-Protein Ligases ,Amino Acid Motifs ,General Physics and Astronomy ,macromolecular substances ,Sciences du Vivant [q-bio]/Biochimie, Biologie Moléculaire ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Ubiquitin ,Signaling proteins ,Cell Line, Tumor ,Humans ,lcsh:Science ,Polyubiquitin ,chemistry.chemical_classification ,DNA ligase ,Multidisciplinary ,biology ,Lysine ,Ubiquitination ,General Chemistry ,Cell biology ,Ubiquitin ligase ,030104 developmental biology ,chemistry ,biology.protein ,lcsh:Q ,030217 neurology & neurosurgery ,DNA ,DNA Damage ,Protein Binding - Abstract
The E3 ubiquitin (Ub) ligase RNF168 plays a critical role in the initiation of the DNA damage response to double-strand breaks (DSBs). The recruitment of RNF168 by ubiquitylated targets involves two distinct regions, Ub-dependent DSB recruitment module (UDM) 1 and UDM2. Here we report the crystal structures of the complex between UDM1 and Lys63-linked diUb (K63-Ub2) and that between the C-terminally truncated UDM2 (UDM2ΔC) and K63-Ub2. In both structures, UDM1 and UDM2ΔC fold as a single α-helix. Their simultaneous bindings to the distal and proximal Ub moieties provide specificity for Lys63-linked Ub chains. Structural and biochemical analyses of UDM1 elucidate an Ub-binding mechanism between UDM1 and polyubiquitylated targets. Mutations of Ub-interacting residues in UDM2 prevent the accumulation of RNF168 to DSB sites in U2OS cells, whereas those in UDM1 have little effect, suggesting that the interaction of UDM2 with ubiquitylated and polyubiquitylated targets mainly contributes to the RNF168 recruitment., E3 ubiquitin ligase RNF168 is important for the repair of DNA double-strand breaks and recognizes ubiquitylated targets through two Ub-dependent DSB recruitment modules UDM1 and UDM2. Here the authors combine crystallography, cell biology and biochemical experiments to reveal how UDM1 and UDM2 interact with polyubiquitin chains.
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- 2017
14. Trm5 and TrmD: Two Enzymes from Distinct Origins Catalyze the Identical tRNA Modification, m¹G37
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Sakurako, Goto-Ito, Takuhiro, Ito, and Shigeyuki, Yokoyama
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Models, Molecular ,tRNA Methyltransferases ,RNA, Transfer ,Trm5 ,TrmD ,Aminoacylation ,Review ,m1G37 ,Crystallography, X-Ray ,tRNA ,Catalysis ,Substrate Specificity - Abstract
The N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs.
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- 2017
15. Structural basis of the interaction between Topoisomerase IIIβ and the TDRD3 auxiliary factor
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Yusuke Sato, Sakurako Goto-Ito, Shuya Fukai, Tomio S. Takahashi, and Atsushi Yamagata
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0301 basic medicine ,Scaffold protein ,Models, Molecular ,Protein Conformation, alpha-Helical ,Recombinant Fusion Proteins ,Genetic Vectors ,Gene Expression ,Sequence alignment ,Spodoptera ,Crystallography, X-Ray ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,Catalytic Domain ,Sf9 Cells ,Animals ,Humans ,A-DNA ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Cloning, Molecular ,Multidisciplinary ,biology ,Chemistry ,Topoisomerase ,RNA ,Nuclear Proteins ,Proteins ,Chromatin ,DNA-Binding Proteins ,030104 developmental biology ,DNA Topoisomerases, Type I ,Structural Homology, Protein ,biology.protein ,Biophysics ,Protein Conformation, beta-Strand ,Carrier Proteins ,Baculoviridae ,Sequence Alignment ,DNA ,Protein Binding - Abstract
Topoisomerase IIIβ (TOP3β) is a DNA/RNA topoisomerase that has been implicated in epigenetic or translational control of gene expression. In cells, TOP3β co-exists with its specific auxiliary factor, TDRD3. TDRD3 serves as a scaffold protein to recruit TOP3β to its DNA/RNA substrates accumulating in specific cellular sites such as methylated chromatins or neural stress granules. Here we report the crystal structures of the catalytic domain of TOP3β, the DUF1767–OB-fold domains of TDRD3 and their complex at 3.44 Å, 1.62 Å and 3.6 Å resolutions, respectively. The toroidal-shaped catalytic domain of TOP3β binds the OB-fold domain of TDRD3. The TDRD3 OB-fold domain harbors the insertion loop, which is protruding from the core structure. Both the insertion loop and core region interact with TOP3β. Our pull-down binding assays showed that hydrophobic characters of the core surface and the amino- and carboxy-terminal regions of the insertion loop are essential for the interaction. Furthermore, by comparison with the structure of the homologous Topoisomerase IIIα (TOP3α)–RMI1 complex, we identified Arg96, Val109, Phe139 and the short insertion loop of TDRD3 as the critical structural elements for the specific interaction with TOP3β to avoid the non-cognate interaction with TOP3α.
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- 2017
16. Crystal structure of Sec10, a subunit of the exocyst complex
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Yusuke Sato, Sakurako Goto-Ito, Atsushi Yamagata, Keiko Kubota, Jianxing Chen, and Shuya Fukai
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0301 basic medicine ,Protein subunit ,Static Electricity ,Vesicular Transport Proteins ,Exocyst ,Sequence alignment ,GTPase ,Crystallography, X-Ray ,Antiparallel (biochemistry) ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Protein structure ,Animals ,Amino Acid Sequence ,Phosphatidylinositol ,Peptide sequence ,Zebrafish ,Multidisciplinary ,Chemistry ,Zebrafish Proteins ,Protein Structure, Tertiary ,Protein Subunits ,030104 developmental biology ,Biophysics ,Sequence Alignment - Abstract
The exocyst complex is a heterooctameric protein complex composed of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84. This complex plays an essential role in trafficking secretory vesicles to the plasma membrane through its interaction with phosphatidylinositol 4,5-bisphosphate and small GTPases. To date, the near-full-length structural information of each subunit has been limited to Exo70, although the C-terminal half structures of Sec6, Sec15 and Exo84 and the structures of the small GTPase-binding domains of Sec3, Sec5 and Exo84 have been reported. Here, we report the crystal structure of the near-full-length zebrafish Sec10 (zSec10) at 2.73 Å resolution. The structure of zSec10 consists of tandem antiparallel helix bundles that form a straight rod, like helical core regions of other exocyst subunits. This structure provides the first atomic details of Sec10, which may be useful for future functional and structural studies of this subunit and the exocyst complex.
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- 2017
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17. Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5
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Sakurako Goto-Ito, Nobukatsu Morooka, Atsushi Yamagata, Yusuke Sato, Ken Sato, and Shuya Fukai
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Protein Conformation, alpha-Helical ,Health, Toxicology and Mutagenesis ,Endosomes ,Plant Science ,Transfection ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,03 medical and health sciences ,0302 clinical medicine ,Protein Domains ,Guanine Nucleotide Exchange Factors ,Humans ,Amino Acid Sequence ,Research Articles ,Adaptor Proteins, Signal Transducing ,030304 developmental biology ,0303 health sciences ,Crystallography ,Ecology ,Hydrogen Bonding ,Guanine Nucleotides ,Protein Transport ,rab GTP-Binding Proteins ,Mutant Proteins ,Crystallization ,030217 neurology & neurosurgery ,Research Article ,HeLa Cells ,Protein Binding - Abstract
The structure of the SH3BP5–Rab11a complex and structure-based mutational analyses reveal structural basis of nucleotide exchange for Rab11 by its specific guanine nucleotide exchange factor., The Rab GTPase family is a major regulator of membrane traffic in eukaryotic cells. The Rab11 subfamily plays important roles in specific trafficking events such as exocytosis, endosomal recycling, and cytokinesis. SH3BP5 and SH3BP5-like (SH3BP5L) proteins have recently been found to serve as guanine nucleotide exchange factors (GEF) for Rab11. Here, we report the crystal structures of the SH3BP5 GEF domain alone and its complex with Rab11a. SH3BP5 exhibits a V-shaped structure comprising two coiled coils. The coiled coil composed of α1, and α4 is solely responsible for the Rab11a binding and GEF activity. SH3BP5 pulls out and deforms switch I of Rab11a so as to facilitate the GDP release from Rab11a. SH3BP5 interacts with the N-terminal region, switch I, interswitch, and switch II of Rab11a. SH3BP5 and SH3BP5L localize to Rab11-positive recycling endosomes and show GEF activity for all of the Rab11 family but not for Rab14. Fluorescence-based GEF assays combined with site-directed mutagenesis reveal the essential interactions between SH3BP5 and Rab11 family proteins for the GEF reaction on recycling endosomes.
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- 2019
18. Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA
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Kazushige Katsura, Takaho Terada, Sakurako Goto-Ito, Mikako Shirouzu, Shigeyuki Yokoyama, Shun-ichi Sekine, Mitsuo Kuratani, Takuhiro Ito, Naoki Shigi, and Hirofumi Nakagawa
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Zinc finger ,TRNA modification ,biology ,Thermus thermophilus ,biology.organism_classification ,Biochemistry ,Thiouridine ,chemistry.chemical_compound ,Pyrococcus horikoshii ,Protein structure ,chemistry ,Structural Biology ,Transfer RNA ,Lysidine ,Molecular Biology - Abstract
In thermophilic bacteria, specific 2-thiolation occurs on the conserved ribothymidine at position 54 (T54) in tRNAs, which is necessary for survival at high temperatures. T54 2-thiolation is achieved by the tRNA thiouridine synthetase TtuA and sulfur-carrier proteins. TtuA has five conserved CXXC/H motifs and the signature PP motif, and belongs to the TtcA family of tRNA 2-thiolation enzymes, for which there is currently no structural information. In this study, we determined the crystal structure of a TtuA homolog from the hyperthermophilic archeon Pyrococcus horikoshii at 2.1 A resolution. The P. horikoshii TtuA forms a homodimer, and each subunit contains a catalytic domain and unique N- and C-terminal zinc fingers. The catalytic domain has much higher structural similarity to that of another tRNA modification enzyme, TilS (tRNAIle2 lysidine synthetase), than to the other type of tRNA 2-thiolation enzyme, MnmA. Three conserved cysteine residues are clustered in the putative catalytic site, which is not present in TilS. An in vivo mutational analysis in the bacterium Thermus thermophilus demonstrated that the three conserved cysteine residues and the putative ATP-binding residues in the catalytic domain are important for the TtuA activity. A positively charged surface that includes the catalytic site and the two zinc fingers is likely to provide the tRNA-binding site. Proteins 2013; 81:1232–1244. © 2013 Wiley Periodicals, Inc.
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- 2013
19. Differentiating analogous tRNA methyltransferases by fragments of the methyl donor
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Shigeyuki Yokoyama, Sakurako Goto-Ito, Georges Lahoud, Ya-Ming Hou, Ken-ichi Yoshida, and Takuhiro Ito
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Models, Molecular ,S-Adenosylmethionine ,Adenosine ,Sequence Homology ,Sequence (biology) ,Plasma protein binding ,Biology ,Models, Biological ,Article ,Substrate Specificity ,chemistry.chemical_compound ,Methionine ,medicine ,Transferase ,Enzyme Inhibitors ,Molecular Biology ,chemistry.chemical_classification ,tRNA Methyltransferases ,Escherichia coli Proteins ,TRNA Methyltransferase ,Peptide Fragments ,TRNA Methyltransferases ,Enzyme ,Biochemistry ,chemistry ,Drug Design ,Methane ,Protein Binding ,medicine.drug - Abstract
Bacterial TrmD and eukaryotic-archaeal Trm5 form a pair of analogous tRNA methyltransferase that catalyze methyl transfer from S-adenosyl methionine (AdoMet) to N1 of G37, using catalytic motifs that share no sequence or structural homology. Here we show that natural and synthetic analogs of AdoMet are unable to distinguish TrmD from Trm5. Instead, fragments of AdoMet, adenosine and methionine, are selectively inhibitory of TrmD rather than Trm5. Detailed structural information of the two enzymes in complex with adenosine reveals how Trm5 escapes targeting by adopting an altered structure, whereas TrmD is trapped by targeting due to its rigid structure that stably accommodates the fragment. Free energy analysis exposes energetic disparities between the two enzymes in how they approach the binding of AdoMet versus fragments and provides insights into the design of inhibitors selective for TrmD.
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- 2011
20. Tertiary structure checkpoint at anticodon loop modification in tRNA functional maturation
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Takuhiro Ito, Sakurako Goto-Ito, Mitsuo Kuratani, Shigeyuki Yokoyama, and Yoshitaka Bessho
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Models, Molecular ,Protein Conformation ,Molecular Conformation ,Biology ,Protein degradation ,Crystallography, X-Ray ,Catalysis ,Protein structure ,RNA, Transfer ,Structural Biology ,Anticodon ,Cysteine ,Codon ,Molecular Biology ,Alanine ,Temperature ,DNA replication ,RNA ,Archaea ,Protein tertiary structure ,Protein Structure, Tertiary ,Cell biology ,Kinetics ,Mutation ,Transfer RNA ,Protein folding ,Linker - Abstract
tRNA precursors undergo a maturation process, involving nucleotide modifications and folding into the L-shaped tertiary structure. The N1-methylguanosine at position 37 (m1G37), 3' adjacent to the anticodon, is essential for translational fidelity and efficiency. In archaea and eukaryotes, Trm5 introduces the m1G37 modification into all tRNAs bearing G37. Here we report the crystal structures of archaeal Trm5 (aTrm5) in complex with tRNA(Leu) or tRNA(Cys). The D2-D3 domains of aTrm5 discover and modify G37, independently of the tRNA sequences. D1 is connected to D2-D3 through a flexible linker and is designed to recognize the shape of the tRNA outer corner, as a hallmark of the completed L shape formation. This interaction by D1 lowers the K(m) value for tRNA, enabling the D2-D3 catalysis. Thus, we propose that aTrm5 provides the tertiary structure checkpoint in tRNA maturation.
- Published
- 2009
21. Structural basis for methyl-donor–dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD
- Author
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Se Won Suh, Shigeyuki Yokoyama, Sakurako Goto-Ito, Isao Masuda, Ya-Ming Hou, Takuhiro Ito, Ken-ichi Yoshida, and Shun-ichi Sekine
- Subjects
Models, Molecular ,S-Adenosylmethionine ,Adenosine ,Guanine ,Methyltransferase ,Molecular Sequence Data ,Biology ,Crystallography, X-Ray ,Methylation ,Ribosome ,Substrate Specificity ,Frameshift mutation ,Structure-Activity Relationship ,RNA, Transfer ,Anticodon ,Moiety ,Transferase ,Thermotoga maritima ,Amino Acid Sequence ,Trefoil knot ,tRNA Methyltransferases ,Binding Sites ,Multidisciplinary ,Base Sequence ,Escherichia coli Proteins ,TRNA Methyltransferase ,Haemophilus influenzae ,Kinetics ,PNAS Plus ,Biochemistry ,Transfer RNA ,Biocatalysis ,Sequence Alignment - Abstract
Significance In bacterial tRNAs with the 36 GG 37 sequence, where positions 36 and 37 are, respectively, the third letter of the anticodon and 3′ adjacent to the anticodon, the modification of N 1 -methylguanosine (m 1 G) at position 37 prevents +1 frameshifts on the ribosome. The m 1 G37 modification is introduced by the enzyme TrmD, which harbors a deep trefoil knot within the S -adenosyl-L-methionine (AdoMet)-binding site. We determined the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. The structure revealed how TrmD, upon AdoMet binding in the trefoil knot, obtains the ability to bind the substrate tRNA, and interacts with G37 and G36 sequentially to transfer the methyl moiety of AdoMet to the N 1 position of G37.
- Published
- 2015
22. Structural basis for ubiquitin recognition by ubiquitin-binding zinc finger of FAAP20
- Author
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Sakurako Goto-Ito, Shinichiro Nakada, Atsuhiko Fukuto, Tomio S. Takahashi, Yusuke Sato, Atsushi Yamagata, Satoshi Tashiro, Yasunori Horikoshi, Shuya Fukai, and Aya Toma
- Subjects
Models, Molecular ,Ubiquitin binding ,Protein Conformation ,DNA polymerase ,Molecular Sequence Data ,lcsh:Medicine ,Deubiquitinating enzyme ,Structure-Activity Relationship ,Protein structure ,Ubiquitin ,Humans ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,lcsh:Science ,Zinc finger ,Multidisciplinary ,biology ,lcsh:R ,Zinc Fingers ,Fanconi Anemia Complementation Group Proteins ,Ubiquitin ligase ,Biochemistry ,Mutation ,biology.protein ,Biophysics ,REV1 ,lcsh:Q ,Sequence Alignment ,Research Article ,Protein Binding - Abstract
Several ubiquitin-binding zinc fingers (UBZs) have been reported to preferentially bind K63-linked ubiquitin chains. In particular, the UBZ domain of FAAP20 (FAAP20-UBZ), a member of the Fanconi anemia core complex, seems to recognize K63-linked ubiquitin chains, in order to recruit the complex to DNA interstrand crosslinks and mediate DNA repair. By contrast, it is reported that the attachment of a single ubiquitin to Rev1, a translesion DNA polymerase, increases binding of Rev1 to FAAP20. To clarify the specificity of FAAP20-UBZ, we determined the crystal structure of FAAP20-UBZ in complex with K63-linked diubiquitin at 1.9 Å resolution. In this structure, FAAP20-UBZ interacts only with one of the two ubiquitin moieties. Consistently, binding assays using surface plasmon resonance spectrometry showed that FAAP20-UBZ binds ubiquitin and M1-, K48- and K63-linked diubiquitin chains with similar affinities. Residues in the vicinity of Ala168 within the α-helix and the C-terminal Trp180 interact with the canonical Ile44-centered hydrophobic patch of ubiquitin. Asp164 within the α-helix and the C-terminal loop mediate a hydrogen bond network, which reinforces ubiquitin-binding of FAAP20-UBZ. Mutations of the ubiquitin-interacting residues disrupted binding to ubiquitin in vitro and abolished the accumulation of FAAP20 to DNA damage sites in vivo. Finally, structural comparison among FAAP20-UBZ, WRNIP1-UBZ and RAD18-UBZ revealed distinct modes of ubiquitin binding. UBZ family proteins could be divided into at least three classes, according to their ubiquitin-binding modes.
- Published
- 2015
23. Structure of Slitrk2-PTPδ complex reveals mechanisms for splicing-dependent trans-synaptic adhesion
- Author
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Tomoyuki Yoshida, Yusuke Sato, Asami Maeda, Tomoko Shiroshima, Shuya Fukai, Sakurako Goto-Ito, Atsushi Yamagata, and Takeshi Uemura
- Subjects
Models, Molecular ,Multidisciplinary ,animal structures ,Binding Sites ,Cell adhesion molecule ,Protein Conformation ,Binding protein ,Receptor-Like Protein Tyrosine Phosphatases, Class 2 ,Adhesion ,Plasma protein binding ,Protein tyrosine phosphatase ,Biology ,Article ,Cell biology ,Repressor Proteins ,Mice ,Structure-Activity Relationship ,Protein structure ,Postsynaptic potential ,RNA splicing ,Synapses ,Animals ,Humans ,Protein Interaction Domains and Motifs ,Protein Binding - Abstract
Selective binding between pre- and postsynaptic adhesion molecules can induce synaptic differentiation. Here we report the crystal structure of a synaptogenic trans-synaptic adhesion complex between Slit and Trk-like family member 2 (Slitrk2) and receptor protein tyrosine phosphatase (RPTP) δ. The structure and site-directed mutational analysis revealed the structural basis of splicing-dependent adhesion between Slitrks and type IIa RPTPs for inducing synaptic differentiation.
- Published
- 2014
24. Trm5 and TrmD: Two Enzymes from Distinct Origins Catalyze the Identical tRNA Modification, m1G37
- Author
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Shigeyuki Yokoyama, Takuhiro Ito, and Sakurako Goto-Ito
- Subjects
0301 basic medicine ,TRNA modification ,biology ,TRNA Methyltransferase ,Guanosine ,Aminoacylation ,biology.organism_classification ,Biochemistry ,Ribosome ,Frameshift mutation ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,0302 clinical medicine ,chemistry ,Transfer RNA ,Molecular Biology ,030217 neurology & neurosurgery ,Archaea - Abstract
The N1-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m1G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs.
- Published
- 2017
25. Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity
- Author
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Yusuke Sato, Fuminori Tokunaga, Keiko Kubota, Shuya Fukai, Jun-ichiro Inoue, Yuri Shibata, Yuji Kubota, Sakurako Goto-Ito, Atsushi Yamagata, Eiji Goto, and Mutsuhiro Takekawa
- Subjects
Models, Molecular ,Biology ,Crystallography, X-Ray ,Conserved sequence ,Deubiquitinating enzyme ,Ubiquitin-Specific Peptidase 7 ,Scissile bond ,Protein structure ,Ubiquitin ,Structural Biology ,Sequence Analysis, Protein ,Humans ,Binding site ,Molecular Biology ,Conserved Sequence ,Binding Sites ,Tumor Suppressor Proteins ,Mutagenesis ,HEK 293 cells ,Zebrafish Proteins ,Cell biology ,Protein Structure, Tertiary ,Kinetics ,HEK293 Cells ,Biochemistry ,biology.protein ,Ubiquitin-Specific Proteases ,Ubiquitin Thiolesterase ,Signal Transduction - Abstract
The tumor suppressor CYLD belongs to a ubiquitin (Ub)-specific protease (USP) family and specifically cleaves Met1- and Lys63-linked polyubiquitin chains to suppress inflammatory signaling pathways. Here, we report crystal structures representing the catalytic states of zebrafish CYLD for Met1- and Lys63-linked Ub chains and two distinct precatalytic states for Met1-linked chains. In both catalytic states, the distal Ub is bound to CYLD in a similar manner, and the scissile bond is located close to the catalytic residue, whereas the proximal Ub is bound in a manner specific to Met1- or Lys63-linked chains. Further structure-based mutagenesis experiments support the mechanism by which CYLD specifically cleaves both Met1- and Lys63-linked chains and provide insight into tumor-associated mutations of CYLD. This study provides new structural insight into the mechanisms by which USP family deubiquitinating enzymes recognize and cleave Ub chains with specific linkage types.
- Published
- 2014
26. Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.
- Author
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Takahashi, Tomio S., Yoshihiro Hirade, Aya Toma, Yusuke Sato, Atsushi Yamagata, Sakurako Goto-Ito, Akiko Tomita, Shinichiro Nakada, and Shuya Fukai
- Subjects
DOUBLE-strand DNA breaks ,UBIQUITINATION ,UBIQUITIN ligases - Abstract
The E3 ubiquitin (Ub) ligase RNF168 plays a critical role in the initiation of the DNA damage response to double-strand breaks (DSBs). The recruitment of RNF168 by ubiquitylated targets involves two distinct regions, Ub-dependent DSB recruitment module (UDM) 1 and UDM2. Here we report the crystal structures of the complex between UDM1 and Lys63- linked diUb (K63-Ub
2 ) and that between the C-terminally truncated UDM2 (UDM2ΔC) and K63-Ub2 . In both structures, UDM1 and UDM2ΔC fold as a single α-helix. Their simultaneous bindings to the distal and proximal Ub moieties provide specificity for Lys63-linked Ub chains. Structural and biochemical analyses of UDM1 elucidate an Ub-binding mechanism between UDM1 and polyubiquitylated targets. Mutations of Ub-interacting residues in UDM2 prevent the accumulation of RNF168 to DSB sites in U2OS cells, whereas those in UDM1 have little effect, suggesting that the interaction of UDM2 with ubiquitylated and polyubiquitylated targets mainly contributes to the RNF168 recruitment. [ABSTRACT FROM AUTHOR]- Published
- 2018
- Full Text
- View/download PDF
27. Molecular Basis of Lys-63-linked Polyubiquitination Inhibition by the Interaction between Human Deubiquitinating Enzyme OTUB1 and Ubiquitin-conjugating Enzyme UBC13*
- Author
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Sakurako Goto-Ito, Yusuke Sato, Keiko Kubota, Shuya Fukai, Rikako Miyamoto, Atsushi Yamagata, and Shinichiro Nakada
- Subjects
DNA repair ,Surface Properties ,Amino Acid Motifs ,Ubiquitin-conjugating enzyme ,Crystallography, X-Ray ,Biochemistry ,Deubiquitinating enzyme ,Cell Line ,Ligases ,Ubiquitin ,Humans ,Protein Interaction Domains and Motifs ,Polyubiquitin ,Protein Structure, Quaternary ,Molecular Biology ,Histone ubiquitination ,biology ,Deubiquitinating Enzymes ,Lysine ,Ubiquitination ,Hydrogen Bonding ,Cell Biology ,Chromatin ,Cell biology ,Isopeptidase activity ,Cysteine Endopeptidases ,Protein Transport ,Amino Acid Substitution ,OTUB1 ,Protein Structure and Folding ,Ubiquitin-Conjugating Enzymes ,biology.protein ,Mutagenesis, Site-Directed ,Hydrophobic and Hydrophilic Interactions ,Protein Processing, Post-Translational ,DNA Damage ,Protein Binding - Abstract
UBC13 is the only known E2 ubiquitin (Ub)-conjugating enzyme that produces Lys-63-linked Ub chain with its cofactor E2 variant UEV1a or MMS2. Lys-63-linked ubiquitination is crucial for recruitment of DNA repair and damage response molecules to sites of DNA double-strand breaks (DSBs). A deubiquitinating enzyme OTUB1 suppresses Lys-63-linked ubiquitination of chromatin surrounding DSBs by binding UBC13 to inhibit its E2 activity independently of the isopeptidase activity. OTUB1 strongly suppresses UBC13-dependent Lys-63-linked tri-Ub production, whereas it allows di-Ub production in vitro. The mechanism of this non-canonical OTUB1-mediated inhibition of ubiquitination remains to be elucidated. Furthermore, the atomic level information of the interaction between human OTUB1 and UBC13 has not been reported. Here, we determined the crystal structure of human OTUB1 in complex with human UBC13 and MMS2 at 3.15 A resolution. The presented atomic-level interactions were confirmed by surface-plasmon resonance spectroscopy with structure-based mutagenesis. The designed OTUB1 mutants cannot inhibit Lys-63-linked Ub chain formation in vitro and histone ubiquitination and 53BP1 assembly around DSB sites in vivo. Finally, we propose a model for how capping of di-Ub by the OTUB1-UBC13-MMS2/UEV1a complex efficiently inhibits Lys-63-linked tri-Ub formation.
- Published
- 2012
28. Get1 stabilizes an open dimer conformation of get3 ATPase by binding two distinct interfaces
- Author
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Yusuke Sato, Sakurako Goto-Ito, Shuya Fukai, Atsushi Yamagata, and Keiko Kubota
- Subjects
Models, Molecular ,Saccharomyces cerevisiae Proteins ,Dimer ,Molecular Sequence Data ,Plasma protein binding ,GET complex ,Saccharomyces cerevisiae ,Crystallography, X-Ray ,Endoplasmic Reticulum ,chemistry.chemical_compound ,Adenosine Triphosphate ,Structural Biology ,Escherichia coli ,Guanine Nucleotide Exchange Factors ,Protein Interaction Domains and Motifs ,Amino Acid Sequence ,Molecular Biology ,Integral membrane protein ,Adenosine Triphosphatases ,Sequence Homology, Amino Acid ,Chemistry ,Endoplasmic reticulum ,Hydrolysis ,Membrane Proteins ,Transport protein ,Protein Structure, Tertiary ,Adenosine Diphosphate ,Transmembrane domain ,Crystallography ,Adaptor Proteins, Vesicular Transport ,Protein Transport ,Proton-Translocating ATPases ,Membrane protein ,Biophysics ,Protein Processing, Post-Translational ,Protein Binding - Abstract
Tail-anchored (TA) proteins are integral membrane proteins that possess a single transmembrane domain near their carboxy terminus. TA proteins play critical roles in many important cellular processes such as membrane trafficking, protein translocation, and apoptosis. The GET complex mediates posttranslational insertion of newly synthesized TA proteins to the endoplasmic reticulum membrane. The GET complex is composed of the homodimeric Get3 ATPase and its heterooligomeric receptor, Get1/2. During insertion, the Get3 dimer shuttles between open and closed conformational states, coupled with ATP hydrolysis and the binding/release of TA proteins. We report crystal structures of ADP-bound Get3 in complex with the cytoplasmic domain of Get1 (Get1CD) in open and semi-open conformations at 3.0- and 4.5-A resolutions, respectively. Our structures and biochemical data suggest that Get1 uses two interfaces to stabilize the open dimer conformation of Get3. We propose that one interface is sufficient for binding of Get1 by Get3, while the second interface stabilizes the open dimer conformation of Get3.
- Published
- 2012
29. Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin
- Author
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Shun-ichi Sekine, Sakurako Goto-Ito, Masashi Hirano, Madoka Nishimoto, Mitsuo Kuratani, Yasushi Hikida, Henri Grosjean, Yuzuru Itoh, Shigeyuki Yokoyama, Yoshitaka Bessho, Takuhiro Ito, Institut de génétique et microbiologie [Orsay] (IGM), and Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS)
- Subjects
MESH: Amino Acids ,Adenosine ,Saccharomyces cerevisiae Proteins ,Protein Conformation ,Saccharomyces cerevisiae ,MESH: tRNA Methyltransferases ,Biology ,Crystallography, X-Ray ,03 medical and health sciences ,Sinefungin ,chemistry.chemical_compound ,MESH: Saccharomyces cerevisiae Proteins ,MESH: Protein Conformation ,Bacterial Proteins ,Structural Biology ,MESH: Anti-Bacterial Agents ,MESH: Protein Binding ,Transferase ,Humans ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Amino Acids ,MESH: Bacterial Proteins ,Molecular Biology ,030304 developmental biology ,0303 health sciences ,tRNA Methyltransferases ,MESH: Humans ,Binding Sites ,MESH: Methanococcaceae ,030302 biochemistry & molecular biology ,Active site ,Methanocaldococcus jannaschii ,Methanococcaceae ,MESH: Adenosine ,MESH: Crystallography, X-Ray ,biology.organism_classification ,TRNA binding ,5-Methylcytidine ,Anti-Bacterial Agents ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,MESH: Binding Sites ,chemistry ,Biochemistry ,Transfer RNA ,biology.protein ,Protein Binding - Abstract
International audience; tRNA:m(5)C methyltransferase Trm4 generates the modified nucleotide 5-methylcytidine in archaeal and eukaryotic tRNA molecules, using S-adenosyl-l-methionine (AdoMet) as methyl donor. Most archaea and eukaryotes possess several Trm4 homologs, including those related to diseases, while the archaeon Methanocaldococcus jannaschii has only one gene encoding a Trm4 homolog, MJ0026. The recombinant MJ0026 protein catalyzed AdoMet-dependent methyltransferase activity on tRNA in vitro and was shown to be the M. jannaschii Trm4. We determined the crystal structures of the substrate-free M. jannaschii Trm4 and its complex with sinefungin at 1.27 A and 2.3 A resolutions, respectively. This AdoMet analog is bound in a negatively charged pocket near helix alpha8. This helix can adopt two different conformations, thereby controlling the entry of AdoMet into the active site. Adjacent to the sinefungin-bound pocket, highly conserved residues form a large, positively charged surface, which seems to be suitable for tRNA binding. The structure explains the roles of several conserved residues that were reportedly involved in the enzymatic activity or stability of Trm4p from the yeast Saccharomyces cerevisiae. We also discuss previous genetic and biochemical data on human NSUN2/hTrm4/Misu and archaeal PAB1947 methyltransferase, based on the structure of M. jannaschii Trm4.
- Published
- 2010
30. Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis
- Author
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Sakurako Goto-Ito, Shigeyuki Yokoyama, Emiko Fusatomi, Rie Shibata, Yoshitaka Bessho, Shun-ichi Sekine, Takuhiro Ito, and Ryohei Ishii
- Subjects
Iron-Sulfur Proteins ,Stereochemistry ,Archaeal Proteins ,Saccharomyces cerevisiae ,Molecular Sequence Data ,Molecular Conformation ,Crystallography, X-Ray ,Catalysis ,Protein Structure, Secondary ,Pyrococcus horikoshii ,chemistry.chemical_compound ,Structural Biology ,Amino Acid Sequence ,chemistry.chemical_classification ,Binding Sites ,biology ,Sequence Homology, Amino Acid ,Nucleosides ,General Medicine ,biology.organism_classification ,Archaea ,Protein tertiary structure ,Enzymes ,Protein Structure, Tertiary ,Crystallography ,Enzyme ,chemistry ,Docking (molecular) ,Transfer RNA ,Cysteine ,Wybutosine - Abstract
Wye bases are tricyclic bases that are found in archaeal and eukaryotic tRNAs. The most modified wye base, wybutosine, which appears at position 37 (the 3'-adjacent position to the anticodon), is known to be important for translational reading-frame maintenance. Saccharomyces cerevisiae TYW1 catalyzes the tri-ring-formation step in wye-base biosynthesis, with the substrate tRNA bearing N(1)-methylated G37. Here, the crystal structure of the archaeal TYW1 homologue from Pyrococcus horikoshii is reported at 2.2 A resolution. The amino-acid sequence of P. horikoshii TYW1 suggested that it is a radical-AdoMet enzyme and the tertiary structure of P. horikoshii TYW1 indeed shares the modified TIM-barrel structure found in other radical-AdoMet enzymes. Radical-AdoMet enzymes generally contain one or two iron-sulfur (FeS) clusters. The tertiary structure of P. horikoshii TYW1 revealed two FeS cluster sites, each containing three cysteine residues. One FeS cluster site was expected from the amino-acid sequence and the other involves cysteine residues that are dispersed throughout the sequence. The existence of two FeS clusters was confirmed from the anomalous Fourier electron-density map. By superposing the P. horikoshii TYW1 tertiary structure on those of other radical-AdoMet enzymes, the AdoMet molecule, which is necessary for the reactions of radical-AdoMet enzymes, was modelled in P. horikoshii TYW1. Surface plots of conservation rates and electrostatic potentials revealed the highly conserved and positively charged active-site hollow. On the basis of the surface properties, a docking model of P. horikoshii TYW1, the tRNA, the FeS clusters and the AdoMet molecule was constructed, with the nucleoside at position 37 of tRNA flipped out from the canonical tRNA structure.
- Published
- 2007
31. Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA
- Author
-
Hirofumi, Nakagawa, primary, Mitsuo, Kuratani, additional, Sakurako, Goto‐Ito, additional, Takuhiro, Ito, additional, Kazushige, Katsura, additional, Takaho, Terada, additional, Mikako, Shirouzu, additional, Shun‐ichi, Sekine, additional, Naoki, Shigi, additional, and Shigeyuki, Yokoyama, additional
- Published
- 2014
- Full Text
- View/download PDF
32. 3B1322 Crystal structure of the bacterial tRNA(m^1G37)-methyltransferase in complex with a substrate tRNA and a methyl donor analog(3B Nucleic acid binding proteins,The 49th Annual Meeting of the Biophysical Society of Japan)
- Author
-
Shigeyuki Yokoyama, Sakurako Goto-Ito, Ken-ichi Yoshida, and Takuhiro Ito
- Subjects
Methyltransferase ,Biochemistry ,Transfer RNA ,Nucleic acid ,Substrate (chemistry) ,Crystal structure ,Methyl donor ,Biology ,DNA-binding protein - Published
- 2011
33. Ubiquitin recognition by UBZ and UMI domains for DNA damage response
- Author
-
Tomio S. Takahashi, Sakurako Goto-Ito, Atsushi Yamagata, Yusuke Sato, Shuya Fukai, and Aya Toma
- Subjects
Inorganic Chemistry ,Ubiquitin ,biology ,Structural Biology ,DNA damage ,biology.protein ,General Materials Science ,Physical and Theoretical Chemistry ,Condensed Matter Physics ,Biochemistry ,Cell biology - Abstract
Double-strand break (DSB) and interstrand crosslink (ICL) are serious damages in DNA. Responses to these DNA damages include ubiquitination of damaged chromatin and other substrates, which recruit protein complexes required for DNA repair. Therefore, many proteins involved in DNA damage response contain ubiquitin-binding modules. For instance, a ubiquitin ligase RNF168, which catalyzes K63-linked polyubiquitination of histone H2A, contains two types of ubiquitin binding motifs, MIU (motif interacting with ubiquitin) and UIM (UIM and MIU-related Ub-binding domain). FAAP20, which recruits Fanconi anemia proteins (crosslink-repair factors), contains a UBZ (ubiquitin-binding zinc finger) domain. To date, mechanisms for ubiquitin recognition by UMI and UBZ domains have remained unclear. In this study, we determined crystal structures of RNF168 UMI and FAAP20 UBZ in complex with ubiquitin at 1.9 Å resolutions, respectively. SPR analyses using UMI and UBZ mutants, which were designed to disrupt Ub binding, confirmed that the observed interactions between Ub and UMI or UBZ are critical for binding. Our structure and the accompanying in-vitro structure-based mutagenesis experiments reveal the structural basis of these important recognition events.
- Published
- 2014
34. Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD.
- Author
-
Takuhiro Ito, Isao Masuda, Ken-ichi Yoshida, Sakurako Goto-Ito, Shun-ichi Sekine, Se Won Suh, Ya-Ming Hou, and Shigeyuki Yokoyama
- Subjects
TRANSFER RNA methyltransferase ,TREFOIL knots ,CRYSTAL structure ,RNA modification & restriction ,X-ray crystallography - Abstract
The deep trefoil knot architecture is unique to the SpoU and tRNA methyltransferase D (TrmD) (SPOUT) family of methyltransferases (MTases) in all three domains of life. In bacteria, TrmD catalyzes the N¹-methylguanosine (m¹G) modification at position 37 in transfer RNAs (tRNAs) with the
36 GG37 sequence, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. The m¹G37-modified tRNA functions properly to prevent +1 frameshift errors on the ribosome. Here we report the crystal structure of the TrmD homodimer in complex with a substrate tRNA and an AdoMet analog. Our structural analysis revealed the mechanism by which TrmD binds the substrate tRNA in an AdoMet-dependent manner. The trefoil-knot center, which is structurally conserved among SPOUT MTases, accommodates the adenosine moiety of AdoMet by loosening/retightening of the knot. The TrmD-specific regions surrounding the trefoil knot recognize the methionine moiety of AdoMet, and thereby establish the entire TrmD structure for global interactions with tRNA and sequential and specific accommodations of G37 and G36, resulting in the synthesis of m¹G37-tRNA. [ABSTRACT FROM AUTHOR]- Published
- 2015
- Full Text
- View/download PDF
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