Genomes and Genes
Experts and Doctors on tertiary protein structure in Kyoto, Japan
Locale: Kyoto, Japan
Topic: tertiary protein structure
Publications141 found, 100 shown here
- Kong S, Suzuki T, Tamura K, Mochizuki N, Hara Nishimura I, Nagatani A. Blue light-induced association of phototropin 2 with the Golgi apparatus. Plant J. 2006;45:994-1005 pubmed..The BL-induced Golgi localization of phot2 may be one of important signaling steps in the phot2 signal transduction pathway. ..
- Morimoto H, Kondoh K, Nishimoto S, Terasawa K, Nishida E. Activation of a C-terminal transcriptional activation domain of ERK5 by autophosphorylation. J Biol Chem. 2007;282:35449-56 pubmed..These results reveal the role of the stimulus-induced ERK5 autophosphorylation in regulation of gene expression. ..
- Hiraoka Y, Yoshida K, Ohno M, Matsuoka T, Kita T, Nishi E. Ectodomain shedding of TNF-alpha is enhanced by nardilysin via activation of ADAM proteases. Biochem Biophys Res Commun. 2008;370:154-8 pubmed publisher..Our results indicate the involvement of NRDc in ectodomain shedding of TNF-alpha, which may be a novel target for anti-inflammatory therapies. ..
- Kohda C, Kawamura I, Baba H, Nomura T, Ito Y, Kimoto T, et al. Dissociated linkage of cytokine-inducing activity and cytotoxicity to different domains of listeriolysin O from Listeria monocytogenes. Infect Immun. 2002;70:1334-41 pubmed..In contrast, the other part of LLO, corresponding to domain 1-3, was essential for IFN-gamma-inducing activity. These findings implied a novel aspect of the function of LLO as a bacterial modulin. ..
- Yamaguchi Y, Katoh H, Negishi M. N-terminal short sequences of alpha subunits of the G12 family determine selective coupling to receptors. J Biol Chem. 2003;278:14936-9 pubmed..Thus, N-terminal short sequences of the G(12) family determine the selective couplings of thrombin and LPA receptors to the Galpha(12) family. ..
- Miyazaki K, Miyamoto H, Mercer D, Hirase T, Martin J, Kojima Y, et al. Involvement of the multidomain regulatory protein XynR in positive control of xylanase gene expression in the ruminal anaerobe Prevotella bryantii B(1)4. J Bacteriol. 2003;185:2219-26 pubmed..bryantii B(1)4. This is the first regulatory protein that demonstrates significant homology with the two-component regulatory protein superfamily and has been shown to be involved in the regulation of polysaccharidase gene expression...
- Ikai N, Yanagida M. Cdc48 is required for the stability of Cut1/separase in mitotic anaphase. J Struct Biol. 2006;156:50-61 pubmed..Cells lose viability during the traverse of anaphase in cdc48 mutant cells. Cdc48 may protect Cut1/separase and Cut2/securin against the instability during polyubiquitination and degradation in the metaphase-anaphase transition. ..
- Kamikawa R, Masuda I, Demura M, Oyama K, Yoshimatsu S, Kawachi M, et al. Mitochondrial group II introns in the raphidophycean flagellate Chattonella spp. suggest a diatom-to-Chattonella lateral group II intron transfer. Protist. 2009;160:364-75 pubmed publisher..Based on parsimonious discussion, Chattonella cox1-i1 and Chattonella cox1-i2 have invaded into the cox1 gene of an ancestral Chattonella cell after diverging from C. subsalsa. ..
- Takahata K. Isolation of carrot Argonaute1 from subtractive somatic embryogenesis cDNA library. Biosci Biotechnol Biochem. 2008;72:900-4 pubmed..C-Ago1 has specific expression during somatic embryogenesis, which indicates that microRNA gene expression controlling system is required for somatic embryogenesis. ..
- Nakamura N, Morinaga H, Kikuchi M, Yonekura S, Ishii N, Yamamoto K, et al. Cloning and characterization of uracil-DNA glycosylase and the biological consequences of the loss of its function in the nematode Caenorhabditis elegans. Mutagenesis. 2008;23:407-13 pubmed publisher..The present experiments also showed that the ung-1 mutant of C.elegans was more resistant to NaHSO(3)-inducing cytosine deamination than wild-type strain. ..
- Fujita H, Katoh H, Ishikawa Y, Mori K, Negishi M. Rapostlin is a novel effector of Rnd2 GTPase inducing neurite branching. J Biol Chem. 2002;277:45428-34 pubmed..Therefore, Rapostlin is the first effector of Rnd2, regulating neurite branch formation. ..
- Ishizaki R, Shin H, Iguchi Ariga S, Ariga H, Nakayama K. AMY-1 (associate of Myc-1) localization to the trans-Golgi network through interacting with BIG2, a guanine-nucleotide exchange factor for ADP-ribosylation factors. Genes Cells. 2006;11:949-59 pubmed
- Miyake A, Takahashi Y, Miwa H, Shimada A, Konishi M, Itoh N. Neucrin is a novel neural-specific secreted antagonist to canonical Wnt signaling. Biochem Biophys Res Commun. 2009;390:1051-5 pubmed publisher..The expression pattern of Neucrin is distinct from that of any Dkk. Neucrin is a unique secreted Wnt antagonist that is predominantly expressed in developing neural tissues. ..
- Izumi K, Nakamura S, Nakano H, Shimura K, Sakagami Y, Oishi S, et al. Characterization of HIV-1 resistance to a fusion inhibitor, N36, derived from the gp41 amino-terminal heptad repeat. Antiviral Res. 2010;87:179-86 pubmed publisher..Denaturing experiments revealed that the stability of the 6-helix bundle of N126K/E137Q is greater than in the wild-type. These results suggest that the stabilizing effect of N126K/E137Q provides resistance to N36 and C34. ..
- Tanaka N, Tani Y, Tada T, Lee Y, Kanaori K, Kunugi S. The roles of conserved amino acids on substrate binding and conformational integrity of ClpB N-terminal domain. Biochemistry. 2006;45:8556-61 pubmed..1 degrees C lower than that of wild-type. Our results revealed that conserved amino acids Thr7 and Ser84 both participated in maintaining the conformational integrity of the ClpB N-terminal domain. ..
- Wakasugi K, Nakano T, Kitatsuji C, Morishima I. Human neuroglobin interacts with flotillin-1, a lipid raft microdomain-associated protein. Biochem Biophys Res Commun. 2004;318:453-60 pubmed..Since Galpha exists within lipid rafts critical for signal transduction and flotillin-1 recruits signaling proteins to lipid rafts, flotillin-1 might recruit Ngb to lipid rafts as a means of preventing neuronal death. ..
- Kato T, Kawahara A, Ashida H, Yamamoto K. Unique peptide:N-glycanase of Caenorhabditis elegans has activity of protein disulphide reductase as well as of deglycosylation. J Biochem. 2007;142:175-81 pubmed..Our biochemical studies revealed that PNG-1 is a unique bifunctional protein possessing two enzyme activities. ..
- Koumoto Y, Shimada T, Kondo M, Hara Nishimura I, Nishimura M. Chloroplasts have a novel Cpn10 in addition to Cpn20 as co-chaperonins in Arabidopsis thaliana. J Biol Chem. 2001;276:29688-94 pubmed..It was proposed that two kinds of co-chaperonins, Cpn20 and chl-Cpn10, work independently in the chloroplast. ..
- Kosugi S, Okamoto H, Tamada A, Sanchez Franco F. A novel peculiar mutation in the sodium/iodide symporter gene in spanish siblings with iodide transport defect. J Clin Endocrinol Metab. 2002;87:3830-6 pubmed..Further, the mutant NIS protein was synthesized, but not properly expressed, on the cell surface, but was mostly accumulated in the cytoplasm, suggesting impaired targeting to the plasma membrane...
- Hoseki J, Sasakawa H, Yamaguchi Y, Maeda M, Kubota H, Kato K, et al. Solution structure and dynamics of mouse ARMET. FEBS Lett. 2010;584:1536-42 pubmed publisher..These results suggest that ARMET may hold a negatively charged molecule using the two positively charged domains. ..
- Matsuo Y, Akiyama N, Nakamura H, Yodoi J, Noda M, Kizaka Kondoh S. Identification of a novel thioredoxin-related transmembrane protein. J Biol Chem. 2001;276:10032-8 pubmed..This activity was abolished when two Cys residues in the active site sequence were mutated to Ser, suggesting that the Trx-like activity of TMX may help relieve ER stress caused by brefeldin A. ..
- Sakai A, Hizume K, Sutani T, Takeyasu K, Yanagida M. Condensin but not cohesin SMC heterodimer induces DNA reannealing through protein-protein assembly. EMBO J. 2003;22:2764-75 pubmed..SMC is eliminated from the completed double-stranded DNA. The ability of heterodimeric SMC to reanneal DNA may be regulated in vivo possibly through the non-SMC heterotrimeric complex. ..
- Saitsu H, Komada M, Suzuki M, Nakayama R, Motoyama J, Shiota K, et al. Expression of the mouse Fgf15 gene is directly initiated by Sonic hedgehog signaling in the diencephalon and midbrain. Dev Dyn. 2005;232:282-92 pubmed..These findings indicate that Fgf15 is directly regulated by Shh signaling through Gli proteins. ..
- Hirai M, Horiguchi M, Ohbayashi T, Kita T, Chien K, Nakamura T. Latent TGF-beta-binding protein 2 binds to DANCE/fibulin-5 and regulates elastic fiber assembly. EMBO J. 2007;26:3283-95 pubmed..These results suggest a novel regulatory mechanism of elastic fiber assembly in which LTBP-2 regulates targeting of DANCE on suitable microfibrils to form elastic fibers...
- Maegawa S, Koide K, Ito K, Akiyama Y. The intramembrane active site of GlpG, an E. coli rhomboid protease, is accessible to water and hydrolyses an extramembrane peptide bond of substrates. Mol Microbiol. 2007;64:435-47 pubmed
- Terawaki S, Tanaka Y, Nagakura T, Hayashi T, Shibayama S, Muroi K, et al. Specific and high-affinity binding of tetramerized PD-L1 extracellular domain to PD-1-expressing cells: possible application to enhance T cell function. Int Immunol. 2007;19:881-90 pubmed..The results suggest that oligomeric PD-L1 extracellular domains may provide a potential means to restore T cell functions in cancer and viral infection in humans. ..
- Shirakawa K, Takaori Kondo A, Yokoyama M, Izumi T, Matsui M, Io K, et al. Phosphorylation of APOBEC3G by protein kinase A regulates its interaction with HIV-1 Vif. Nat Struct Mol Biol. 2008;15:1184-91 pubmed publisher..These data imply that PKA-mediated phosphorylation of A3G can regulate the interaction between A3G and Vif. ..
- Kanehara K, Ito K, Akiyama Y. YaeL (EcfE) activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA. Genes Dev. 2002;16:2147-55 pubmed publisher..Thus, YaeL is positively required for the sigma(E) extracytoplasmic stress response...
- Ishizaki K, Shimizu Ueda Y, Okada S, Yamamoto M, Fujisawa M, Yamato K, et al. Multicopy genes uniquely amplified in the Y chromosome-specific repeats of the liverwort Marchantia polymorpha. Nucleic Acids Res. 2002;30:4675-81 pubmed..These observations suggest that the Y chromosome evolved by co-amplifying protein-coding genes with unique repeat sequences. ..
- Hosokawa N, Kamiya Y, Kamiya D, Kato K, Nagata K. Human OS-9, a lectin required for glycoprotein endoplasmic reticulum-associated degradation, recognizes mannose-trimmed N-glycans. J Biol Chem. 2009;284:17061-8 pubmed publisher..Thus, we propose a model for mannose trimming and the requirement for hOS-9 lectin activity in glycoprotein ERAD in which N-glycans lacking the terminal mannose from the C branch are recognized by hOS-9 and targeted for degradation. ..
- Yamanaka H, Nishida E. Wnt11 stimulation induces polarized accumulation of Dishevelled at apical adherens junctions through Frizzled7. Genes Cells. 2007;12:961-7 pubmed..Our results suggest that Wnt11-induced polarized accumulation of Frizzled7 and Dishevelled at adherens junctions underlies the formation and maintenance of apicobasal cell polarity. ..
- Morito D, Hirao K, Oda Y, Hosokawa N, Tokunaga F, Cyr D, et al. Gp78 cooperates with RMA1 in endoplasmic reticulum-associated degradation of CFTRDeltaF508. Mol Biol Cell. 2008;19:1328-36 pubmed publisher..Our data demonstrates that gp78 cooperates with RMA1 with E4-like activity in the ERAD of CFTRDeltaF508. ..
- Watabe Uchida M, Masuda A, Shimada N, Endo M, Shimamura K, Yasuda K, et al. Novel metalloprotease-disintegrin, meltrin epsilon (ADAM35), expressed in epithelial tissues during chick embryogenesis. Dev Dyn. 2004;230:557-68 pubmed..Basolateral localization of Meltrin epsilon in these epithelial cells suggests its unique roles in the organization of the epithelial tissues and development of the sensory organs and the gut. ..
- Koga H, Ohshima T, Shimotohno K. Enhanced activation of tax-dependent transcription of human T-cell leukemia virus type I (HTLV-I) long terminal repeat by TORC3. J Biol Chem. 2004;279:52978-83 pubmed..These results provide important clues toward understanding the molecular mechanism of Tax-dependent transcriptional activation of the HTLV-I LTR. ..
- Kakizawa T, Koide Yoshida S, Kimura T, Uchimura H, Hayashi Y, Saito K, et al. Fmoc-based solid phase chemical synthesis of 71-meric neuregulin 1-beta1, an epidermal growth factor-like domain. J Pept Sci. 2008;14:261-6 pubmed..The biological activity of the synthesized NRG1-beta1 was confirmed by ligand-induced tyrosine phosphorylation on Chinese hamster ovary (CHO) cells expressing ErbB-4. ..
- Kaku N, Matsuda K, Tsujimura A, Kawata M. Characterization of nuclear import of the domain-specific androgen receptor in association with the importin alpha/beta and Ran-guanosine 5'-triphosphate systems. Endocrinology. 2008;149:3960-9 pubmed publisher..Our data suggest that the nuclear import of AR is regulated by the interplay between each domain of the AR. ..
- Lee K, Ohyama T, Yajima N, Tsubuki S, Yonehara S. MST, a physiological caspase substrate, highly sensitizes apoptosis both upstream and downstream of caspase activation. J Biol Chem. 2001;276:19276-85 pubmed..These findings suggest that MST1 and MST2 play a role in apoptosis both upstream and downstream of caspase activation. ..
- Wakabayashi M, Ito T, Mitsushima M, Aizawa S, Ueda K, Amachi T, et al. Interaction of lp-dlg/KIAA0583, a membrane-associated guanylate kinase family protein, with vinexin and beta-catenin at sites of cell-cell contact. J Biol Chem. 2003;278:21709-14 pubmed..Together these findings suggest that lp-dlg/KIAA0583 is a novel scaffolding protein that can link the vinexin-vinculin complex and beta-catenin at sites of cell-cell contact. ..
- Mima J, Narita Y, Chiba H, Hayashi R. The multiple site binding of carboxypeptidase Y inhibitor (IC) to the cognate proteinase. Implications for the biological roles of the phosphatidylethanolamine-binding protein. J Biol Chem. 2003;278:29792-8 pubmed..Considering the fact that mouse PEBP has recently been identified as a novel thrombin inhibitor, the binding that characterizes the CPY-IC complex could be a common feature of PEBPs. ..
- Tatsumi R, Sekiya S, Nakanishi R, Mizutani M, Kojima S, Sokawa Y. Function of ubiquitin-like domain of chicken 2'-5'-oligoadenylate synthetase in conformational stability. J Interferon Cytokine Res. 2003;23:667-76 pubmed..Thus, OAS-B carrying the mutated UbL domain is unstable compared with OAS-A in vitro and in vivo, and the wt UbL domain may contribute to the stability of the protein structure of ChOAS. ..
- Fujita K, Kobayashi K, Iwamatsu A, Takeuchi M, Kumagai H, Yamamoto K. Molecular cloning of Mucor hiemalis endo-beta-N-acetylglucosaminidase and some properties of the recombinant enzyme. Arch Biochem Biophys. 2004;432:41-9 pubmed
- Nishi E, Hiraoka Y, Yoshida K, Okawa K, Kita T. Nardilysin enhances ectodomain shedding of heparin-binding epidermal growth factor-like growth factor through activation of tumor necrosis factor-alpha-converting enzyme. J Biol Chem. 2006;281:31164-72 pubmed..These results indicate the essential role of NRDc in HB-EGF ectodomain shedding and reveal how the shedding is regulated by the modulation of sheddase activity. ..
- Takahashi K, Niidome T, Akaike A, Kihara T, Sugimoto H. Phosphorylation of amyloid precursor protein (APP) at Tyr687 regulates APP processing by alpha- and gamma-secretase. Biochem Biophys Res Commun. 2008;377:544-549 pubmed publisher..These results suggest that phosphorylation of APP at Tyr687 regulates APP processing by alpha- and gamma-secretases, determining the expression level of AICD. ..
- Tanaka T, Fukui T, Fujiwara S, Atomi H, Imanaka T. Concerted action of diacetylchitobiose deacetylase and exo-beta-D-glucosaminidase in a novel chitinolytic pathway in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Biol Chem. 2004;279:30021-7 pubmed publisher..This is the first elucidation of an archaeal chitin catabolic pathway and defines a novel mechanism for dimer processing using a combination of deacetylation and cleavage, distinct from any previously known pathway...
- Inaba K, Takahashi Y, Ito K. Reactivities of quinone-free DsbB from Escherichia coli. J Biol Chem. 2005;280:33035-44 pubmed..We discuss the significance of having such multiple reaction pathways for the DsbB-dependent DsbA oxidation. ..
- Kondoh K, Terasawa K, Morimoto H, Nishida E. Regulation of nuclear translocation of extracellular signal-regulated kinase 5 by active nuclear import and export mechanisms. Mol Cell Biol. 2006;26:1679-90 pubmed..These results reveal the mechanism by which the activating phosphorylation of ERK5 induces its nuclear import and suggest a novel example of a phosphorylation-dependent control mechanism for nucleocytoplasmic shuttling of proteins. ..
- Tsukihara T, Honda Y, Sakai R, Watanabe T, Watanabe T. Mechanism for oxidation of high-molecular-weight substrates by a fungal versatile peroxidase, MnP2. Appl Environ Microbiol. 2008;74:2873-81 pubmed publisher..This is the first study of a direct mechanism for oxidation of high-molecular-weight substrates by a fungal peroxidase using a homologous gene expression system. ..
- Ushioda R, Hoseki J, Araki K, Jansen G, Thomas D, Nagata K. ERdj5 is required as a disulfide reductase for degradation of misfolded proteins in the ER. Science. 2008;321:569-72 pubmed publisher..Thus, ERdj5 is a member of a supramolecular ERAD complex that recognizes and unfolds misfolded proteins for their efficient retrotranslocation. ..
- Shirakawa R, Higashi T, Tabuchi A, Yoshioka A, Nishioka H, Fukuda M, et al. Munc13-4 is a GTP-Rab27-binding protein regulating dense core granule secretion in platelets. J Biol Chem. 2004;279:10730-7 pubmed..Thus, Rab27 regulates the dense core granule secretion in platelets by employing its binding protein, Munc13-4. ..
- Kurihara S, Oda S, Kato K, Kim H, Koyanagi T, Kumagai H, et al. A novel putrescine utilization pathway involves gamma-glutamylated intermediates of Escherichia coli K-12. J Biol Chem. 2005;280:4602-8 pubmed
- Su J, Takeda K, Tamura S, Fujiki Y, Miki K. Crystal structure of the conserved N-terminal domain of the peroxisomal matrix protein import receptor, Pex14p. Proc Natl Acad Sci U S A. 2009;106:417-21 pubmed publisher..Collectively, Phe-35 and Phe-52 are essential for the Pex14p functions, including the interaction between Pex14p and Pex5p. ..
- Niida A, Wang Z, Tomita K, Oishi S, Tamamura H, Otaka A, et al. Design and synthesis of downsized metastin (45-54) analogs with maintenance of high GPR54 agonistic activity. Bioorg Med Chem Lett. 2006;16:134-7 pubmed..This may provide an approach to reverse the pro-metastatic effect of metastin deletion in multiple malignant tumors. ..
- Mimori Kiyosue Y, Grigoriev I, Sasaki H, Matsui C, Akhmanova A, Tsukita S, et al. Mammalian CLASPs are required for mitotic spindle organization and kinetochore alignment. Genes Cells. 2006;11:845-57 pubmed..This local stabilization of microtubules is essential for the formation of normal metaphase spindle, completion of anaphase and cytokinesis. ..
- Koyanagi T, Katayama T, Suzuki H, Kumagai H. Altered oligomerization properties of N316 mutants of Escherichia coli TyrR. J Bacteriol. 2008;190:8238-43 pubmed publisher..ADP was substituted for ATP in the oligomer formation of TyrR(N316D). ..
- Tsukita S, Furuse M, Itoh M. Multifunctional strands in tight junctions. Nat Rev Mol Cell Biol. 2001;2:285-93 pubmed..New insights into the molecular architecture of tight junctions allow us to now discuss the structure and functions of this unique cell-cell adhesion apparatus in molecular terms. ..
- Shimaoka T, Nakayama T, Kume N, Takahashi S, Yamaguchi J, Minami M, et al. Cutting edge: SR-PSOX/CXC chemokine ligand 16 mediates bacterial phagocytosis by APCs through its chemokine domain. J Immunol. 2003;171:1647-51 pubmed..Thus, SR-PSOX/CXCL16 may play an important role in facilitating uptake of various pathogens and chemotaxis of T and NKT cells by APCs through its chemokine domain. ..
- Shigemoto T, Kageyama M, Hirai R, Zheng J, Yoneyama M, Fujita T. Identification of loss of function mutations in human genes encoding RIG-I and MDA5: implications for resistance to type I diabetes. J Biol Chem. 2009;284:13348-54 pubmed publisher..These results provide new insights into the structure-function relationship of RIG-I-like receptors as well as into human RIG-I-like receptor polymorphisms, antiviral innate immunity, and autoimmune diseases. ..
- Tenno M, Saeki A, Kézdy F, Elhammer A, Kurosaka A. The lectin domain of UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1 is involved in O-glycosylation of a polypeptide with multiple acceptor sites. J Biol Chem. 2002;277:47088-96 pubmed..This suggests a cooperative involvement of each repeat unit in the glycosylation of polypeptides with multiple acceptor sites. ..
- Goshima G, Kiyomitsu T, Yoda K, Yanagida M. Human centromere chromatin protein hMis12, essential for equal segregation, is independent of CENP-A loading pathway. J Cell Biol. 2003;160:25-39 pubmed..RNAi for hMis6, like that of a kinetochore kinesin CENP-E, induces mitotic arrest. Kinetochore localization of hMis12 is unaffected by CENP-A RNAi, demonstrating an independent pathway of CENP-A in human kinetochores. ..
- Nakagiri S, Murakami A, Takada S, Akiyama T, Yonehara S. Viral FLIP enhances Wnt signaling downstream of stabilized beta-catenin, leading to control of cell growth. Mol Cell Biol. 2005;25:9249-58 pubmed..Thus, viral FLIP E8 not only inhibits death receptor-mediated apoptosis but also enhances Wnt signaling pathways that are closely related to those of both ontogenesis and oncogenesis. ..
- Hirano Y, Hossain M, Takeda K, Tokuda H, Miki K. Structural studies of the Cpx pathway activator NlpE on the outer membrane of Escherichia coli. Structure. 2007;15:963-76 pubmed..Furthermore, two monomers in the asymmetric unit form an unusual 3D domain-swapped dimer. These findings indicate that tertiary and/or quaternary structural instability may be responsible for Cpx pathway activation. ..
- Matsuo N, Hoshino M, Yoshizawa M, Nabeshima Y. Characterization of STEF, a guanine nucleotide exchange factor for Rac1, required for neurite growth. J Biol Chem. 2002;277:2860-8 pubmed
- Kanazawa N, Tashiro K, Inaba K, Miyachi Y. Dendritic cell immunoactivating receptor, a novel C-type lectin immunoreceptor, acts as an activating receptor through association with Fc receptor gamma chain. J Biol Chem. 2003;278:32645-52 pubmed..The identification of this activating immunoreceptor provides an example of signaling via a dendritic cell-expressed C-type lectin receptor. ..
- Oka Y, Matsushita T, Mochizuki N, Quail P, Nagatani A. Mutant screen distinguishes between residues necessary for light-signal perception and signal transfer by phytochrome B. PLoS Genet. 2008;4:e1000158 pubmed publisher..Alignment with the recently described three-dimensional structure of the PAS-GAF domain of a bacterial phytochrome suggests that these four mutations reside in the vicinity of the phytochrome light-sensing knot. ..
- Otsuka S, Iwasaka S, Yoneda Y, Takeyasu K, Yoshimura S. Individual binding pockets of importin-beta for FG-nucleoporins have different binding properties and different sensitivities to RanGTP. Proc Natl Acad Sci U S A. 2008;105:16101-6 pubmed publisher..Single-molecule force measurement using the entire molecule of an NPC from a Xenopus oocyte also implies that the reduction of the affinity by RanGTP really occurs at the nucleoplasmic side of the entire NPC. ..
- Watanabe S, Arai T, Matsumi R, Atomi H, Imanaka T, Miki K. Crystal structure of HypA, a nickel-binding metallochaperone for [NiFe] hydrogenase maturation. J Mol Biol. 2009;394:448-59 pubmed publisher..In addition, the hexameric structure of HypA is formed in the crystal packing. Several hydrogen bonds and hydrophobic interactions stabilize the hexamer interface. These findings suggest the functional diversity of HypA proteins...
- Yoshima T, Yura T, Yanagi H. The trimerization domain of human heat shock factor 2 is able to interact with nucleoporin p62. Biochem Biophys Res Commun. 1997;240:228-33 pubmed..These data suggest the possibility that p62 is involved in the activation or regulation of HSF2. ..
- Komori H, Masui R, Kuramitsu S, Yokoyama S, Shibata T, Inoue Y, et al. Crystal structure of thermostable DNA photolyase: pyrimidine-dimer recognition mechanism. Proc Natl Acad Sci U S A. 2001;98:13560-5 pubmed publisher..This structural data for the photolyase-thymine complex allow us to propose a detailed model for the pyrimidine-dimer recognition mechanism...
- Chuma S, Hiyoshi M, Yamamoto A, Hosokawa M, Takamune K, Nakatsuji N. Mouse Tudor Repeat-1 (MTR-1) is a novel component of chromatoid bodies/nuages in male germ cells and forms a complex with snRNPs. Mech Dev. 2003;120:979-90 pubmed..These results suggest that MTR-1, which would provide novel insights into evolutionary comparison of nuages, functions in assembling snRNPs into cytoplasmic granules in germ cells. ..
- Wakatsuki S, Kurisaki T, Sehara Fujisawa A. Lipid rafts identified as locations of ectodomain shedding mediated by Meltrin beta/ADAM19. J Neurochem. 2004;89:119-23 pubmed..These results indicate that localization of Mel beta in lipid rafts is critical for its ectodomain shedding. ..
- Hara S, Kiyokawa E, Iemura S, Natsume T, Wassmer T, Cullen P, et al. The DHR1 domain of DOCK180 binds to SNX5 and regulates cation-independent mannose 6-phosphate receptor transport. Mol Biol Cell. 2008;19:3823-35 pubmed publisher..These data suggest that DOCK180 regulates CI-MPR trafficking via SNX5 and that this function is independent of its guanine nucleotide exchange factor activity toward Rac1. ..
- Iwaya N, Kuwahara Y, Fujiwara Y, Goda N, Tenno T, Akiyama K, et al. A common substrate recognition mode conserved between katanin p60 and VPS4 governs microtubule severing and membrane skeleton reorganization. J Biol Chem. 2010;285:16822-9 pubmed publisher..A common mechanism is evolutionarily conserved between two distinct cellular events, one that drives microtubule severing and the other involving membrane skeletal reorganization. ..
- Nakatogawa H, Mori H, Matsumoto G, Ito K. Characterization of a mutant form of SecA that alleviates a SecY defect at low temperature and shows a synthetic defect with SecY alteration at high temperature. J Biochem. 2000;127:1071-9 pubmed..The data also suggest that the conformation of the central region of SecA is important for the regulation of ATP hydrolysis and for the productive interaction of SecA with SecY...
- Tanaka A, Tanabe K, Morita M, Kurisu M, Kasiwayama Y, Matsuo M, et al. ATP binding/hydrolysis by and phosphorylation of peroxisomal ATP-binding cassette proteins PMP70 (ABCD3) and adrenoleukodystrophy protein (ABCD1). J Biol Chem. 2002;277:40142-7 pubmed..PMP70 and ALDP were also phosphorylated at a tyrosine residue(s). ATP binding/hydrolysis by and phosphorylation of PMP70 and ALDP are involved in the regulation of fatty acid transport into peroxisomes...
- Matsushita T, Mochizuki N, Nagatani A. Dimers of the N-terminal domain of phytochrome B are functional in the nucleus. Nature. 2003;424:571-4 pubmed..These findings indicate that the C-terminal domain attenuates the activity of phyB rather than positively transducing the signal. ..
- Yamagishi N, Ishihara K, Saito Y, Hatayama T. Hsp105 but not Hsp70 family proteins suppress the aggregation of heat-denatured protein in the presence of ADP. FEBS Lett. 2003;555:390-6 pubmed..Thus, Hsp105/110 family proteins are suggested to function as a substitute for Hsp70 family proteins to suppress the aggregation of denatured proteins in cells under severe stress, in which the cellular ATP level decreases markedly. ..
- Ohashi E, Murakumo Y, Kanjo N, Akagi J, Masutani C, Hanaoka F, et al. Interaction of hREV1 with three human Y-family DNA polymerases. Genes Cells. 2004;9:523-31 pubmed..Thus, our results suggest that hREV1 plays a pivotal role in the multi-enzyme, multi-step process of translesion DNA synthesis. ..
- Kakinuma T, Ichikawa H, Tsukada Y, Nakamura T, Toh B. Interaction between p230 and MACF1 is associated with transport of a glycosyl phosphatidyl inositol-anchored protein from the Golgi to the cell periphery. Exp Cell Res. 2004;298:388-98 pubmed..Our results suggest that p230, through its interaction with MACF1, provides the molecular link for transport of GPI-anchored proteins along the microtubule and actin cytoskeleton from the TGN to the cell periphery. ..
- Nishi E, Klagsbrun M. Heparin-binding epidermal growth factor-like growth factor (HB-EGF) is a mediator of multiple physiological and pathological pathways. Growth Factors. 2004;22:253-60 pubmed
- Adachi M, Inoko A, Hata M, Furuse K, Umeda K, Itoh M, et al. Normal establishment of epithelial tight junctions in mice and cultured cells lacking expression of ZO-3, a tight-junction MAGUK protein. Mol Cell Biol. 2006;26:9003-15 pubmed..These findings indicate that ZO-3 is dispensable in vivo in terms of individual viability, epithelial differentiation, and the establishment of TJs, at least in the laboratory environment. ..
- Yanagida Ishizaki Y, Takei T, Ishizaki R, Imakagura H, Takahashi S, Shin H, et al. Recruitment of Tom1L1/Srcasm to endosomes and the midbody by Tsg101. Cell Struct Funct. 2008;33:91-100 pubmed..Taken into account the topological equivalency among the events of the MVB formation, viral egress from the cell, and cytokinesis, the data obtained here suggest that Tom1L1 is implicated in these three distinct cellular processes. ..
- Higashida C, Suetsugu S, Tsuji T, Monypenny J, Narumiya S, Watanabe N. G-actin regulates rapid induction of actin nucleation by mDia1 to restore cellular actin polymers. J Cell Sci. 2008;121:3403-12 pubmed publisher..Taken together, we propose that transient accumulation of G-actin works as a cue to promote mDia1-catalyzed actin nucleation to execute rapid reassembly of actin filaments. ..
- Rashid N, Cornista J, Ezaki S, Fukui T, Atomi H, Imanaka T. Characterization of an archaeal cyclodextrin glucanotransferase with a novel C-terminal domain. J Bacteriol. 2002;184:777-84 pubmed..In contrast, the cyclization activity of CGT(Tk)DeltaC was abolished. The results indicate that the presence of the structurally novel C-terminal domain is essential for CGT(Tk) to properly catalyze the cyclization reaction...
- Ishikawa H, Yun B, Takahashi S, Hori H, Matts R, Ishimori K, et al. NO-induced activation mechanism of the heme-regulated eIF2alpha kinase. J Am Chem Soc. 2002;124:13696-7 pubmed
- Yonekura K, Maki S, Morgan D, DeRosier D, Vonderviszt F, Imada K, et al. The bacterial flagellar cap as the rotary promoter of flagellin self-assembly. Science. 2000;290:2148-52 pubmed..This represents one of the most dynamic movements in protein structures. ..
- Nishimura M, Kakizaki M, Ono Y, Morimoto K, Takeuchi M, Inoue Y, et al. JEAP, a novel component of tight junctions in exocrine cells. J Biol Chem. 2002;277:5583-7 pubmed..The present results indicate that JEAP is a novel component of TJs, which is specifically expressed in exocrine cells. ..