Experts and Doctors on x ray crystallography in Suita, Ōsaka, Japan


Locale: Suita, Ōsaka, Japan
Topic: x ray crystallography

Top Publications

  1. Nakagawa A, Miyazaki N, Taka J, Naitow H, Ogawa A, Fujimoto Z, et al. The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins. Structure. 2003;11:1227-38 pubmed
    ..These interactions suggest how the 900 protein components are built into a higher-ordered virus core structure. ..
  2. Sugiyama S, Vassylyev D, Matsushima M, Kashiwagi K, Igarashi K, Morikawa K. Crystal structure of PotD, the primary receptor of the polyamine transport system in Escherichia coli. J Biol Chem. 1996;271:9519-25 pubmed
  3. Uchida T, Yamasaki T, Eto S, Sugawara H, Kurisu G, Nakagawa A, et al. Crystal structure of the hemolytic lectin CEL-III isolated from the marine invertebrate Cucumaria echinata: implications of domain structure for its membrane pore-formation mechanism. J Biol Chem. 2004;279:37133-41 pubmed
    ..This conformational change may be responsible for oligomerization of CEL-III molecules and hemolysis in the erythrocyte membranes. ..
  4. You D, Fukuchi S, Nishikawa K, Koga Y, Takano K, Kanaya S. Protein thermostabilization requires a fine-tuned placement of surface-charged residues. J Biochem. 2007;142:507-16 pubmed
    ..This result suggests that charged residues of natural thermostable proteins are strictly posted on the surface with optimal interactions and without repulsive interactions. ..
  5. Tsunaka Y, Takano K, Matsumura H, Yamagata Y, Kanaya S. Identification of single Mn(2+) binding sites required for activation of the mutant proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray crystallography. J Mol Biol. 2005;345:1171-83 pubmed
    ..The binding position of the first manganese ion is probably forced to shift to site 1 or site 2 upon binding of the second manganese ion. ..
  6. Unno H, Ichimaida F, Suzuki H, Takahashi S, Tanaka Y, Saito A, et al. Structural and mutational studies of anthocyanin malonyltransferases establish the features of BAHD enzyme catalysis. J Biol Chem. 2007;282:15812-22 pubmed
  7. Tanaka S, Matsumura H, Koga Y, Takano K, Kanaya S. Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation. J Mol Biol. 2007;372:1055-69 pubmed publisher
    ..65 A resolution. This structure is virtually identical with that of the autoprocessed form, indicating that the interaction between the two domains is highly intensive and specific...
  8. Takahashi R, Nakamura S, Nakazawa T, Minoura K, Yoshida T, Nishi Y, et al. Structure and reaction mechanism of human nicotinamide phosphoribosyltransferase. J Biochem. 2010;147:95-107 pubmed publisher
    ..The structures and catalytic mechanism thus revealed are also discussed in connection with the multiple biological functions of NMPRTase. ..
  9. Ogawa A, Takayama Y, Sakai H, Chong K, Takeuchi S, Nakagawa A, et al. Structure of the carboxyl-terminal Src kinase, Csk. J Biol Chem. 2002;277:14351-4 pubmed
    ..These observations suggest that Csk can be regulated through coupling of the SH2 and kinase domains and that Csk provides a novel built-in activation mechanism for cytoplasmic tyrosine kinases. ..

More Information


  1. Satoh A, Konishi S, Tamura H, Stickland H, Whitney H, Smith A, et al. Substrate-induced closing of the active site revealed by the crystal structure of pantothenate synthetase from Staphylococcus aureus. Biochemistry. 2010;49:6400-10 pubmed publisher
    ..Therefore, the complex structure seems to represent a catalytic state poised for in-line nucleophilic attack on PA. These data also offer an alternative strategy for designing novel compounds that selectively inhibit PS activity. ..
  2. Ariyoshi M, Nishino T, Iwasaki H, Shinagawa H, Morikawa K. Crystal structure of the holliday junction DNA in complex with a single RuvA tetramer. Proc Natl Acad Sci U S A. 2000;97:8257-62 pubmed
  3. Tanaka S, Matsumura H, Koga Y, Takano K, Kanaya S. Identification of the interactions critical for propeptide-catalyzed folding of Tk-subtilisin. J Mol Biol. 2009;394:306-19 pubmed publisher
    ..We propose that Glu201-mediated interactions are critical for initiation of Tkpro-catalyzed folding of Tk-subtilisin. ..
  4. Kurisu G, Nishiyama D, Kusunoki M, Fujikawa S, Katoh M, Hanke G, et al. A structural basis of Equisetum arvense ferredoxin isoform II producing an alternative electron transfer with ferredoxin-NADP+ reductase. J Biol Chem. 2005;280:2275-81 pubmed
    ..The structural differences between FdI and FdII therefore result in functional differences that may influence partitioning of electrons into different redox metabolic pathways...
  5. Akita F, Chong K, Tanaka H, Yamashita E, Miyazaki N, Nakaishi Y, et al. The crystal structure of a virus-like particle from the hyperthermophilic archaeon Pyrococcus furiosus provides insight into the evolution of viruses. J Mol Biol. 2007;368:1469-83 pubmed
    ..The structure of PfV provides a previously undescribed example of viral relationships across the three domains of life (Eukarya, Bacteria, and Archaea). ..
  6. Katsumi R, Koga Y, You D, Matsumura H, Takano K, Kanaya S. Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007;63:126-9 pubmed
    ..7 A(3) Da(-1) and the solvent content was 54.1%. The protein was also cocrystallized with substrates and diffraction data were collected to 2.7 A resolution. ..
  7. Li S, Nakagawa A, Tsukihara T. Ni2+ binds to active site of hen egg-white lysozyme and quenches fluorescence of Trp62 and Trp108. Biochem Biophys Res Commun. 2004;324:529-33 pubmed
    ..Based on these results, we have proposed that Ni2+ quenches the fluorescence of Trp62 and Trp108 due to the binding of Ni2+ to the active site of lysozyme. ..
  8. Takano K, Katagiri Y, Mukaiyama A, Chon H, Matsumura H, Koga Y, et al. Conformational contagion in a protein: structural properties of a chameleon sequence. Proteins. 2007;68:617-25 pubmed publisher
    ..We propose this "conformational contagion" as a new nonlocal determinant factor in protein structure and misfolding related to protein conformational diseases...
  9. Miyazaki N, Hagiwara K, Naitow H, Higashi T, Cheng R, Tsukihara T, et al. Transcapsidation and the conserved interactions of two major structural proteins of a pair of phytoreoviruses confirm the mechanism of assembly of the outer capsid layer. J Mol Biol. 2005;345:229-37 pubmed publisher
    ..This is the first report on the molecular biological proof of the mechanism of the assembly of the double-layered capsids with disparate icosahedral lattices...
  10. Tanaka M, Chon H, Angkawidjaja C, Koga Y, Takano K, Kanaya S. Protein core adaptability: crystal structures of the cavity-filling variants of Escherichia coli RNase HI. Protein Pept Lett. 2010;17:1163-9 pubmed
  11. Aoki S, Watanabe Y, Sanagawa M, Setiawan A, Kotoku N, Kobayashi M. Cortistatins A, B, C, and D, anti-angiogenic steroidal alkaloids, from the marine sponge Corticium simplex. J Am Chem Soc. 2006;128:3148-9 pubmed
    ..0018 muM) against HUVECs, in which the selective index was more than 3000-fold in comparison with that of normal fibroblast or several tumor cell lines. ..
  12. Tanaka S, Takeuchi Y, Matsumura H, Koga Y, Takano K, Kanaya S. Crystal structure of Tk-subtilisin folded without propeptide: requirement of propeptide for acceleration of folding. FEBS Lett. 2008;582:3875-8 pubmed publisher
    ..17 and 1.8min(-1) at 30 degrees C in the absence and presence of Tk-propeptide, respectively, indicating that Tk-subtilisin does not require Tk-propeptide for folding but requires it for acceleration of folding. ..
  13. Yagi H, Kajiwara N, Iwabuchi T, Izumi K, Yoshida M, Akutsu H. Stepwise propagation of the ATP-induced conformational change of the F1-ATPase beta subunit revealed by NMR. J Biol Chem. 2009;284:2374-82 pubmed publisher
    ..Actually, MgATP induced a conformational change around Tyr-307 (311 for MF1beta), whereas MgADP did not. The significance of these findings is discussed in connection with the catalytic rotation of F1-ATPase. ..
  14. Bando S, Takano T, Yubisui T, Shirabe K, Takeshita M, Nakagawa A. Structure of human erythrocyte NADH-cytochrome b5 reductase. Acta Crystallogr D Biol Crystallogr. 2004;60:1929-34 pubmed
    ..The structures around 15 mutation sites of the human reductase have been examined for the influence of residue substitutions using the program ROTAMER. Five mutations in the FAD-binding domain seem to be related to cytochrome b(5). ..
  15. Nishino T, Komori K, Ishino Y, Morikawa K. Dissection of the regional roles of the archaeal Holliday junction resolvase Hjc by structural and mutational analyses. J Biol Chem. 2001;276:35735-40 pubmed publisher
  16. Apostolov R, Yonezawa Y, Standley D, Kikugawa G, Takano Y, Nakamura H. Membrane attachment facilitates ligand access to the active site in monoamine oxidase A. Biochemistry. 2009;48:5864-73 pubmed publisher
    ..Our results are also in accordance with mutational analysis which shows that modifications of interdomain hinge residues decrease the activity of rat MAOA in solution. ..
  17. Tamura H, Saito Y, Ashida H, Kai Y, Inoue T, Yokota A, et al. Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis. Acta Crystallogr D Biol Crystallogr. 2009;65:942-51 pubmed publisher
    ..Based on these results, the characteristic structural features of DK-MTP-1P enolase are discussed. ..
  18. Ohta K, Muramoto K, Shinzawa Itoh K, Yamashita E, Yoshikawa S, Tsukihara T. X-ray structure of the NO-bound Cu(B) in bovine cytochrome c oxidase. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010;66:251-3 pubmed publisher
    ..Electron density for the NO molecule was observed close to Cu(B). The refined structure indicates that NO is bound to Cu(B) in a side-on manner. ..
  19. Okada C, Yamashita E, Lee S, Shibata S, Katahira J, Nakagawa A, et al. A high-resolution structure of the pre-microRNA nuclear export machinery. Science. 2009;326:1275-9 pubmed publisher
    ..RNA recognition by Exp-5:RanGTP does not depend on RNA sequence, implying that Exp-5:RanGTP can recognize a variety of pre-miRNAs. ..
  20. Tamura H, Ashida H, Koga S, Saito Y, Yadani T, Kai Y, et al. Crystallization and preliminary X-ray analysis of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:147-50 pubmed publisher
    ..3, b = 91.5, c = 107.0 A, beta = 90.8 degrees. The asymmetric unit contained four molecules of DK-MTP-1P enolase, with a V(M) value of 2.2 A(3) Da(-1) and a solvent content of 43%. ..
  21. Mukai Y, Shibata H, Nakamura T, Yoshioka Y, Abe Y, Nomura T, et al. Structure-function relationship of tumor necrosis factor (TNF) and its receptor interaction based on 3D structural analysis of a fully active TNFR1-selective TNF mutant. J Mol Biol. 2009;385:1221-9 pubmed publisher
    ..This phage display technique can be used to efficiently construct functional mutants for analysis of the TNF structure-function relationship, which might facilitate in silico drug design based on receptor selectivity. ..
  22. Ishikawa M, Tsuchiya D, Oyama T, Tsunaka Y, Morikawa K. Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex. EMBO J. 2004;23:2745-54 pubmed
    ..This channelling mechanism could be applied to other beta-oxidation multienzymes, as revealed from the homology model of the human mitochondrial trifunctional enzyme complex. ..
  23. Wakamatsu T, Kitamura Y, Kotera Y, Nakagawa N, Kuramitsu S, Masui R. Structure of RecJ exonuclease defines its specificity for single-stranded DNA. J Biol Chem. 2010;285:9762-9 pubmed publisher
    ..In addition, the structure of the RecJ-Mn(2+) complex suggests that the hydrolysis reaction catalyzed by RecJ proceeds through a two-metal ion mechanism. ..
  24. You D, Chon H, Koga Y, Takano K, Kanaya S. Crystal structure of type 1 ribonuclease H from hyperthermophilic archaeon Sulfolobus tokodaii: role of arginine 118 and C-terminal anchoring. Biochemistry. 2007;46:11494-503 pubmed
  25. Ishino S, Oyama T, Yuasa M, Morikawa K, Ishino Y. Mutational analysis of Pyrococcus furiosus replication factor C based on the three-dimensional structure. Extremophiles. 2003;7:169-75 pubmed
    ..These results contribute to our general understanding of the structure-function relationship of the RFC molecule for the clamp-loading event. ..
  26. Son S, Ma J, Kondou Y, Yoshimura M, Yamashita E, Tsukihara T. Structure of human monoamine oxidase A at 2.2-A resolution: the control of opening the entry for substrates/inhibitors. Proc Natl Acad Sci U S A. 2008;105:5739-44 pubmed publisher
    ..We report on the observation of the structure-function relationship between a transmembrane helical anchor and an extra-membrane domain. ..
  27. Kimata Ariga Y, Kurisu G, Kusunoki M, Aoki S, Sato D, Kobayashi T, et al. Cloning and characterization of ferredoxin and ferredoxin-NADP+ reductase from human malaria parasite. J Biochem. 2007;141:421-8 pubmed
    ..falciparum Fd in a reconstituted system of NADPH-dependent cytochrome c reduction. These results indicate that an NADPH-FNR-Fd cascade is operative in the apicoplast of human malaria parasites. ..
  28. Saijo Hamano Y, Imada K, Minamino T, Kihara M, Shimada M, Kitao A, et al. Structure of the cytoplasmic domain of FlhA and implication for flagellar type III protein export. Mol Microbiol. 2010;76:260-8 pubmed publisher
    ..These results along with further mutation analyses suggest that a dynamic domain motion of FlhA(C) is essential for protein export...
  29. Ben Ammar Y, Takeda S, Sugawara M, Miyano M, Mori H, Wakabayashi S. Crystallization and preliminary crystallographic analysis of the human calcineurin homologous protein CHP2 bound to the cytoplasmic region of the Na+/H+ exchanger NHE1. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:956-8 pubmed
    ..The crystals diffract to 2.7 A and belong to a tetragonal space group, with unit-cell parameters a = b = 49.96, c = 103.20 A. ..
  30. Sugi T, Oyama T, Muto T, Nakanishi S, Morikawa K, Jingami H. Crystal structures of autoinhibitory PDZ domain of Tamalin: implications for metabotropic glutamate receptor trafficking regulation. EMBO J. 2007;26:2192-205 pubmed
    ..Our study suggests a novel regulatory mechanism of the PDZ domain, by which Tamalin switches between the trafficking-inhibited and -active forms depending on mGluR association. ..
  31. Angkawidjaja C, Matsumura H, Koga Y, Takano K, Kanaya S. X-ray crystallographic and MD simulation studies on the mechanism of interfacial activation of a family I.3 lipase with two lids. J Mol Biol. 2010;400:82-95 pubmed publisher
    ..These results suggest that Ca1 functions as a hook for stabilization of a fully opened conformation of lid1 and for initiation of subsequent opening of lid2. ..
  32. Tsukihara T, Aoyama H, Yamashita E, Tomizaki T, Yamaguchi H, Shinzawa Itoh K, et al. The whole structure of the 13-subunit oxidized cytochrome c oxidase at 2.8 A. Science. 1996;272:1136-44 pubmed
    ..Possible channels for chemical protons to produce H2O, for removing the produced water, and for O2, respectively, were identified. ..
  33. Irikura D, Kumasaka T, Yamamoto M, Ago H, Miyano M, Kubata K, et al. Cloning, expression, crystallization, and preliminary X-ray analysis of recombinant mouse lipocalin-type prostaglandin D synthase, a somnogen-producing enzyme. J Biochem. 2003;133:29-32 pubmed
    ..8, and c = 105.3 A. The selenomethionyl crystals obtained with citrate belong to orthorhombic space group C222(1) with lattice constants a = 45.5, b = 66.8, and c = 104.5 A. The native crystals diffracted beyond 2.1 A resolution. ..
  34. Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K. Crystal structure and functional implications of Pyrococcus furiosus hef helicase domain involved in branched DNA processing. Structure. 2005;13:143-53 pubmed
    ..Hence, our findings provide a structural basis for the functional mechanisms of this helicase/nuclease family. ..
  35. Akiyama M, Takeda S, Kokame K, Takagi J, Miyata T. Crystal structures of the noncatalytic domains of ADAMTS13 reveal multiple discontinuous exosites for von Willebrand factor. Proc Natl Acad Sci U S A. 2009;106:19274-9 pubmed publisher
  36. Muto T, Tsuchiya D, Morikawa K, Jingami H. Site-specific unglycosylation to improve crystallization of the metabotropic glutamate receptor 3 extracellular domain. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:236-41 pubmed publisher
    ..0, b = 97.5, c = 108.1 A, beta = 93.0 degrees . Assuming the presence of two protomers per crystallographic asymmetric unit, the Matthews coefficient V(M) was calculated to be 3.5 A(3) Da(-1) and the solvent content was 65%. ..
  37. Shionyu Mitsuyama C, Ito Y, Konno A, Miwa Y, Ogawa T, Muramoto K, et al. In vitro evolutionary thermostabilization of congerin II: a limited reproduction of natural protein evolution by artificial selection pressure. J Mol Biol. 2005;347:385-97 pubmed
    ..The results showed that the artificial pressure made congerin II partially reproduce the natural evolution of congerin I...
  38. Iwata K, Matsuura T, Sakurai K, Nakagawa A, Goto Y. High-resolution crystal structure of beta2-microglobulin formed at pH 7.0. J Biochem. 2007;142:413-9 pubmed
    ..We consider that the enhanced fibrillation is more directly coupled with the decreased stability leading to the increased propensity of exposing amyloidogenic regions. ..
  39. Sakurai K, Shimada H, Hayashi T, Tsukihara T. Substrate binding induces structural changes in cytochrome P450cam. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:80-3 pubmed publisher
    ..Camphor binding induces rotation of Thr101 to form a hydrogen bond that acts as a hydrogen donor to a peripheral haem propionate. This bonding contributes to the redox-potential change. ..
  40. Yamada K, Kunishima N, Mayanagi K, Ohnishi T, Nishino T, Iwasaki H, et al. Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8. Proc Natl Acad Sci U S A. 2001;98:1442-7 pubmed publisher
  41. Muto T, Tsuchiya D, Morikawa K, Jingami H. Structures of the extracellular regions of the group II/III metabotropic glutamate receptors. Proc Natl Acad Sci U S A. 2007;104:3759-64 pubmed
    ..We propose a general activation mechanism of the dimeric receptor coupled with both ligand-binding and interprotomer rearrangements. ..
  42. Shiraki T, Kodama T, Jingami H, Kamiya N. Rational discovery of a novel interface for a coactivator in the peroxisome proliferator-activated receptor gamma: theoretical implications of impairment in type 2 diabetes mellitus. Proteins. 2005;58:418-25 pubmed
    ..Thus, our model provides structural insight into the impairment of PPARgamma function in type 2 diabetes mellitus. ..
  43. Tanaka H, Kato K, Yamashita E, Sumizawa T, Zhou Y, Yao M, et al. The structure of rat liver vault at 3.5 angstrom resolution. Science. 2009;323:384-8 pubmed publisher
    ..Interactions between the 42-turn-long cap-helix domains are key to stabilizing the particle. The shoulder domain is structurally similar to a core domain of stomatin, a lipid-raft component in erythrocytes and epithelial cells...
  44. Inoue T, Okino N, Kakuta Y, Hijikata A, Okano H, Goda H, et al. Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase. J Biol Chem. 2009;284:9566-77 pubmed publisher
    ..Furthermore, insights into the actions of PaCD and eukaryotic neutral CDases as an exotoxin and mediators of sphingolipid signaling are also revealed, respectively. ..
  45. Unno M, Mizushima T, Morimoto Y, Tomisugi Y, Tanaka K, Yasuoka N, et al. The structure of the mammalian 20S proteasome at 2.75 A resolution. Structure. 2002;10:609-18 pubmed
    ..We also determined the site of the nuclear localization signals in the molecule. A model of the immunoproteasome was predicted from this constitutive structure. ..
  46. Tokuoka K, Kusakari Y, Krungkrai S, Matsumura H, Kai Y, Krungkrai J, et al. Structural basis for the decarboxylation of orotidine 5'-monophosphate (OMP) by Plasmodium falciparum OMP decarboxylase. J Biochem. 2008;143:69-78 pubmed
    ..The structural basis of substrate or product binding to PfOMPDC will help to uncover the decarboxylation mechanism and facilitate structure-based optimization of antimalarial drugs. ..
  47. Nakaishi A, Hirose M, Yoshimura M, Oneyama C, Saito K, Kuki N, et al. Structural insight into the specific interaction between murine SHPS-1/SIRP alpha and its ligand CD47. J Mol Biol. 2008;375:650-60 pubmed
  48. Nishimura M, Kaminishi T, Takemoto C, Kawazoe M, Yoshida T, Tanaka A, et al. Crystal structure of human ribosomal protein L10 core domain reveals eukaryote-specific motifs in addition to the conserved fold. J Mol Biol. 2008;377:421-30 pubmed publisher
    ..Characteristic interactions among Arg90-Trp171-Arg139 guide the C-terminal part outside of the central fold, implying that the eukaryote-specific C-terminal extension localizes on the outer side of the ribosome. ..
  49. Foophow T, Tanaka S, Angkawidjaja C, Koga Y, Takano K, Kanaya S. Crystal structure of a subtilisin homologue, Tk-SP, from Thermococcus kodakaraensis: requirement of a C-terminal beta-jelly roll domain for hyperstability. J Mol Biol. 2010;400:865-77 pubmed publisher
    ..We propose that attachment of a beta-jelly roll domain to the C-terminus is one of the strategies of the proteins from hyperthermophiles to adapt to high-temperature environment...
  50. Naumov P, Kowalik J, Solntsev K, Baldridge A, Moon J, Kranz C, et al. Topochemistry and photomechanical effects in crystals of green fluorescent protein-like chromophores: effects of hydrogen bonding and crystal packing. J Am Chem Soc. 2010;132:5845-57 pubmed publisher
  51. Koga Y, Katsumi R, You D, Matsumura H, Takano K, Kanaya S. Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form. FEBS J. 2008;275:2632-43 pubmed publisher
    ..These results suggest that the ion pairs in the alpha16 helix contribute to the stabilization of Tk-GK in a cooperative manner. ..
  52. Yabe T, Yamashita E, Kikuchi A, Morimoto K, Nakagawa A, Tsukihara T, et al. Structural analysis of Arabidopsis CnfU protein: an iron-sulfur cluster biosynthetic scaffold in chloroplasts. J Mol Biol. 2008;381:160-73 pubmed publisher
    ..We propose that such a structural framework is important for CnfU to function as a Fe-S cluster biosynthetic scaffold. ..
  53. Yagi H, Kajiwara N, Tanaka H, Tsukihara T, Kato Yamada Y, Yoshida M, et al. Structures of the thermophilic F1-ATPase epsilon subunit suggesting ATP-regulated arm motion of its C-terminal domain in F1. Proc Natl Acad Sci U S A. 2007;104:11233-8 pubmed publisher
    ..These results suggest that the epsilon C-terminal domain can undergo an arm-like motion in response to an ATP concentration change and thereby contribute to regulation of F(o)F(1)-ATP synthase...
  54. Tanaka S, Saito K, Chon H, Matsumura H, Koga Y, Takano K, et al. Crystal structure of unautoprocessed precursor of subtilisin from a hyperthermophilic archaeon: evidence for Ca2+-induced folding. J Biol Chem. 2007;282:8246-55 pubmed publisher
  55. Yamagata Y, Ogasahara K, Hioki Y, Lee S, Nakagawa A, Nakamura H, et al. Entropic stabilization of the tryptophan synthase alpha-subunit from a hyperthermophile, Pyrococcus furiosus. X-ray analysis and calorimetry. J Biol Chem. 2001;276:11062-71 pubmed publisher
    ..Rather, the increase in ion pairs, decrease in cavity volume, and entropic effects due to shortening of the polypeptide chain play important roles in extremely high stability in Pf-alpha-subunit...
  56. Yamada K, Miyata T, Tsuchiya D, Oyama T, Fujiwara Y, Ohnishi T, et al. Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery. Mol Cell. 2002;10:671-81 pubmed
  57. Lee S, Ogasahara K, Ma J, Nishio K, Ishida M, Yamagata Y, et al. Conformational Changes in the tryptophan synthase from a hyperthermophile upon alpha2beta2 complex formation: crystal structure of the complex. Biochemistry. 2005;44:11417-27 pubmed publisher
    ..4) The changes in the conformations of both the alpha and beta subunits due to complex formation contributed to the stabilization of the subunit association, which is critical for the stimulation of the enzymatic activities...
  58. Nishio K, Morimoto Y, Ishizuka M, Ogasahara K, Tsukihara T, Yutani K. Conformational changes in the alpha-subunit coupled to binding of the beta 2-subunit of tryptophan synthase from Escherichia coli: crystal structure of the tryptophan synthase alpha-subunit alone. Biochemistry. 2005;44:1184-92 pubmed
    ..This also confirms the prediction of the conformational changes based on the thermodynamic analysis for the association between the alpha- and beta-subunits. ..
  59. Toma S, Chong K, Nakagawa A, Teranishi K, Inouye S, Shimomura O. The crystal structures of semi-synthetic aequorins. Protein Sci. 2005;14:409-16 pubmed
    ..The differences of various semi-synthetic aequorins in Ca(2+)-sensitivity and reaction rate are explained by the capability of the involved groups and structures to undergo conformational changes in response to the Ca(2+)-binding...
  60. Xie Y, Inoue T, Seike N, Matsumura H, Kanbayashi K, Itoh K, et al. Crystallization and preliminary X-ray crystallographic studies of dissimilatory nitrite reductase isolated from Hyphomicrobium denitrificans A3151. Acta Crystallogr D Biol Crystallogr. 2004;60:2383-6 pubmed
    ..X-ray diffraction data were collected to 3.5 A resolution. To solve the crystal structure of HdNIR, the multiwavelength anomalous dispersion (MAD) method and the molecular-replacement method are currently being used...
  61. Inoue T, Irikura D, Okazaki N, Kinugasa S, Matsumura H, Uodome N, et al. Mechanism of metal activation of human hematopoietic prostaglandin D synthase. Nat Struct Biol. 2003;10:291-6 pubmed
    ..This effect explains a four-fold reduction in the K(m) of the enzyme for GSH. The structure provides insights into how Ca2+ or Mg2+ binding activates human hematopoietic PGD synthase. ..
  62. Lin L, Nakano H, Nakamura S, Uchiyama S, Fujimoto S, Matsunaga S, et al. Crystal structure of Pyrococcus horikoshii PPC protein at 1.60 A resolution. Proteins. 2007;67:505-7 pubmed
  63. Tomizaki T, Yamashita E, Yamaguchi H, Aoyama H, Tsukihara T, Shinzawa Itoh K, et al. Structure analysis of bovine heart cytochrome c oxidase at 2.8 A resolution. Acta Crystallogr D Biol Crystallogr. 1999;55:31-45 pubmed
    ..The hierarchy of the structural organization of the enzyme complex has been proposed on the basis of intersubunit interactions. ..
  64. Ichiyanagi K, Ishino Y, Ariyoshi M, Komori K, Morikawa K. Crystal structure of an archaeal intein-encoded homing endonuclease PI-PfuI. J Mol Biol. 2000;300:889-901 pubmed publisher
    ..For the double-strand break, the two strands in the DNA duplex were cleaved by PI-PfuI with different efficiencies. We suggest that the cleavage of each strand is catalyzed by each of the two non-equivalent active sites...
  65. Fukuzumi S, Inada O, Satoh N, Suenobu T, Imahori H. Significant enhancement of electron transfer reduction of NAD(+) analogues by complexation with scandium ion and the detection of the radical intermediate-scandium ion complex. J Am Chem Soc. 2002;124:9181-8 pubmed
    ..The electron self-exchange rates of the MPP(*)/MPP(+) system have been determined from the ESR line width variation and are compared with those of the ABNA(*)/ABNA(+) system...
  66. Nakano H, Yoshida T, Uchiyama S, Kawachi M, Matsuo H, Kato T, et al. Structure and binding mode of a ribosome recycling factor (RRF) from mesophilic bacterium. J Biol Chem. 2003;278:3427-36 pubmed
    ..This is just the reverse of a model that is now widely accepted. However, the new model is in better agreement with published biological findings. ..
  67. Ma J, Yoshimura M, Yamashita E, Nakagawa A, Ito A, Tsukihara T. Structure of rat monoamine oxidase A and its specific recognitions for substrates and inhibitors. J Mol Biol. 2004;338:103-14 pubmed
    ..This study also presents that MAOA has a transmembrane helix at the C-terminal region. This is the first crystal structure of membrane protein with an isolated transmembrane helix. ..
  68. Inanobe A, Matsuura T, Nakagawa A, Kurachi Y. Structural diversity in the cytoplasmic region of G protein-gated inward rectifier K+ channels. Channels (Austin). 2007;1:39-45 pubmed
    ..These structural elements are located at the interface with the plasma membrane. Therefore, these structural elements could associate with the Kir channel transmembrane helices and be involved in the regulation of Kir channel gating. ..
  69. Ammar Y, Takeda S, Hisamitsu T, Mori H, Wakabayashi S. Crystal structure of CHP2 complexed with NHE1-cytosolic region and an implication for pH regulation. EMBO J. 2006;25:2315-25 pubmed
    ..These findings suggest that CHP serves as an obligatory subunit that is required both for supporting the basic activity and regulating the pH-sensing of NHE1 via interactions between distinct parts of these proteins. ..
  70. Asahara H, Koizumi T, Mochizuki E, Oshima T. Two conformers of 10,11-dihydro-5H-dibenzo[a,d]cycloheptene spiro-linked with homobenzoquinone epoxide. Acta Crystallogr C. 2006;62:o136-8 pubmed
    ..The conformational structures of these isomers have been compared with those of the corresponding isomers of the unepoxidized homobenzoquinone. ..
  71. Hong D, Gozu M, Hasegawa K, Naiki H, Goto Y. Conformation of beta 2-microglobulin amyloid fibrils analyzed by reduction of the disulfide bond. J Biol Chem. 2002;277:21554-60 pubmed
    ..Taken together, the disulfide bond once exposed to the solvent upon acid denaturation may be progressively buried in the interior of the amyloid fibrils during its formation. ..
  72. Minamino T, Imada K, Tahara A, Kihara M, Macnab R, Namba K. Crystallization and preliminary X-ray analysis of Salmonella FliI, the ATPase component of the type III flagellar protein-export apparatus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006;62:973-5 pubmed
    ..4 A resolution. Anomalous difference Patterson maps of Os-derivative and Pt-derivative crystals showed significant peaks in their Harker sections, indicating that both derivatives are suitable for structure determination. ..
  73. Fei M, Yamashita E, Inoue N, Yao M, Yamaguchi H, Tsukihara T, et al. X-ray structure of azide-bound fully oxidized cytochrome c oxidase from bovine heart at 2.9 A resolution. Acta Crystallogr D Biol Crystallogr. 2000;56:529-35 pubmed
    ..1995), Nature (London), 376, 660-669], which lacks one of the three imidazole ligands to Cu(B). ..
  74. Hashimoto H, Nishioka M, Fujiwara S, Takagi M, Imanaka T, Inoue T, et al. Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1. J Mol Biol. 2001;306:469-77 pubmed publisher
    ..The stabilization of the melted DNA structure at the forked-point may be correlated with the high PCR performance of KOD DNA polymerase, which is due to low error rate, high elongation rate and processivity...
  75. Sugawara H, Kusunoki M, Kurisu G, Fujimoto T, Aoyagi H, Hatakeyama T. Characteristic recognition of N-acetylgalactosamine by an invertebrate C-type Lectin, CEL-I, revealed by X-ray crystallographic analysis. J Biol Chem. 2004;279:45219-25 pubmed
    ..Mutational analyses, in which Gln70 and/or Arg115 were replaced by alanine, confirmed that these residues contributed to GalNAc recognition in a cooperative manner...
  76. Nagata A, Ohnishi H, Yoshimura M, Ogawa A, Ujita S, Adachi H, et al. Crystallization and preliminary X-ray analysis of rat SHPS-1. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006;62:189-91 pubmed
    ..Preliminary X-ray diffraction data were collected from SHPS-1 crystals to 2.8 A resolution and reduced to primitive hexagonal space group P622. Unit-cell parameters are a = b = 100.5, c = 101.3 A. ..
  77. Matsumura H, Takahashi H, Inoue T, Yamamoto T, Hashimoto H, Nishioka M, et al. Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1. Proteins. 2006;63:711-5 pubmed publisher
  78. Yamamoto T, Matsuda T, Sakamoto N, Matsumura H, Inoue T, Morikawa M, et al. Crystallization and preliminary X-ray analysis of TBP-interacting protein from the hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1. Acta Crystallogr D Biol Crystallogr. 2003;59:372-4 pubmed
    ..83, c = 86.41 A, and diffract to 2.2 A using synchrotron radiation. MAD data was collected and a Bijvoet difference Patterson map showed strong peaks sufficient to determine the positions of the Se atoms...
  79. Suga M, Maeda S, Nakagawa S, Yamashita E, Tsukihara T. A description of the structural determination procedures of a gap junction channel at 3.5 A resolution. Acta Crystallogr D Biol Crystallogr. 2009;65:758-66 pubmed publisher
  80. Akiyama M, Takeda S, Kokame K, Takagi J, Miyata T. Production, crystallization and preliminary crystallographic analysis of an exosite-containing fragment of human von Willebrand factor-cleaving proteinase ADAMTS13. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009;65:739-42 pubmed publisher
    ..Diffraction data sets were collected using the SPring-8 beamline. Two ADAMTS13-DTCS crystals with distinct unit-cell parameters generated data sets to 2.6 and 2.8 A resolution, respectively. ..
  81. Lee S, Sekimoto T, Yamashita E, Nagoshi E, Nakagawa A, Imamoto N, et al. The structure of importin-beta bound to SREBP-2: nuclear import of a transcription factor. Science. 2003;302:1571-5 pubmed
    ..Importin-beta changes its conformation to reveal a pseudo-twofold symmetry on its surface structure so that it can accommodate a symmetric dimer molecule. Importin-beta may use a similar strategy to recognize other dimeric cargoes. ..
  82. Nishida H, Tsuchiya D, Ishino Y, Morikawa K. Overexpression, purification and crystallization of an archaeal DNA ligase from Pyrococcus furiosus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005;61:1100-2 pubmed
    ..7 A resolution. They belong to the monoclinic space group P2(1), with unit-cell parameters a = 61.1, b = 88.3, c = 63.4 A, beta = 108.9 degrees. The asymmetric unit contains one ligase molecule. ..
  83. Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K. Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition. Structure. 2001;9:197-204 pubmed
    ..This model accounts for how Hjc recognizes and resolves the junction DNA in a specific manner. Mutational and biochemical analyses highlight the importance of some loops and the amino terminal region in interaction with DNA. ..
  84. Takano K, Tsuchimori K, Yamagata Y, Yutani K. Effect of foreign N-terminal residues on the conformational stability of human lysozyme. Eur J Biochem. 1999;266:675-82 pubmed
  85. Hashimoto H, Nishioka M, Inoue T, Fujiwara S, Takagi M, Imanaka T, et al. Crystallization and preliminary X-ray crystallographic analysis of archaeal O6-methylguanine-DNA methyltransferase. Acta Crystallogr D Biol Crystallogr. 1998;54:1395-6 pubmed
    ..3 A3 Da-1 and a solvent content of 48% by volume. A full set of X-ray diffraction data was collected to 2.0 A Bragg spacings from the native crystal...