Experts and Doctors on binding sites in Japan

Summary

Locale: Japan
Topic: binding sites

Top Publications

  1. Sato M, Kitazawa T, Iwai T, Seki J, Sakato N, Kato J, et al. Isolation of chicken-bek and a related gene; identification of structural variation in the ligand-binding domains of the FGF-receptor family. Oncogene. 1991;6:1279-83 pubmed
    ..Furthermore, another bek-like gene was isolated and the expressions of its mRNA and protein product were analysed in tissues and cultured cells. ..
  2. Ye L, Li Y, Fukami Kobayashi K, Go M, Konishi T, Watanabe A, et al. Diversity of a ribonucleoprotein family in tobacco chloroplasts: two new chloroplast ribonucleoproteins and a phylogenetic tree of ten chloroplast RNA-binding domains. Nucleic Acids Res. 1991;19:6485-90 pubmed
    ..The first and second introns interrupt the first CS-RBD and the third intron does the second CS-RBD. The position of the first intron site is the same as that in the human hnRNP A1 protein gene. ..
  3. Miwa Y, Horiguchi T, Shigesada K. Structural and functional dissections of transcription termination factor rho by random mutagenesis. J Mol Biol. 1995;254:815-37 pubmed
  4. Nakamura F, Mino T, Yamamoto J, Naka M, Tanaka T. Identification of the regulatory site in smooth muscle calponin that is phosphorylated by protein kinase C. J Biol Chem. 1993;268:6194-201 pubmed
    ..Thus Thr184 is the preferred site of phosphorylation and is functionally the most important of the sites phosphorylated by protein kinase C in smooth muscle calponin. ..
  5. Matsuda M, Ota S, Tanimura R, Nakamura H, Matuoka K, Takenawa T, et al. Interaction between the amino-terminal SH3 domain of CRK and its natural target proteins. J Biol Chem. 1996;271:14468-72 pubmed
    ..The result suggests that the amino acid at position +1 also contributes to the high affinity binding of the peptides to the SH3 domain of Grb2, but not to that of CRK. ..
  6. Shirayama M, Matsui Y, Toh e A. Dominant mutant alleles of yeast protein kinase gene CDC15 suppress the lte1 defect in termination of M phase and genetically interact with CDC14. Mol Gen Genet. 1996;251:176-85 pubmed
    ..We postulate that the cooperative action of Cdc14 and Cdc15 plays an essential role in the termination of M phase. ..
  7. Asano T, Morishita R, Ueda H, Asano M, Kato K. GTP-binding protein gamma12 subunit phosphorylation by protein kinase C--identification of the phosphorylation site and factors involved in cultured cells and rat tissues in vivo. Eur J Biochem. 1998;251:314-9 pubmed
    ..Phosphorylated gamma12 was also detected in various tissues of untreated rats. Its decrease by pertussis toxin treatment also suggested the involvement of G(i/o) in vivo. ..
  8. Tokunaga C, Kuroda S, Tatematsu K, Nakagawa N, Ono Y, Kikkawa U. Molecular cloning and characterization of a novel protein kinase C-interacting protein with structural motifs related to RBCC family proteins. Biochem Biophys Res Commun. 1998;244:353-9 pubmed
    ..These results suggest that RBCK1 protein might be a transcription factor that has a role in the signaling pathway through PKC. ..
  9. Imada K, Inagaki K, Matsunami H, Kawaguchi H, Tanaka H, Tanaka N, et al. Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 A resolution: the role of Glu88 in the unique substrate-recognition mechanism. Structure. 1998;6:971-82 pubmed
    ..The acidic tip of Glu88 is likely to interact with the nicotinamide mononucleotide (NMN) ribose of NAD+ in the ternary complex. This structure clearly explains the substrate specificity of IPMDH. ..

More Information

Publications483 found, 100 shown here

  1. Kamijo Y, Soma K, Yosimura K, Ohwada T. Acute mercuric chloride poisoning: effect of co-ingested milk on outcome and continued hyperamylasemia. Vet Hum Toxicol. 2001;43:277-9 pubmed
    ..Delayed absorption and weakened corrosive effect may have resulted from the binding of mercuric chloride to thiol-containing proteins in milk, improving the clinical outcome. ..
  2. Yamada S, Ono T, Mizuno A, Nemoto T. A hydrophobic segment within the C-terminal domain is essential for both client-binding and dimer formation of the HSP90-family molecular chaperone. Eur J Biochem. 2003;270:146-54 pubmed
  3. Fujita H, Fujii R, Aratani S, Amano T, Fukamizu A, Nakajima T. Antithetic effects of MBD2a on gene regulation. Mol Cell Biol. 2003;23:2645-57 pubmed
    ..Interestingly, coimmunoprecipitation assays demonstrated that MBD2a binding to RHA was not associated with histone deacetylase 1. Our results indicate a novel role for MBD2a in gene regulation. ..
  4. Kikuchi Y, Uno S, Yoshimura Y, Otabe K, Iida S, Oheda M, et al. A bivalent single-chain Fv fragment against CD47 induces apoptosis for leukemic cells. Biochem Biophys Res Commun. 2004;315:912-8 pubmed
    ..Interestingly, MABL scFv-15 dimer did not cause hemagglutination. This apoptosis-inducing dimer appears to be a lead candidate for novel leukemic therapy. ..
  5. Ohsugi T, Horie R, Kumasaka T, Ishida A, Ishida T, Yamaguchi K, et al. In vivo antitumor activity of the NF-kappaB inhibitor dehydroxymethylepoxyquinomicin in a mouse model of adult T-cell leukemia. Carcinogenesis. 2005;26:1382-8 pubmed
    ..These results suggest that DHMEQ induces apoptosis in HTLV-I-transformed cells in vivo, resulting in inhibition of tumor formation and organ infiltration, thereby enhancing survival. ..
  6. Tamada T, Honjo E, Maeda Y, Okamoto T, Ishibashi M, Tokunaga M, et al. Homodimeric cross-over structure of the human granulocyte colony-stimulating factor (GCSF) receptor signaling complex. Proc Natl Acad Sci U S A. 2006;103:3135-40 pubmed
    ..The Ig-like domain cross-over structure necessary for GCSF-R activation is consistent with previously reported thermodynamic and mutational analyses. ..
  7. Okumura N, Terasawa F, Haneishi A, Fujihara N, Hirota Kawadobora M, Yamauchi K, et al. B:b interactions are essential for polymerization of variant fibrinogens with impaired holes 'a'. J Thromb Haemost. 2007;5:2352-9 pubmed
    ..These results demonstrate that B:b interactions are critical for polymerization of variant fibrinogens with impaired holes 'a'. Based on these data, we propose a model wherein B:b interactions participate in protofibril formation. ..
  8. Yoshida E, Hidaka M, Fushinobu S, Koyanagi T, Minami H, Tamaki H, et al. Role of a PA14 domain in determining substrate specificity of a glycoside hydrolase family 3 ?-glucosidase from Kluyveromyces marxianus. Biochem J. 2010;431:39-49 pubmed publisher
    ..The present study is the first which reveals the structural basis of the interaction between the PA14 domain and a carbohydrate. ..
  9. Okamoto N, Mizote K, Honda H, Saeki A, Watanabe Y, Yamaguchi Miyamoto T, et al. Funiculosin variants and phosphorylated derivatives promote innate immune responses via the Toll-like receptor 4/myeloid differentiation factor-2 complex. J Biol Chem. 2017;292:15378-15394 pubmed publisher
    ..We conclude that FNC-RED and its synthetic derivative represent a novel category of murine and human TLR4/MD-2 agonist. ..
  10. Zhang X, Ohta Y. Antimutagenicity of cell fractions of microorganisms on potent mutagenic pyrolysates. Mutat Res. 1993;298:247-53 pubmed
    ..The cultured broth and freeze-dried cytoplasms of yeast cells showed bio-antimutagenicity towards Trp-P-1, but those of all bacteria tested did not...
  11. Kanazawa H, Fujimoto S, Ohara A. On the mechanism of inactivation of active papain by ascorbic acid in the presence of cupric ions. Biol Pharm Bull. 1994;17:789-93 pubmed
    ..OH), is to promote the conversion of Cu+ into Cu2+, and that an active SH group of papain is site-specifically modified by the .OH, resulting in inactivation of the enzyme...
  12. Yamato I, Kotani M, Oka Y, Anraku Y. Site-specific alteration of arginine 376, the unique positively charged amino acid residue in the mid-membrane-spanning regions of the proline carrier of Escherichia coli. J Biol Chem. 1994;269:5720-4 pubmed
  13. Sugino K, Kurosawa N, Nakamura T, Takio K, Shimasaki S, Ling N, et al. Molecular heterogeneity of follistatin, an activin-binding protein. Higher affinity of the carboxyl-terminal truncated forms for heparan sulfate proteoglycans on the ovarian granulosa cell. J Biol Chem. 1993;268:15579-87 pubmed
  14. Yamaguchi H, Kato H, Hata Y, Nishioka T, Kimura A, Oda J, et al. Three-dimensional structure of the glutathione synthetase from Escherichia coli B at 2.0 A resolution. J Mol Biol. 1993;229:1083-100 pubmed
    ..The ATP binding site is surrounded by two sets of the structural motif that belong to those respective domains. Each motif consists of an anti-parallel beta-sheet and a glycine-rich loop. ..
  15. Hirayama T, Shinozaki K. A cdc5+ homolog of a higher plant, Arabidopsis thaliana. Proc Natl Acad Sci U S A. 1996;93:13371-6 pubmed
    ..In addition, we cloned a PCR fragment corresponding to the DNA binding domain of human Cdc5-like protein. These results strongly suggest that Cdc5-like protein exists in all eukaryotes and may function in cell cycle regulation. ..
  16. Matsumoto A, Masuhara M, Mitsui K, Yokouchi M, Ohtsubo M, Misawa H, et al. CIS, a cytokine inducible SH2 protein, is a target of the JAK-STAT5 pathway and modulates STAT5 activation. Blood. 1997;89:3148-54 pubmed
    ..Thus, CIS is a feedback modulator of STAT5; its expression is induced by STAT5 and it negatively modulates STAT5 activation. ..
  17. Katsutani S, Fujimoto T, Noda M, Shimomura T, Takafuta T, Kimura A, et al. Cloning and characterization of the gene encoding the murine glycoprotein V: the conserved thrombin-cleavable protein on platelet surface. Thromb Res. 1998;92:43-51 pubmed
    ..In the survey of other organs, GPV was not expressed at all. These results demonstrate that GPV is highly conserved, thrombin-cleavable protein beyond the species, and is a specific protein in the platelet-megakaryocyte lineage. ..
  18. Nagata Y, Kiefer F, Watanabe T, Todokoro K. Activation of hematopoietic progenitor kinase-1 by erythropoietin. Blood. 1999;93:3347-54 pubmed
    ..We therefore conclude that Epo induces activation of both HPK1 and HS1, whereas cellular stresses activate only HS1, and that the HPK1-JNK/SAPK pathway is involved in Epo-induced growth and differentiation signals. ..
  19. Yokosaki Y, Matsuura N, Sasaki T, Murakami I, Schneider H, Higashiyama S, et al. The integrin alpha(9)beta(1) binds to a novel recognition sequence (SVVYGLR) in the thrombin-cleaved amino-terminal fragment of osteopontin. J Biol Chem. 1999;274:36328-34 pubmed
    ..These results demonstrate that the linear sequence SVVYGLR directly binds to alpha(9)beta(1) and is responsible for alpha(9)beta(1)-mediated cell adhesion to the NH(2)-terminal fragment of osteopontin. ..
  20. Hibino Y. [Functional arrangement of genomic DNA and structure of nuclear matrix]. Yakugaku Zasshi. 2000;120:520-33 pubmed
    ..We will discuss screening of drugs that interact with nuclear matrix proteins and influence nuclear events. ..
  21. Liu W, Wang J, Mitsui K, Shen H, Tsurugi K. Interaction of the GTS1 gene product with glyceraldehyde- 3-phosphate dehydrogenase 1 required for the maintenance of the metabolic oscillations of the yeast Saccharomyces cerevisiae. Eur J Biochem. 2002;269:3560-9 pubmed
    ..Thus, we hypothesized that Gts1p plays a role in the regulation of metabolic oscillation by interacting with the TDH1 product, GAPDH1, in yeast. ..
  22. Dai P, Shinagawa T, Nomura T, Harada J, Kaul S, Wadhwa R, et al. Ski is involved in transcriptional regulation by the repressor and full-length forms of Gli3. Genes Dev. 2002;16:2843-8 pubmed
    ..Furthermore, a Ski mutation enhanced the digit abnormalities caused by the Gli3 gene mutation. Thus, Ski plays an important role in pattern formation. ..
  23. He L, Ban Y, Miyata S, Kitashiba H, Moriguchi T. Apple aminopropyl transferase, MdACL5 interacts with putative elongation factor 1-alpha and S-adenosylmethionine synthase [corrected]. Biochem Biophys Res Commun. 2008;366:162-7 pubmed
    ..Results from Y2H and RNA gel blot analysis suggested the involvement of MdACL5 and eEF-1A or SAMS complexes in the plant growth and development of the organized tissues and/or organs. ..
  24. Nishimura T, Iino T, Mitsuya M, Bamba M, Watanabe H, Tsukahara D, et al. Identification of novel and potent 2-amino benzamide derivatives as allosteric glucokinase activators. Bioorg Med Chem Lett. 2009;19:1357-60 pubmed publisher
    ..In vivo pharmacokinetic and acute in vivo efficacy studies of compound 18 are also described. ..
  25. Kato Y, Kimoto F, Susa T, Nakayama M, Ishikawa A, Kato T. Pituitary homeodomain transcription factors HESX1 and PROP1 form a heterodimer on the inverted TAAT motif. Mol Cell Endocrinol. 2010;315:168-73 pubmed publisher
  26. Mawaribuchi S, Yoshimoto S, Ohashi S, Takamatsu N, Ito M. Molecular evolution of vertebrate sex-determining genes. Chromosome Res. 2012;20:139-51 pubmed publisher
  27. Bessho T, Morii S, Kusumoto T, Shinohara T, Noda M, Uchiyama S, et al. Characterization of the novel Trypanosoma brucei inosine 5'-monophosphate dehydrogenase. Parasitology. 2013;140:735-45 pubmed publisher
    ..Our results show that TbIMPDH is different from its mammalian counterpart and thus may be a good target for further studies on anti-trypanosomal drugs. ..
  28. Nureki O, Suzuki K, Hara Yokoyama M, Kohno T, Matsuzawa H, Ohta T, et al. Glutamyl-tRNA synthetase from Thermus thermophilus HB8. Molecular cloning of the gltX gene and crystallization of the overproduced protein. Eur J Biochem. 1992;204:465-72 pubmed
    ..The crystals diffract X-rays beyond 0.35 nm. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters of a = 8.64 nm, b = 8.86 nm and c = 8.49 nm. ..
  29. Okano Y, Sugimoto Y, Fukuoka M, Matsui A, Nagata K, Nozawa Y. Identification of rat cDNA encoding hck tyrosine kinase from megakaryocytes. Biochem Biophys Res Commun. 1991;181:1137-44 pubmed
  30. Tao K, Zou C, Fujita N, Ishihama A. Mapping of the OxyR protein contact site in the C-terminal region of RNA polymerase alpha subunit. J Bacteriol. 1995;177:6740-4 pubmed
    ..These results suggest that these two regions comprise the contact surfaces on the alpha subunit for OxyR. ..
  31. Iwata S, Kamata K, Yoshida S, Minowa T, Ohta T. T and R states in the crystals of bacterial L-lactate dehydrogenase reveal the mechanism for allosteric control. Nat Struct Biol. 1994;1:176-85 pubmed
    ..The proposed mechanism can explain activation by chemical modification and mutagenesis, as well as suggesting why vertebrate counterparts are not allosteric...
  32. Song K, Miyazaki M, Okunishi H, Ishii K, Takai S, Shiota N, et al. Localization and quantitation of active renin in monkey kidney by radioinhibitor binding and in vitro autoradiography. Am J Hypertens. 1994;7:529-35 pubmed
    ..This technique permits specific labeling of the catalytic site of renin in the monkey kidney sections. ..
  33. Sato H, Kinoshita T, Takino T, Nakayama K, Seiki M. Activation of a recombinant membrane type 1-matrix metalloproteinase (MT1-MMP) by furin and its interaction with tissue inhibitor of metalloproteinases (TIMP)-2. FEBS Lett. 1996;393:101-4 pubmed
    ..Tissue inhibitor of metalloproteinases (TIMP)-2 inhibited activation of progelatinase A by forming a stable complex with activated MT1-MMP. ..
  34. Osada S, Izawa M, Koyama T, Hirai S, Ohno S. A domain containing the Cdc42/Rac interactive binding (CRIB) region of p65PAK inhibits transcriptional activation and cell transformation mediated by the Ras-Rac pathway. FEBS Lett. 1997;404:227-33 pubmed
    ..PAK/RD is a good tool to investigate the signaling pathways in which Rac and Cdc42 are involved. ..
  35. Itoh K, Chiba T, Takahashi S, Ishii T, Igarashi K, Katoh Y, et al. An Nrf2/small Maf heterodimer mediates the induction of phase II detoxifying enzyme genes through antioxidant response elements. Biochem Biophys Res Commun. 1997;236:313-22 pubmed
    ..The nrf2-deficient mice may prove to be a very useful model for the in vivo analysis of chemical carcinogenesis and resistance to anti-cancer drugs. ..
  36. Kawai T, Matsumoto M, Takeda K, Sanjo H, Akira S. ZIP kinase, a novel serine/threonine kinase which mediates apoptosis. Mol Cell Biol. 1998;18:1642-51 pubmed
    ..Therefore, both ZIP and DAP kinases represent a novel kinase family, which mediates apoptosis through their catalytic activities. ..
  37. Shimizu K, Chiba S, Hosoya N, Kumano K, Saito T, Kurokawa M, et al. Binding of Delta1, Jagged1, and Jagged2 to Notch2 rapidly induces cleavage, nuclear translocation, and hyperphosphorylation of Notch2. Mol Cell Biol. 2000;20:6913-22 pubmed
    ..Moreover, the findings of rapid cleavage, nuclear translocation, and phosphorylation of Notch2 after ligand binding facilitate the understanding of the Notch signaling. ..
  38. Mardy S, Miura Y, Endo F, Matsuda I, Indo Y. Congenital insensitivity to pain with anhidrosis (CIPA): effect of TRKA (NTRK1) missense mutations on autophosphorylation of the receptor tyrosine kinase for nerve growth factor. Hum Mol Genet. 2001;10:179-88 pubmed
    ..Our data may aid in developing a drug which targets the clinically devastating 'complex regional pain syndrome'...
  39. Ozaki Kuroda K, Nakanishi H, Ohta H, Tanaka H, Kurihara H, Mueller S, et al. Nectin couples cell-cell adhesion and the actin scaffold at heterotypic testicular junctions. Curr Biol. 2002;12:1145-50 pubmed
    ..These results indicate that the nectin-afadin system plays essential roles in coupling cell-cell adhesion and the cortical actin scaffold at SspJs and in subsequent sperm morphogenesis. ..
  40. Marui J, Kitamoto N, Kato M, Kobayashi T, Tsukagoshi N. Transcriptional activator, AoXlnR, mediates cellulose-inductive expression of the xylanolytic and cellulolytic genes in Aspergillus oryzae. FEBS Lett. 2002;528:279-82 pubmed
    ..Moreover, AoXlnR was newly found to mediate the cellulose-inductive expression of the xylanolytic genes as well as the cellulolytic genes. ..
  41. Watanabe S, Ichimura T, Fujita N, Tsuruzoe S, Ohki I, Shirakawa M, et al. Methylated DNA-binding domain 1 and methylpurine-DNA glycosylase link transcriptional repression and DNA repair in chromatin. Proc Natl Acad Sci U S A. 2003;100:12859-64 pubmed
    ..These data suggest that MBD1 cooperates with MPG for transcriptional repression and DNA repair. We hypothesize that MBD1 functions as a reservoir for MPG and senses the base damage in chromatin ..
  42. Tanaka T, Okuda T, Yamamoto Y. Characterization of the CYP3A4 active site by homology modeling. Chem Pharm Bull (Tokyo). 2004;52:830-5 pubmed
    ..These results suggest that this model is reliable enough to be used in the design of compounds for removing undesirable CYP3A4 inhibition. ..
  43. Murakami S, Nakashima R, Yamashita E, Matsumoto T, Yamaguchi A. Crystal structures of a multidrug transporter reveal a functionally rotating mechanism. Nature. 2006;443:173-9 pubmed
    ..The voluminous binding pocket is aromatic and allows multi-site binding. The structures indicate that drugs are exported by a three-step functionally rotating mechanism in which substrates undergo ordered binding change. ..
  44. Inomata K, Khawn H, Chen L, Kinoshita H, Zienicke B, Molina I, et al. Assembly of Agrobacterium phytochromes Agp1 and Agp2 with doubly locked bilin chromophores. Biochemistry. 2009;48:2817-27 pubmed publisher
    ..In Agp1, the Pfr chromophore is most likely in the C5 Z anti stereochemistry. We propose that the stereochemistry of the C5 methine bridge might differ between different phytochromes, most particularly in the Pfr form. ..
  45. Otagiri M. [Study on binding of drug to serum protein]. Yakugaku Zasshi. 2009;129:413-25 pubmed
    ..Finally, cases in which protein binding displacement can be applied to medical fields will also be introduced. ..
  46. Sakurai T, Misaka T, Ishiguro M, Masuda K, Sugawara T, Ito K, et al. Characterization of the beta-D-glucopyranoside binding site of the human bitter taste receptor hTAS2R16. J Biol Chem. 2010;285:28373-8 pubmed publisher
    ..This study characterizes the molecular interaction between hTAS2R16 and beta-D-glucopyranoside and will also facilitate rational design of bitter blockers...
  47. Takahashi K, Tagami U, Shimba N, Kashiwagi T, Ishikawa K, Suzuki E. Crystal structure of Bifidobacterium Longum phosphoketolase; key enzyme for glucose metabolism in Bifidobacterium. FEBS Lett. 2010;584:3855-61 pubmed publisher
    ..In silico docking studies of B. longum phosphoketolase with its substrate enable us to propose a model for substrate binding. ..
  48. Yanagita H, Urano E, Matsumoto K, Ichikawa R, Takaesu Y, Ogata M, et al. Structural and biochemical study on the inhibitory activity of derivatives of 5-nitro-furan-2-carboxylic acid for RNase H function of HIV-1 reverse transcriptase. Bioorg Med Chem. 2011;19:816-25 pubmed publisher
    ..Since there is still much room for modification of the compounds at the part opposite the nitro-furan moiety, further chemical conversion will lead to improvement of compound potency and specificity. ..
  49. Fujisawa M, Nakano T, Ito Y. Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation. BMC Plant Biol. 2011;11:26 pubmed publisher
    ..These findings clarify the crucial role of RIN in the transcriptional regulation of ripening initiation and progression. ..
  50. Wei T, Miyazaki N, Uehara Ichiki T, Hibino H, Shimizu T, Netsu O, et al. Three-dimensional analysis of the association of viral particles with mitochondria during the replication of Rice gall dwarf virus. J Mol Biol. 2011;410:436-46 pubmed publisher
    ..Our analysis demonstrates the three-dimensional arrangement and molecular basis for the mitochondrial proximity of RGDV particles during viral replication. ..
  51. Fujimoto Z, Suzuki N, Kishine N, Ichinose H, Momma M, Kimura A, et al. Carbohydrate-binding architecture of the multi-modular ?-1,6-glucosyltransferase from Paenibacillus sp. 598K, which produces ?-1,6-glucosyl-?-glucosaccharides from starch. Biochem J. 2017;474:2763-2778 pubmed publisher
    ..Ps6TG31A appears to have enhanced transglucosylation activity facilitated by its carbohydrate-binding modules and substrate-binding cleft that positions the substrate and acceptor sugar for the transglucosylation. ..
  52. Matsuoka Y, Nishizawa K, Yano T, Shibata M, Ando S, Takahashi T, et al. Two different protein kinases act on a different time schedule as glial filament kinases during mitosis. EMBO J. 1992;11:2895-902 pubmed
    ..These results suggest that cdc2 kinase acts as a glial filament kinase only at the G2-M phase transition while other glial filament kinases are probably activated at the cleavage furrow before final separation of the daughter cells. ..
  53. Mizuno H, Morimoto Y, Tsukihara T, Matsumoto T, Takase K. Crystallization and preliminary X-ray studies of wild type and catalytic-site mutant alpha-amylase from Bacillus subtilis. J Mol Biol. 1993;234:1282-3 pubmed
    ..6 A, b = 74.4 A, c = 116.7 A. Structural studies of both wild-type and mutant proteins will provide a basis for understanding the catalytic mechanism of alpha-amylase. ..
  54. Hu C, Kariya K, Tamada M, Akasaka K, Shirouzu M, Yokoyama S, et al. Cysteine-rich region of Raf-1 interacts with activator domain of post-translationally modified Ha-Ras. J Biol Chem. 1995;270:30274-7 pubmed
    ..These results suggest that the activator domain of Ha-Ras participates in activation of Raf-1 through interaction with CRR and that post-translational modifications of Ha-Ras are required for this interaction. ..
  55. Fujii Y, Shimizu T, Kusumoto M, Kyogoku Y, Taniguchi T, Hakoshima T. Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences. EMBO J. 1999;18:5028-41 pubmed
    ..Our results provide new insights into the structure and function of this family of transcription factors. ..
  56. Takeba Y, Nagafuchi H, Takeno M, Kashiwakura J, Suzuki N. Txk, a member of nonreceptor tyrosine kinase of Tec family, acts as a Th1 cell-specific transcription factor and regulates IFN-gamma gene transcription. J Immunol. 2002;168:2365-70 pubmed
    ..Thus, Txk is expressed on Th1/Th0 cells with the IFN-gamma production and acts as a Th1 cell-specific transcription factor. ..
  57. Sugimoto H, Sugahara M, FOLSCH H, Koide Y, Nakatsu F, Tanaka N, et al. Differential recognition of tyrosine-based basolateral signals by AP-1B subunit mu1B in polarized epithelial cells. Mol Biol Cell. 2002;13:2374-82 pubmed
    ..Our results suggest that mu1B interacts with different classes of basolateral targeting signals in distinct ways. ..
  58. Fujimoto Z, Kaneko S, Kuno A, Kobayashi H, Kusakabe I, Mizuno H. Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86. J Biol Chem. 2004;279:9606-14 pubmed
    ..CBM13 was shown to bind xylose or xylooligosaccharides reversibly by using nonsymmetric sugars as the ligands. The independent multiple sites in CBM13 may increase the probability of substrate binding...
  59. Sakamoto H, Maruyama K, Sakuma Y, Meshi T, Iwabuchi M, Shinozaki K, et al. Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high-salinity stress conditions. Plant Physiol. 2004;136:2734-46 pubmed
    ..These results suggest that AZF2 and STZ function as transcriptional repressors to increase stress tolerance following growth retardation. ..
  60. Katoh M, Katoh M. Comparative genomics on Wnt7a orthologs. Oncol Rep. 2005;13:777-80 pubmed
    ..Therefore, biological functions of rodent Wnt7a are not always consistent with those of human WNT7A due to promoter evolution. This is the first report on the rat Wnt7a gene and comparative genomics for Wnt7a orthologs. ..
  61. Shiba T, Kakuda S, Ishiguro M, Morita I, Oka S, Kawasaki T, et al. Crystal structure of GlcAT-S, a human glucuronyltransferase, involved in the biosynthesis of the HNK-1 carbohydrate epitope. Proteins. 2006;65:499-508 pubmed
  62. Enoki Y, Sakurai H. Diversity in DNA recognition by heat shock transcription factors (HSFs) from model organisms. FEBS Lett. 2011;585:1293-8 pubmed publisher
    ..Further analysis of alternatively spliced HSF isoforms showed the importance of the C-terminal region in HSF-HSE interaction. ..
  63. Someya T, Baba S, Fujimoto M, Kawai G, Kumasaka T, Nakamura K. Crystal structure of Hfq from Bacillus subtilis in complex with SELEX-derived RNA aptamer: insight into RNA-binding properties of bacterial Hfq. Nucleic Acids Res. 2012;40:1856-67 pubmed publisher
    ..These findings provide novel insight into how the Hfq homologue recognizes RNA. ..
  64. Yamada T, Kurihara K, Ohnishi Y, Tamada T, Tomoyori K, Masumi K, et al. Neutron and X-ray crystallographic analysis of the human ?-thrombin-bivalirudin complex at pD 5.0: protonation states and hydration structure of the enzyme-product complex. Biochim Biophys Acta. 2013;1834:1532-8 pubmed publisher
    ..In addition to the active site, the hydration structures of the S1 subsite and the Exosite I, which are involved in the recognition of bivalirudin, are presented. ..
  65. Satou Y, Miyazato P, Ishihara K, Yaguchi H, Melamed A, Miura M, et al. The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome. Proc Natl Acad Sci U S A. 2016;113:3054-9 pubmed publisher
    ..The presence of an ectopic CTCF-BS introduced by the retrovirus in tens of thousands of genomic locations has the potential to cause widespread abnormalities in host cell chromatin structure and gene expression. ..
  66. Watanabe K, Kitamura K, Iha H, Suzuki Y. Primary structure of the oligo-1,6-glucosidase of Bacillus cereus ATCC7064 deduced from the nucleotide sequence of the cloned gene. Eur J Biochem. 1990;192:609-20 pubmed
    ..carlsbergensis alpha-glucosidase and Aspergillus oryzae alpha-amylase. ..
  67. Ushida C, Aiba H. Helical phase dependent action of CRP: effect of the distance between the CRP site and the -35 region on promoter activity. Nucleic Acids Res. 1990;18:6325-30 pubmed
    ..We conclude that stereospecific positioning of CRP and RNA polymerase on the DNA helix is strictly required for CRP action. The data support a model that CRP stimulates transcription by directly contacting RNA polymerase. ..
  68. Makino Y, Yamamoto K, Tsuji T. Specific lectin bindings to oval cells and proliferated bile ductules. Gastroenterol Jpn. 1988;23:658-65 pubmed
  69. Takeshima H, Yamazawa T, Ikemoto T, Takekura H, Nishi M, Noda T, et al. Ca(2+)-induced Ca2+ release in myocytes from dyspedic mice lacking the type-1 ryanodine receptor. EMBO J. 1995;14:2999-3006 pubmed
    ..Although RyR-3 does not mediate excitation-contraction coupling of the skeletal muscle type, we propose that RyR-3 may induce intracellular Ca2+ release in response to a Ca2+ rise with a high threshold. ..
  70. Imamura Y, Koga T, Higuchi T, Otagiri M, Sugino E, Hibino S, et al. Catalytic properties of carbonyl reductase from rabbit liver for analogs of acetohexamide and 4-acetylpyridine. Biochem Mol Biol Int. 1994;33:893-9 pubmed
    ..It is reasonable to postulate that a hydrophobic pocket is located in the substrate-binding domain of the enzyme. ..
  71. Suzuki H, Kishimoto K, Yoshimoto T, Yamamoto S, Kanai F, Ebina Y, et al. Site-directed mutagenesis studies on the iron-binding domain and the determinant for the substrate oxygenation site of porcine leukocyte arachidonate 12-lipoxygenase. Biochim Biophys Acta. 1994;1210:308-16 pubmed
    ..A double mutation of Val-418 and -419 to Ile and Met increased the ratio of 15- and 12-lipoxygenase activities from 0.1 to 5.7. ..
  72. Totsuka A, Fukazawa C. Expression and mutation of soybean beta-amylase in Escherichia coli. Eur J Biochem. 1993;214:787-94 pubmed
    ..Therefore, neither His93 nor Asp348 may participate in the catalytic reaction directly. ..
  73. Tanaka T, Oda J, Yamaguchi H, Katsube Y. [Structural and functional analysis on glutathione-synthetase]. Tanpakushitsu Kakusan Koso. 1993;38:1579-88 pubmed
  74. Kim S, Makino K, Amemura M, Shinagawa H, Nakata A. Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli. J Bacteriol. 1993;175:1316-24 pubmed
    ..Transcription from the P1 promoter required the phoB function and was induced by phosphate limitation, while transcription from the P2 promoter was independent of phoB and constitutive under tested conditions. ..
  75. Igarashi K, Isohara T, Kato T, Shigeta K, Yamano T, Uno I. Tyrosine 1213 of Flt-1 is a major binding site of Nck and SHP-2. Biochem Biophys Res Commun. 1998;246:95-9 pubmed
    ..Nck also binds to Y1333 of Flt-1. These results suggest that Nck, SHP-2, PLC gamma, and PI3K play important roles in Flt-1 signal transduction and that Y1213 of Flt-1 is a major binding site of PI3K, Nck, and SHP-2. ..
  76. Suzuki H, Nishiyama K, Tokuda H. Coupled structure changes of SecA and SecG revealed by the synthetic lethality of the secAcsR11 and delta secG::kan double mutant. Mol Microbiol. 1998;29:331-41 pubmed
    ..We conclude that SecG and SecA undergo a coupled structure change, that is critical for efficient protein translocation. ..
  77. Kato M, Mizuno T, Shimizu T, Hakoshima T. Refined structure of the histidine-containing phosphotransfer (HPt) domain of the anaerobic sensor kinase ArcB from Escherichia coli at 1.57 A resolution. Acta Crystallogr D Biol Crystallogr. 1999;55:1842-9 pubmed
    ..One water molecule was buried in the protein core and contributed to the rigidity of the HPt domain, cooperating in the coordination of the zinc ion. ..
  78. Sakakibara H, Hayakawa A, Deji A, Gawronski S, Sugiyama T. His-Asp phosphotransfer possibly involved in the nitrogen signal transduction mediated by cytokinin in maize: molecular cloning of cDNAs for two-component regulatory factors and demonstration of phosphotransfer activity in vitro. Plant Mol Biol. 1999;41:563-73 pubmed
    ..These results indicate that His-Asp phosphotransfer may be involved in the transduction of nitrogen signals mediated by cytokinin, and that multiple response regulators participate in the signaling pathways. ..
  79. Inoshita S, Takeda K, Hatai T, Terada Y, Sano M, Hata J, et al. Phosphorylation and inactivation of myeloid cell leukemia 1 by JNK in response to oxidative stress. J Biol Chem. 2002;277:43730-4 pubmed
    ..JNK-dependent phosphorylation and thus inactivation of Mcl-1 may be one of the mechanisms through which oxidative stress induces cellular damage. ..
  80. Chuang V, Otagiri M. How do fatty acids cause allosteric binding of drugs to human serum albumin?. Pharm Res. 2002;19:1458-64 pubmed
    ..4-kDa peptide was observed. Long-chain fatty acids regulate the binding properties of HSA in a complex manner, in which a simultaneous competitive and allosteric mechanism operates and which mainly involves domain I. ..
  81. Samata K, Yamagishi T, Ichihara T, Nanaumi K, Ikeda T, Ikeya H, et al. Establishment and characterization of a mouse FM3A cell mutant resistant to topoisomerase II-inhibitor NC-190. Cancer Chemother Pharmacol. 2002;50:367-72 pubmed
    ..These results indicate that the NC-190-resistant cell line FM/NC-R contains a mutated DNA topoisomerase IIalpha. ..
  82. Fujita M, Fujita Y, Maruyama K, Seki M, Hiratsu K, Ohme Takagi M, et al. A dehydration-induced NAC protein, RD26, is involved in a novel ABA-dependent stress-signaling pathway. Plant J. 2004;39:863-76 pubmed
    ..Furthermore, RD26 activated a promoter of its target gene in Arabidopsis protoplasts. These results indicate that RD26 functions as a transcriptional activator in ABA-inducible gene expression under abiotic stress in plants. ..
  83. Iitaka C, Miyazaki K, Akaike T, Ishida N. A role for glycogen synthase kinase-3beta in the mammalian circadian clock. J Biol Chem. 2005;280:29397-402 pubmed
    ..Recombinant GSK-3beta can phosphorylate PER2 in vitro. GSK-3beta promotes the nuclear translocation of PER2 in COS1 cells. The present data suggest that GSK-3beta plays important roles in mammalian circadian clock. ..
  84. Katoh M, Katoh M. Integrative genomic analyses of WNT11: transcriptional mechanisms based on canonical WNT signals and GATA transcription factors signaling. Int J Mol Med. 2009;24:247-51 pubmed
    ..Canonical WNT-to-WNT11 signaling loop is involved in cellular migration during embryogenesis as well as tumor invasion during carcinogenesis. ..
  85. Yoshida T, Tsuge H, Konno H, Hisabori T, Sugano Y. The catalytic mechanism of dye-decolorizing peroxidase DyP may require the swinging movement of an aspartic acid residue. FEBS J. 2011;278:2387-94 pubmed publisher
    ..On the basis of these results, we propose a swing mechanism in compound I formation. When DyP reacts with hydrogen peroxide, OD2 swings towards an optimal position to accept the proton from hydrogen peroxide bound to the heme iron. ..
  86. Suzuki T, Yoshinaga N, Tanabe S. Interleukin-6 (IL-6) regulates claudin-2 expression and tight junction permeability in intestinal epithelium. J Biol Chem. 2011;286:31263-71 pubmed publisher
    ..IL-6 increases Cdx2 protein expression, which is suppressed by the inhibition of MEK and PI3K. These observations may reveal an important mechanism by which IL-6 can undermine the integrity of the intestinal barrier. ..
  87. Shinoda Y, Fujita K, Saito S, Matsui H, Kanto Y, Nagaura Y, et al. Acyl-CoA binding domain containing 3 (ACBD3) recruits the protein phosphatase PPM1L to ER-Golgi membrane contact sites. FEBS Lett. 2012;586:3024-9 pubmed publisher
    ..These results suggested that ACBD3 plays a pivotal role in ceramide transport regulation at the ER-Golgi interface. ..
  88. Yamada M, Tamada T, Takeda K, Matsumoto F, Ohno H, Kosugi M, et al. Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: new insights into regulation of efficient electron transfer. J Mol Biol. 2013;425:4295-306 pubmed publisher
    ..Furthermore, crystallographic analysis by the cryo-trapping method suggests that re-oxidation follows a two-step mechanism. These results provide structural insights into the catalytic cycle of b5R. ..
  89. Kumagai K, Kawano Kawada M, Hanada K. Phosphoregulation of the ceramide transport protein CERT at serine 315 in the interaction with VAMP-associated protein (VAP) for inter-organelle trafficking of ceramide in mammalian cells. J Biol Chem. 2014;289:10748-60 pubmed publisher
  90. Nakano N, Maeyama K, Sakata N, Itoh F, Akatsu R, Nakata M, et al. C18 ORF1, a novel negative regulator of transforming growth factor-? signaling. J Biol Chem. 2014;289:12680-92 pubmed publisher
    ..Thus, we defined C18ORF1 as a surveillant of steady state TGF-? signaling, whereas TMEPAI might help C18ORF1 to inhibit TGF-? signaling in a coordinated manner when cells are stimulated with high levels of TGF-?. ..
  91. Aihara H, Ito Y, Kurumizaka H, Terada T, Yokoyama S, Shibata T. An interaction between a specified surface of the C-terminal domain of RecA protein and double-stranded DNA for homologous pairing. J Mol Biol. 1997;274:213-21 pubmed
    ..Combined with our previous results, these provide direct evidence that the defined region in the C-terminal domain furnishes a binding surface for DNA. ..
  92. Tanimura S, Ohtsuka S, Mitsui K, Shirouzu K, Yoshimura A, Ohtsubo M. MDM2 interacts with MDMX through their RING finger domains. FEBS Lett. 1999;447:5-9 pubmed
    ..Interaction of MDMX with MDM2 through the C-terminal RING finger domains resulted in inhibiting degradation of MDM2. These data indicate that MDMX functions as a regulator of MDM2. ..