seminar2003

2nd Annual Meeting of
Structural - Biological Whole Cell Project of Thermus thermophilus HB8

1-15. Progress Reports of Systematic Preparation of Thermus thermophilus HB8 Proteins in RIKEN Harima Institute
　　1. Comparative analaysis of Thermus thermophilus HB8 proteins

　　　　Ryoji MASUI et al.

　　2. Construction of Expression Plasmid

　　　　Yumiko INOUE, Kazuko AGARI, Miwa OHMORI, Takeshi NAGIRA, Toshi ARIMA, Yukihide KOUSUMI et al.

　　3. Protein Expression

　　　　Kayoko MATSUMOTO, Tomomi KIYAMA et al.

　　4. Protein Purification - Methods and Progress

　　　　Shinya SATOH, Keiko HORITA, Sonomi YAMAMOTO, Akio EBIHARA et al.

　　5. Purification Report 1

　　　　Nobuko MAOKA et al.

　　6. Purification Report 2

　　　　Aiko KASHIHARA et al.

　　7. Purification Report 3

　　　　Fujie SHINKAI et al.

　　8. Purification Report 4

　　　　Emi ISHIDO et al.

　　9. Purification Report 5

　　　　Masami NISHIDA et al.

　　10. Protein Crystallization

　　　　Hitoshi IINO, Shuka IBA et al.

　　11. List of Structural and Functional Analyses

　　　　Noriko NAKAGAWA et al.

　　12. DNA Microarray Analysis

　　　　Aiko KASHIHARA et al.

　　13. Experimental Database

　　　　Yoshihiro AGARI et al.

　　14. Home Page of Thermus thermophilus HB8

　　　　Fumie KAMADA et al.

　　15. Organization Chart of Research Group

　　　　Sae FUKUDA et al.

16. Development of Full-automated Macromolecular Crystallization /Observation Robot System

Hideyuki Miyatake¹, Seong-Hoon Kim¹ and Kunio Miki^1,2

(¹ RIKEN Harima Inst., ² Grad. Sch. of Sci., Kyoto Univ)

17. High-throughput Protein Crystallization in RIKEN Highthroughput Factory

Nobuo OKAZAKI¹, Yuuki NAKAMURA¹, Maki KUMEI¹,Tomoyuki TANAKA¹, Nigar BABAYEVA¹, Takashi MATSUMOTO, Mika MIZOGUCHI¹, Tooru HANAMURA¹ and Mitsuaki SUGAHARA^1,2

(RIKEN Harima Inst. ¹Highthroughput Factory Large scale protein crystallization team, ²Structural Biophysics Lab.)

19. High Throughput Protein Crystallography at RIKEN Structural Genomics Beamlines

Masaki Yamamoto¹, Go Ueno^1,2, Raita Hirose^1,2, Koh Ida^1,3, Hiroyuki Kanda^1,4, Takashi Kumasaka^1,5, Masashi Miyano¹and Tetsuya Ishikawa¹

(¹SPring-8/RIKEN, ²Rigaku co., ³Yokohama City University, ⁴Shimane University, ⁵ Tokyo Institute of Technology)

20. Structural and Functional Analyses of RecR Protein

Masayoshi HONDA^1,2, Mayuko ISHIDA³, Sundaresan Rajesh^2,4, Satoko ISHIBE^2,4,5, Yutaka ITO^1,2,4,5, Tsutomu MIKAWA^1,2,4,5,6, and Takehiko SHIBATA^1,2,4,5

(¹Grad. Sch. of Integrated Sci., Yokohama City Univ., ²Bio-supramol. Struct. -Func. Group, RIKEN, ³Japan Women's Univ.,⁴Cellular & Molecular Biol. Lab. RIKEN, ⁵CREST/JST, ⁶Structurome Res. Group, RIKEN/Harima Institute)

21. NMR analysis of the interactions of Thermus thermophilus RecO with RecF pathway proteins

Jin INOUE^1,2, Masayoshi HONDA^1,2, Sundaresan Rajesh^2,3, Yutaka ITO^1,2,3,4, Tsutomu MIKAWA^1,2,3,4,5, Takehiko SHIBATA^1,2,3,4

(¹Grad. Sch. of Integrated Sci., Yokohama City Univ., ²Bio-supramol. Struct Func. Group, RIKEN, ³Cellular & Molecular Biol. Lab. RIKEN, ⁴CREST/JST, ⁵Structurome Res. Group, RIKEN/Harima Institute)

22. Thermus thermophilus MutS2, a MutS Homologue, Possesses an Endonuclease Activity Effected by MutL

Kenji FUKUI¹, Ryoji MASUI^1,2, and Seiki KURAMITSU^1,2

(¹ Grad. Sch. Sci., Osaka Univ.,² RIKEN Harima Inst.)

23. Structural and Functional Analyses of DNA Repair Enzyme, MutM - DNA Complex

Noriko NAKAGAWA¹, Chikako OTSUKA², Mitsuhiro NISHIMURA², Yukihide KOUSUMI¹, Ryoji MASUI^1,2, Seiki KURAMITSU^1,2

(¹ RIKEN Harima Inst., ² Grad. Sch. of Sci., Osaka Univ)

24. Nucleotide Excision Repair System of Thermus thermophilus HB8
- Initial Steps of the Reaction by UvrABC Excinuclease -

Ikumi SAITO¹, Noriko NAKAGAWA², Ryoji MASUI^1,2, and Seiki KURAMITSU^1,2

(¹ Grad. Sch. Sci., Osaka Univ., ²RIKEN Harima Inst.)

25. Structural and Sequence Comparisons Arising from the Solution Structure of the Transcription Elongation Factor NusG from Thermus thermophilus

Paul REAY¹, Kazuhiko YAMASAKI^1,2, Takaho TERADA^2,3, Seiki KURAMITSU^3,4, Mikako SHIROUZU^2,3and Shigeyuki YOKOYAMA^2,3,5

(¹Age Dimension Research Center, AIST, ² RIKEN GSC, ³ RIKEN Harima Inst., ⁴ Grad. Sch. of Sci., Osaka Univ., ⁵ Grad. Sch. of Sci., Univ. of Tokyo)

26. Structural Basis of the tRNA-dependent Amino-acid Activation by Glutamyl-tRNA Synthetase

Shun-ichi Sekine¹, Osamu Nureki^1,2, Daniel Y. Dubois³, Stephane Bernier⁴, Robert Chenevert⁴, Jacques Lapointe³, Dmitry G. Vassylyev¹ and Shigeyuki Yokoyama^1,2,5

(¹ Cellular Signaling Laboratory and Structurome Group, RIKEN Harima Inst., ² Grad. Sch. of Sci., Univ. of Tokyo, Departements de Biochimie et Microbiologie and of ⁴ Chimie, Faculte des Sciences et de Genie, CREFSIP, Universite, ⁵ Genomic Sciences Center, RIKEN Yokohama Inst.)

27. Crystal Structure of Cysteinyl-tRNA synthetase from Thermus Thermophilus HB8

Takashi Nakama ^1,4, Osamu Nureki4, Seiki Kuramitsu ^2,3, Shigeyuki Yokoyama ^1,2,4

( ¹ RIKEN GSC, ² RIKEN Harima Inst., ³ Grad. Sch. of Sci., Osaka Univ., ⁴ Grad. Sch. of Sci., Univ. of Tokyo)

28. Amino Acid Residues Responsible for S-Adenosyl-L-Methionine Binding in tRNA (Gm18) Methyltransferase from Thermus themophilus HB8

Kazunori WATANABE

(Faculty of Eng., Ehime Univ.)

29. Molecular Evolution of tRNA (m¹G37) Methyltransferases in Thermophilc Eubacteria

Hiroshi TAKEDA

(Faculty of Eng., Ehime Univ.)

30. Thermus thermophilus-Specific Polyamines Are Essentially Required for Gm18 modification of tRNA at Extreme High Temperature.

Hiroyuki HORI

(Faculty of Eng., Ehime Univ.)

31. tRNA Identity of Hyperthermophilic Archaeon, Aeropyrum pernix K1

Tsunemi HASEGAWA¹, Junji YOKOZAWA¹, Yoshiyuki NAGAOKA¹, Jun IWAKI¹, Koji OKAMOTO¹, Takuya UMEHARA¹, Yutaka KAWARABAYASI², Yoshinori KOYAMA² and Atsushi KUNO¹

(¹ Fac. of Sci., Yamagata Univ., ² Nat. Inst. Adv. Ind. Sci. Tech.)

32. Large-scale Preparation System for Structural Analysis of New Functional Proteins and Proteins Involved in Transcription and Translation of Thermus thermophilus HB8

Takaho TERADA^1,2, Mikako SHIROUZU^1,2, Takanori KIGAWA¹, Mio INOUE¹, Mie GOTO¹, Keiko TSUGANEZAWA¹, Ryoko USHIKOSH^I1, Ayako TATSUGUCHI¹, Yuki KAMEWARI¹, Hiroaki HAMANA¹, Naomi OBAYASHI¹, Hiroko UDA¹, Hideaki TANAKA¹, Yukiko KINOSHITA¹, Miki IDAKA¹, Miyuki KATO¹, Machiko YAMAGUCHI-HIRAFUJI¹, Satoru WATANABE¹, Naoko SHINYA¹, Noriko NAKAGAWA², Ryoji MASUI^2,3, Seiki KURAMITSU^2,3 and Shigeyuki YOKOYAMA^1,2,4

(¹ RIKEN GSC, ² RIKEN Harima Institute, ³ Grad. Sch. of Sci., Osaka Univ., ⁴ Grad. Sch. of Sci., Univ. of Tokyo)

33. Crystal Structures of the Conserved Hypothetical Proteins from Thermus thermophilus HB8

Mikako SHIROUZU^1,2, Miki IDAKA¹, Miyuki KATO¹, Mutsuko NIINO-KUKIMOTO¹, Azusa SETO¹, Kazutaka MURAYAMA¹, Takaho TERADA^1,2, Seiki KURAMITSU^2,3 and Shigeyuki YOKOYAMA^1,2,4

(¹ RIKEN GSC, ² RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ, ⁴ Grad. Sch. of Sci., Univ. of Tokyo)

34. Crystal Structure of TT1561 of Thermus thermophilus HB8

Miyuki KATO-MURAYAMA¹, Mikako SHIROUZU^1,2, Takaho TERADA^1,2, Kazutaka MURAYAMA¹, Seiki KURAMITSU^2,3 and Shigeyuki YOKOYAMA^1,2,4

(¹ RIKEN GSC, ² RIKEN Harima Inst., ³ Grad. Sch. of Sci., Osaka Univ, ⁴ Grad. Sch. of Sci., Univ. of Tokyo)

35. Crystal Structure of TT1467 from Thermus thermophilus HB8

Miki Idaka¹, Takaho,Terada^1,2, Kazutaka Murayama¹, Hiroto Yamaguch¹, Osamu Nurek⁴, Ryuichiro Ishitan⁴, Seiki Kuramitsu^2,3, Mikako Shirouzu^1,2 and Shigeyuki Yokoyama^1,2,4

(¹ RIKEN GSC, ² RIKEN Harima Inst., ³ Grad. Sch. of Sci., Osaka Univ, ⁴ Grad. Sch. of Sci., Univ. of Tokyo)

36. Crystal structure of TT1696 from Thermus thermophilus HB8

Miki Idaka¹, Kazutaka Murayama¹, Hiroto Yamaguchi¹, Takaho Terada^1,2, Seiki Kuramitsu^2,3, Mikako Shirouzu^1,2, Shigeyuki Yokoyama^1,2,4

(¹ RIKEN GSC, ² RIKEN Harima Inst., ³ Grad. Sch. of Sci., Osaka Univ, ⁴ Grad. Sch. of Sci., Univ. of Tokyo)

37. Proteomics Analysis of Thermus thermophilus HB8 and Identification of Binding Proteins Using Mass Spectrometry

Ryoichi ARAI^1,2, Madoka NISHIMOTO¹, Yumi SAITO¹, Mitsutoshi TOYAMA¹, Chie TAKEMOTO-HORI¹, Takaho TERADA¹, Seiki KURAMITSU^2,3, Mikako SHIROUZU^1,2 and Sigeyuki YOKOYAMA^1,2,4

(¹RIKEN GSC, ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ., ⁴Grad. Sch. of Sci., Univ. of Tokyo)

38. Functional Analysis of Hypothetical Proteins from Thermus Thermophilus HB8

Mitsutoshi TOYAMA¹, Ryoichi ARAI^1,2, Madoka NISHIMOTO¹, Takaho TERADA¹, Seiki KURAMITSU^2,3, Mikako SHIROUZU^1,2 and Sigeyuki YOKOYAMA^1,2,4

(¹RIKEN GSC, ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ., ⁴Grad. Sch. of Sci., Univ. of Tokyo)

39. Crystal Basis for the tmRNA-SmpB Tagging and Ribosomal Rescue System

Yoshitaka BESSHO¹, Rie SHIBATA¹, Hiroaki SAKAI¹, Kazutaka MURAYAMA¹, Shun-ichi SEKINE², Chie TAKEMOTO-HORI¹, Mikako SHIROUZU^1,2, Seiki KURAMITSU^2,3, Shigeyuki YOKOYAMA^1,2,4

(¹RIKEN GSC, ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ., ⁴Grad. Sch. of Sci., Univ. of Tokyo)

40. Purification and Crystallization of SmpB, a tmRNA-binding Protein Essential for Ribosomal Trans-translation

Rie SHIBATA¹, Yoshitaka BESSHO¹, Masahito KAWAZOE¹, Chie TAKEMOTO-HORI¹, Hiroaki SAKAI¹, Kazutaka MURAYAMA¹, Shun-ichi SEKINE², Mikako SHIROUZU^1,2, Seiki KURAMITSU^2,3, Shigeyuki YOKOYAMA^1,2,4

(¹RIKEN GSC, ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ., ⁴Grad. Sch. of Sci., Univ. of Tokyo)

41. Crystal Structure of Ribosomal Protein L11 Methyltransferase PrmA

Tatsuya KAMINISHI^1,2, Hiroaki SAKAI¹, Chie TAKEMOTO-HORI¹, Noriko NAKAGAWA³, Nobuko MAOKA³, Seiki KURAMITSU^1,3,4, Mikako SHIROUZU^1,3 and Shigeyuki YOKOYAMA^1,2,3

(¹RIKEN GSC, ²Grad. Sch. Sci., Univ. of Tokyo,³RIKEN Harima Inst., ⁴Grad. Sch. Sci., Osaka Univ.)

42. The Crystal Structure of Thermus thermophilus Elongation Factor P

Kyoko HANAWA-SUETSUGU¹, Shun-ichi SEKINE², Hiroaki SAKAI¹, Chie TAKEMOTO-HORI¹, Takaho TERADA^1,2, Seiki KURAMITSU^2,3, Mikako SHIROUZU^1,2 and Shigeyuki YOKOYAMA^1,2,4

(¹RIKEN GSC, ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ., ⁴Grad. Sch. of Sci., Univ. of Tokyo)

43. Crystallization and preliminary X-ray diffraction analysis of ribosome-associated factor EF-G-2 from Thermus thermophilus HB8

Hongfei Wang¹, Shun-ichi Sekine^2, Chie Takemoto- Hori¹, Kazutaka Murayama¹, Takaho Terada^1,2, Mikako Shirouzu^1,2, Seiki Kuramitsu^2,3, Shigeyuki Yokoyama^1,2,4

(¹RIKEN GSC, ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ., ⁴Grad. Sch. of Sci., Univ. of Tokyo)

44. Analysis of Thermus thermophilus HB8 Ribosomal and Related Proteins

Chie TAKEMOTO-HORI¹, Hiroshi NAKAYAMA², Ryogo AKASAKA¹, Mikako SHIROUZU^1,3, Seiki KURAMITSU^3,5, Hiroshi HIROTA¹, Koji TAKIO ^2,3 and Shigeyuki YOKOYAMA^1,3,4

(¹RIKEN GSC, ²RIKEN Discovery Research Inst., ³RIKEN Harima Inst., ⁴Grad. Sch. of Sci., Univ. of Tokyo, ⁵Grad. Sch. of Sci., Osaka Univ.)

46. Crystal Structure of the Conserved Hypothetical Protein TT1751 from Thermus thermophilus HB8 at 2.0 Å Resolution

Seiichiro KISHISHITA¹, Ayako TATSUGUCHI¹, Ryoko USHIKOSHI¹, Takaho TERADA¹, Seiki KURAMITSU^2,3, Sam-Yong PARK⁴, Jeremy R. H. TAME⁴, Kengo KINOSHITA^1,4,5, Haruki NAKAMURA^1,6, Mikako SHIROUZU^1,3 and Shigeyuki YOKOYAMA^1,3,7

(¹RIKEN GSC, ²Grad. Sch. of Sci., Osaka Univ., ³RIKEN Harima Inst., ⁴Yokohama City Univ., ⁵PRESTO, ⁶Inst. of Protein Research, Osaka Univ., ⁷Grad. Sch. of Sci., Univ. of Tokyo)

47. Crystal Structure of the Conserved Protein TT1542 from Thermus thermophilus HB8

Noriko HANDA¹, Takaho TERADA^1,2, Yuki KAMEWARI¹, Hiroaki HAMANA¹, Jeremy R. H. TAME³, Sam-Yong PARK³, Kengo KINOSHITA^1,3,4, Motonori Ota⁵, Haruki NAKAMURA^1,6, Seiki KURAMITSU^2,7, Mikako SHIROUZU^1,2 and Shigeyuki YOKOYAMA^1,2,8

(¹RIKEN GSC, ²RIKEN Harima Inst., ³Yokohama City Univ., ⁴PRESTO,⁵Tokyo Inst. of Tech, ⁶Inst. of Protein Research, Osaka Univ., ⁷Grad. Sch. of Sci., Osaka Univ., ⁸Grad. Sch. of Sci., Univ. of Tokyo)

48. Structural and Functional Analyses of Nudix Protein Ndx1

Takayoshi IWAI^1,2, Noriko NAKAGAWA¹, Ryoji MASUI^1,2and Seiki KURAMITSU^1,2

(¹RIKEN Harima Inst., ²Grad. Sch. Sci., Osaka Univ)

49. Functional Analysis of Ndx3 Hydrolase from Thermus thermophilus HB8

Takashi NISHIKUBO¹, Takayoshi IWAI¹, Ryoji MASUI^1,2 and Seiki KURAMITSU^1,2

(¹Grad. Sch. of Sci., Osaka Univ., ²RIKEN Harima Inst.)

50. Crystal Structure of Binary and Ternary Complexes of ADP-ribose Pyrophosphatase from Thermus thermophilus HB8: Insights into the Catalytic Mechanism

Sachiko YOSHIBA¹, Takushi OOGA¹, Noriko NAKAGAWA², Ryoji MASUI^1,2, and Seiki KURAMITSU^1,2

(¹Grad. Sch. Sci., Osaka Univ., ²RIKEN Harima Inst.)

51. Analysis of Catalytic Mechanism of Ndx4, a Nudix Protein from Thermus thermophilus HB8

Takushi OOGA¹, Sachiko YOSHIBA¹, Takayoshi IWAI¹, Ryoji MASUI^1,2, and Seiki KURAMITU^1,2

(¹Grad. Sch. Sci., Osaka Univ., ²RIKEN Harima Inst.)

52. Functional Analysis of dNTP Triphosphohydrolase

Naoyuki KONDO¹, Ryoji MASUI^1,2, and Seiki KURAMITSU^1,2

(¹Grad. Sch. Sci., Osaka Univ., ²RIKEN Harima Inst.)

53. Structural Analysis of the Interaction with Thermus thermophilus P450 (CYP175A1) and its Redox Partner Protein

Yukihide KOUSUMI¹, Noriko NAKAGAWA¹, Maki KANEKO², Ryoji MASUI^1,2, Hitoshi YAMAMOTO², Norikazu UEYAMA² and Seiki KURAMITSU^1,2

(¹RIKEN Harima Inst., ²Grad. Sch. of Sci., Osaka Univ.)

54. Purification of Thermus thermophilus HB 8 Ferredoxin, and an Interaction with Cytochrome P450

Maki KANEKO¹, Yukihide KOUSUMI ³, Taka-aki OKAMURA¹, Hitoshi YAMOTO^1,3, Ryoji MASUI^2,3, Seiki KURAMITSU^2,3 and Norikazu UEYAMA¹

(¹Department of Macro Molecular Science, and ²Department of Biology, Grad. Sch. of Sci., Osaka Univ.,³RIKEN Harima Inst.)

55. X-ray Crystallographic Study of Enzymes on Amino Acid Metabolic Pathways

Ken Hirotsu^1,2, Rie Omi^1,2, Ikuko Miyahara^1,2 and Masaru Goto^3,1

(¹Grad. Sch. of Sci., Osaka City Univ., ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ.)

56. Open-Closed Conformational Change of Threonine Synthase from Thermus thermophilus HB8

Rie Omi^1,2, Masaru Goto^1,3, Ikuko Miyahara^1,2, Hiroyuki Mizuguchi⁴, Hideyuki Hayashi⁴, Hiroyuki Kagamiyama⁴ and Ken Hirotsu^1,2

(¹Grad. Sch. of Sci., Osaka City Univ., ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ., ⁴Dept. of Biochem., Osaka medical college)

57. Characterization and Crystal Structure of Threonine Dehydrogenase from Thermus thermophilus HB8

Tadayuki Yao^1,2, Rie Omi^1,2, Masaru Goto^1,3, I. Miyahara^1,2 and K. Hirotsu^1,2

(¹Grad. Sch. of Sci., Osaka City Univ., ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ)

58. Argininosuccinate Synthetase: Structure of Enzyme･ATP･Substrates and Stereochemistry of the Reaction

Masaru Goto^1,2, Rie Omi^2,3, Ikuko Miyahara^2,3, Sugahara Mitsuaki², and Ken Hirotsu^2,3

(¹Grad. Sch. of Sci., Osaka Univ., ²RIKEN Harima Inst.,³Grad. Sch. of Sci., Osaka City Univ.)

59. X-Ray Crystallographic Study of Acetylornithine Aminotransferase

Mitsuyoshi Matsumura^1,2, Masaru Goto^1,3, Rie Omi^1,2, Ikuko Miyahara^1,2, and Ken Hirotsu^1,2

(¹Dept. of Chem., Osaka City Univ., ²RIKEN Harima Inst., ³Dept. of Biol., Osaka Univ.)

60. Crystal Analysis of Chorismate Mutase from Thermus thermophilus

Eiji Inagaki¹, Yumi Tokunaga¹, Chizuru Tsuzuki¹, Takashi Matsumoto¹, Seiki KURAMITSU², Shigeyuki YOKOYAMA^2,4, Masashi MIYANO^1,3 and Tahir H. TAHIROV¹

(¹Highthroughput Factory, ²Structurome Research Group, ³Structural Biophysics Laboratory RIKEN Harima Institute; ⁴RIKEN Genomic Sciences Center)

61. Crystal Structure of a Lysine Biosynthesis Enzyme, LysX, from Thermus thermophilus HB8

Hiroaki SAKAI¹, Marina N. VASSYLYEVA^1,2, Takanori MATSUURA¹, Shun-ichi SEKINE², Kazumi GOTOH³, Makoto NISHIYAMA³, Takaho TERADA^1,2, Mikako SHIROUZU^1,2, Seiki KURAMITSU^2,4, Dmitry G. VASSYLYEV ², Shigeyuki YOKOYAMA^1,2,5

(¹RIKEN GSC, ²RIKEN Harima Inst., ³Biotech. Research Center, Univ. of Tokyo, ⁴Grad. Sch. of Sci., Osaka Univ., ⁵Grad. Sch. of Sci., Univ. of Tokyo)

62. Characterization of α-Aminoadipate Aminotransferase, an Enzyme Involved in Lysine Biosynthesis in Extreme Thermophile Bacterium

Takashi MIYAZAKI, Junichi MIYAZAKI, Hisakazu YAMANE, and Makoto NISHIYAMA

(Biotechnology Research Center, The University of Tokyo)

63. Functional analysis of the Pyrococcus horikoshii putative lysine biosynthesis gene cluster by in vivo genome engineering

Lombo T., Nakamura A. and Hoshino T.

(Institute of Applied Biochemistry, University of Tsukuba)

64. Organization of the genes of purine nucleotide biosynthetic pathwa
- Approach from 3D structure of gene products -

Gen-ichi SAMPEI^1,2, Hisaaki YANAI^1,2, Takeshi ISHII^1,2, Hiroya KAWAI^2,3, Yoko FUKAI ^2,3, Mayumi KANAGAWA^2,3 and Gota KAWAI^2,3

(¹University of Electro-Communications, ²RIKEN Harima Inst.,³Chiba Institute of Technology)

65. Crystallographic analysis of proteins of purine nucleotides biosynthetic pathway

Mayumi KANAGAWA^1,2, Hisaaki YANAI^2,3, Takeshi ISHII^2,3, Hiroya KAWAI^1,2 , Yoko FUKAI^1,2, Gota KAWAI^{1, 2} and Gen-ichi SAMPEI^{2, 3}

(¹Chiba Institute of Technology, ²RIKEN Harima Inst., ³University of Electro-Communications)

66. Crystal structure of GMP synthetase (GuaA) from Thermus thermophilus HB8

Hisaaki YANAI^1,2，Takeshi ISHII^1,2，Hiroya KAWAI^2,3，Yoko FUKAI^2,3，Mayumi KANAGAWA^2,3，Gota KAWAI^2,3 and Gen-ichi SAMPEI^1,2

(¹University of Electro-Communications, ²RIKEN Harima Inst., ³Chiba Institute of Technology)

67. Structural and Functional Analysis of NDP Kinase from Thermus thermophilus HB8

Shunsaku TAKEISHI¹, Noriko NAKAGAWA², Ryoji MASUI^1,2, and Seiki KURAMITSU^1,2

(¹Grad. Sch. Sci., Osaka Univ., ²RIKEN Harima Inst.)

68. X-ray Crystallographic Study of CTP Synthase

Masaru Goto^1,3, Rie Omi^1,2, Ikuko Miyahara^1,2, and Ken Hirotsu^1,2

(¹Grad. Sch. of Sci., Osaka City Univ., ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ.)

69. Crystal Analysis of β-Ketoacyl-ACP Synthase from Thermus thermophilus

Eiji Inagaki¹, Masumi Maekawa¹, Chizu Kuroishi¹, Seiki KURAMITSU², Shigeyuki YOKOYAMA^2,4, Masashi MIYANO^1,3 and Tahir H. TAHIROV¹

(¹Highthroughput Factory, ²Structurome Research Group, ³Structural Biophysics Laboratory RIKEN Harima Institute;⁴RIKEN Genomic Sciences Center)

70. Biotin-dependent Enzymes in Archaeota

Hiroki Kondo^1,2, Kaori Hisada², Shinji Sueda²

⁽¹RIKEN Harima Inst.,²Kyushu Inst. Tech.)

71. Three-dimensional structure of the biotin carboxylase subunit of pyruvate carboxylase

Kaori Hisada¹, Md. Nurul Islam¹, Shinji Sueda¹, Hiroki Kondo^1,2

(¹Kyushu Inst. Tech., ²RIKEN Harima Inst.)

72. Functional Analysis and Crystallization of Geranylgeranylglyceryl Phosphate Synthase from a Thermoacidophilic Archaeon, Thermoplasma acidophilum

Naoki Nemoto¹, Norio Kudo², Masaru Tanokura², Tairo Oshima¹, and Akihiko Yamagishi¹

(¹Dep. of Mol. Biol., Tokyo University of Pharmacy and Life Science, ²Dep. of Appl. Biol. Chem. Grad. Sch. of Agr. and Life Sci., The University of Tokyo)

73. Reaction Mechanism of GTP Cyclohydrolase I

Yoko TANAKA^1,2, Noriko NAKAGAWA¹, Ryoji MASUI^1,2, and Seiki KURAMITSU^1,2

(¹RIKEN Harima Inst., ²Grad. Sch. Sci., Osaka Univ.)

74. Crystal Structure of the menG Gene Product from Thermus thermophilis HB8

Peter H. REHSE¹, Masumi MAEKAWA¹, Mika MIZOGUCHI¹, Mayumi SUGAHARA¹, Seiki KURAMITSU², Shigeyuki YOKOYAMA^2,4, Masashi MIYANO^1,3 and Tahir H. TAHIROV¹

(¹Highthroughput Factory,²Structurome Research Group,³Structural Biophysics Laboratory RIKEN Harima Institute; ⁴RIKEN Genomic Sciences Center)

75. The Crystal Structure of Adenylyltransferase from Thermus themophilus

Hitomi TAKAHASHI¹, Eiji Inagaki¹, Yayoi FUJIMOTO¹, Chizu KUROISHI¹, Yuki NAKAMURA¹, Fumio ARISAKA⁴, Katsuhide YUTANI¹, Seiki KURAMITSU², Shigeyuki YOKOYAMA^2,5, Masashi MIYANO^1,3 and Tahir H. TAHIROV¹

(¹Highthroughput Factory, ²Structurome Research Group, ³Structural Biophysics Laboratory RIKEN Harima Institute;⁴Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology; ⁵RIKEN Genomic Sciences Center)

76. Crystal Structure of TT1252 from Thermus thermophilus

Azusa SETO¹, Kazutaka MURAYAMA¹, Mitsutoshi TOYAMA¹, Akio EBIHARA², Noriko NAKAGAWA², Seiki KURAMITSU^2,3, Mikako SHIROUZU^1,2, Shigeyuki YOKOYAMA^1,2,4

(¹RIKEN GSC, ²RIKEN Harima Inst., ³Grad. Sch. of Sci., Osaka Univ., ⁴Grad. Sch. of Sci., Univ. of Tokyo)

77. Crystal Structure of Pantothenate Synthetase from Thermus thermophilus HB8

Bagautdin BAGAUTDINOV¹, Emiko MATSUNAGA¹, Mayumi SUGAHARA¹, Tohru HANAMURA¹, Seiki KURAMITSU², Shigeyuki YOKOYAMA^2,4, Masashi MIYANO^1,3 and Tahir H. TAHIROV¹

(¹Highthroughput Factory, ²Structurome Research Group,³Structural Biophysics Laboratory RIKEN Harima Institute; ⁴RIKEN Genomic Sciences Center)

78. Crystal Structure of Phosphomethylpyrimidine Kinase (ThiD) from Thermus thermophilus HB8

Bagautdin BAGAUTDINOV¹, Yoko UKITA¹, Naoko TAKAHASHI¹, Nobio OKAZAKI ¹, Seiki KURAMITSU², Shigeyuki YOKOYAMA^2,4, Masashi MIYANO^1,3 and Tahir H. TAHIROV¹

(¹Highthroughput Factory, ²Structurome Research Group, ³Structural Biophysics Laboratory RIKEN Harima Institute; ⁴RIKEN Genomic Sciences Center)

79. Structural and Functional Analysis of ATP Sulfurylase from Thermus thermophilus HB8

Yuichi Taguchi¹, Masakazu Sugishima¹, and Keiichi Fukuyama^1,2

(¹Sch. Sci., Osaka Univ., ²RIKEN Harima Inst Grad.)

80. Crystallization and Preliminary Crystallographic Analysis of Short-Chain Dehydrogenase/Reductase (SDR) Family Proteins

Tomoyasu KICHISE¹, Tamao HISANO¹, Kazuki TAKEDA¹, Kunio MIKI^1,2

(¹RIKEN Harima Inst., ²Grad. Sch. Sci., Kyoto Univ)

81. Crystallization and Preliminary X-ray Analysis of Chloromuconate Cycloisomerase

Tamao Hisano¹, Hideyuki Miyatake¹, and Kunio Miki^1,2

(¹RIKEN Harima Inst., ²Grad. Sch. Sci., Kyoto Univ.)

82. Crystal Structure of NADP-dependent 3-hydroxyisobutyrate dehydrogenase from Thermus thermophilus HB8

Neratur K. LOKANATH¹, Ikuya SHIROMIZU¹, Yuichi NODAKE¹, Mitsuaki SUGUHARA¹, Shigeyuki YOKOYAMA², Seiki KURAMITSU², Masashi MIYANO¹, Naoki KUNISHIMA¹

(¹Highthroughput Factory and ²Structurome Research Group, RIKEN at SPring-8)

83. Crystallization and preliminary X-ray analysis of small component of 4-hydroxyphenylacetate 3-monooxygenase (HpaC) from Thermus thermophilus HB8 and cofactor complexes

Seong-Hoon KIM¹, Hideyuki MIYATAKE¹, Tamao HISANO¹, and Kunio MIKI^1,2

(¹ RIKEN Harima Inst., ² Grad. Sch. of Sci., Kyoto Univ.)

84. Ligand-induced conformational changes and a reaction intermediate in branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8

Tadashi NAKAI^1,2, Noriko NAKAGAWA¹, Nobuko MAOKA¹, Ryoji MASUI^1,2, Seiki KURAMITSU^1,2, Nobuo KAMIYA¹

(¹ RIKEN Harima Inst./SPring-8,² Grad. Sch. of Sci., Osaka Univ.)

85. Functional Analysis of 2-keto-3-deoxygluconate kinase

Noriyasu OHSHIMA¹, Yoko UKITA¹, Tahir H. TAHIROV¹, Eiji INAGAKI¹, Yasuhiro KAJIHARA², Shigeyuki YOKOYAMA³, Seiki KURAMITSU³, Masashi MIYANO¹and Koji TAKIO¹

(¹ RIKEN Harima Inst. Highthroughput Factory, ² Grad. Sch. of Sci., Yokohama City Univ., ³ RIKEN Harima Inst. Structurome Research Group)

86. The Crystal Structure of Succinyl-CoA synthetase a-subunit from Thermus themophilus

Hitomi TAKAHASHI¹, Yumi TOKUNAGA¹, Chizu KUROISHI¹, Nigar BABAYEVA¹, Seiki KURAMITSU², Shigeyuki YOKOYAMA^2,4, Masashi MIYANO^1,3 and Tahir H. TAHIROV¹

(¹ Highthroughput Factory, ² Structurome Research Group,³ Structural Biophysics Laboratory RIKEN Harima Institute; ⁴ RIKEN Genomic Sciences Center)

87. Crystallographic analysis of malate dehydrogenase mutant with coenzyme specificity toward NADP

Takeo TOMITA, Hisakazu YAMANEand Makoto NISHIYAMA

(Biotechnology Research Center, The University of Tokyo )

88. Crystallographic studies of ATP-binding subunits of ABC transporters from Thermus thermophilus HB8

Kazuki TAKEDA¹, Hideyuki MIYATAKE¹, Kunio MIKI^1,2

(¹ RIKEN Harima Inst., ² Grad. Sch. of Sci., Kyoto Univ)

89. FRET analysis of protein translocase from Thermus thermophilus HB8

Hiroyuki MORI^1,2, Tomoya TSUKAZAKI^1,2, Ryoji MASUI^3,4 , Seiki KURAMITSU^{3, 4}, Shigeyuki YOKOYAMA^{4, 5}, Arthur E. JOHNSON⁶, Yoshiaki KIMURA^2,7, Yoshinori AKIYAMA^{1, 2} and Koreaki ITO^1,2

(¹ Inst. Virus Res., Kyoto Univ., ² CREST, JST, ³ Grad. Sch. Sci., Osaka Univ., ⁴RIKEN, ⁵ Grad. Sch. Sci., Univ. Tokyo, ⁶ Texas A&M Univ., ⁷ BERI)

90. Thermus thermophilus SecYE Complex for Structural Studies of Protein Translocation Channel

Tomoya TSUKAZAKI^1,2, Hiroyuki MORI¹, Dmitry G. VASSYLYEV³, Yoshiaki KIMURA⁴, Seiki KURAMITSU^3,5, Shigeyuki YOKOYAMA^3,6 and Koreaki ITO^1,2

(¹ Inst. Virus Res., Kyoto Univ., ² CREST, JST, ³ RIKEN, ⁴BERI, ⁵ Grad. Sch. Sci., Osaka Univ.,⁶ Grad. Sch. Sci., Univ. Tokyo)

91. Crystallization and Preliminary X-ray Analysis of Peptide Deformylase from Thermus thermophilus HB8

Masayuki Kamo¹, Norio Kudo¹, WooCheol Lee¹, Hiroyuki Motoshima², Masaru Tanokura^1,2

(¹ Dept. of Appl. Biol. Chem., Grad. Sch. of Agr. and Life Sci. The Univ. of Tokyo, ² RIKEN Harima Inst.)

92. Structural biological study on environmental sensing/adaptation proteins of T. thermophilus HB8

Hideyuki Miyatake¹, Seong-Hoon Kim¹, Kunio Miki^1,2

(¹ RIKEN Harima Inst., ² Grad. Sch. of Sci., Kyoto Univ.)

93. Crystal structure determination of Alanine Racemase from Thermus Thermophilus HB8

Shintaro Misaki^{1, 2}, Shinya Sato², Satoshi Uemae³, Takashi Tamura^{2, 3}, Kenji Inagaki^{2, 3}

(¹ Pharmaceutical Consortium for Protein Structure Analysis,²RIKEN Harima Inst., ³ Faculty of Agriculture, Okayama Univ.)

94. Crystal Structure of the Divalent Cation Tolerence Protein (CutA) from Thermus thermophilus HB8

Bagautdin BAGAUTDINOV¹, Azusa TAKEDA¹, Chizuru TSUZUKI¹, Tonoyuki TANAKA¹, Seiki KURAMITSU², Shigeyuki YOKOYAMA^2,4, Masashi MIYANO^1,3 and Tahir H. TAHIROV¹

(¹ Highthroughput Factory, ² Structurome Research Group, ³ Structural Biophysics Laboratory RIKEN Harima Institute; ⁴RIKEN Genomic Sciences Center)

95. Structure of Osmotically Inducible Protein C from Thermus thermophilis HB8

Peter H. REHSE¹, Sayuri ISHIJIMA¹, Seiki KURAMITSU², Shigeyuki YOKOYAMA^2,4, Masashi MIYANO^1,3 and Tahir H. TAHIROV¹

(¹Highthroughput Factory, ² Structurome Research Group, ³ Structural Biophysics Laboratory RIKEN Harima Institute; ⁴ RIKEN Genomic Sciences Center)

96. Whole cell simulation environment for Thermus thermophilus

Mariko HATAKEYAMA^1,2, Takuji KAWASAKI³, Takashi NAKA⁴, Shuhei KIMURA¹, Kaori IDE^1,2, Fumikazu KONISHI^1,2, Shigeyuki YOKOYAMA^2,5,6, Seiki KURAMITSU^2,7, Akihiko KONAGAYA^1,2

(¹ Bioinformatics G., RIKEN GSC, ² RIKEN Harima Inst., ³ Fuji Res. Inst. Corp., ⁴ Dept. of Comp. Sci., Kyusyu Sangyo Univ., ⁵ Protein Res. G., RIKEN GSC, ⁶ Grad. Sch. of Sci., Univ. of Tokyo, ⁷ Grad. Sch. of Sci., Osaka Univ.)

97. GRID environment building toward the genetic information, function, and network analysis for Thermus thermophilus

Fumikazu KONISHI^1,2,Akinobu FUKUZAKI¹, Takeshi NAGASHIMA¹, Kaori IDE^1,2, Mariko HATAKEYAMA^1,2, Shigeyuki YOKOYAMA ^2,3,4, Seiki KURAMITSU^2,5, Akihiko KONAGAYA^1,2

(¹ Bioinformatics G., RIKEN GSC, ² RIKEN Harima Inst., ³Protein Res. G., RIKEN GSC, ⁴ Grad. Sch. of Sci., Univ. of Tokyo,⁵ Grad. Sch. of Sci., Osaka Univ.)

98. ORF annotation system for Thermus thermophilus

Akinobu FUKUZAKI¹, Takeshi NAGASHIMA¹, Kaori IDE^1,2, Fumikazu KONISHI^1,2, Mariko HATAKEYAMA^1,2, Shigeyuki YOKOYAMA ^2,3,4, Seiki KURAMITSU^2,5, Akihiko KONAGAYA^1,2

(¹ Bioinformatics G., RIKEN GSC, ² RIKEN Harima Inst., ³ Protein Res. G., RIKEN GSC,⁴ Grad. Sch. of Sci., Univ. of Tokyo, ⁵ Grad. Sch. of Sci., Osaka Univ.)

100. Structural Characterization of Neutral and Acidic Glycolipids from Thermus thermophilus HB8

Yasuo SUDA^1,2, Fumiaki OKAZAKI³, Yushi HASEGAWA³, Seiji AKACHI³, Koichi FUKASE³, Susumu KOKUBO², Seiki KURAMITSU^1,3 and Shoichi KUSUMOTO³

(¹RIKEN Harima Inst., ² Grad. Sch. of Sci. & Eng., Kagoshima Univ., Grad. Sch. of Sci., Osaka Univ.)

101. Low molecular weight and high copy vector pKMH052 for Thermus thermophilus HB27

Hideo KOBAYASHI¹, Asaomi KUWAE², Hideaki MASEDA¹, Akira NAKAMURA¹ , Takayuki HOSHINO¹

(¹ Tsukuba Univ., ² Kitasato Univ.)

102. Gene assembly-A new field of genome engineering using Bacillus subtilis GenoMe (BGM) vector is opened up

Kenji TSUGE, Kuniko MATSUI, Mitsuhiro ITAYA

(Mitsubishi Kagaku Inst. Life Sci.)

103. Crystal Structures of The Two components of 4-Hydroxyphenylacetate 3-monooxygenase from Thermus thermophilus

Seon-Hoon Kim¹, Hideyuki Miyatake¹, Tamao Hisano¹, and Kunio Miki^1,2

(¹ RIKEN Harima Inst., ² Grad. Sch. Sci., Kyoto Univ.)

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