Koreaki Ito

Summary

Affiliation: Kyoto University
Country: Japan

Publications

  1. pmc YaeL (EcfE) activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA
    Kazue Kanehara
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Genes Dev 16:2147-55. 2002
  2. pmc Mutational analysis of transmembrane regions 3 and 4 of SecY, a central component of protein translocase
    Hiroyuki Mori
    Institute for Virus Research, Kyoto University, Sakyo ku, Kyoto 606 8507, Japan
    J Bacteriol 186:3960-9. 2004
  3. pmc Conformational transition of Sec machinery inferred from bacterial SecYE structures
    Tomoya Tsukazaki
    Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta cho, Midori ku, Yokohama shi, Kanagawa 226 8501, Japan
    Nature 455:988-91. 2008
  4. ncbi request reprint Ribosome-based protein folding systems are structurally divergent but functionally universal across biological kingdoms
    Koreaki Ito
    Institute for Virus Research, and CREST of Japan Science and Technology Agency, Kyoto University, Kyoto 606 8507, Japan
    Mol Microbiol 57:313-7. 2005
  5. ncbi request reprint Cellular functions, mechanism of action, and regulation of FtsH protease
    Koreaki Ito
    Institute for Virus Research, Kyoto University, Sakyo ku, Kyoto 606 8507, Japan
    Annu Rev Microbiol 59:211-31. 2005
  6. ncbi request reprint Reactivities of quinone-free DsbB from Escherichia coli
    Kenji Inaba
    Institute for Virus Research, Kyoto University, and CREST of Japan Science and Technology Agency, Kyoto 606 8507, Japan
    J Biol Chem 280:33035-44. 2005
  7. ncbi request reprint Reconstitution of membrane proteolysis by FtsH
    Yoshinori Akiyama
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    J Biol Chem 278:18146-53. 2003
  8. ncbi request reprint The intramembrane active site of GlpG, an E. coli rhomboid protease, is accessible to water and hydrolyses an extramembrane peptide bond of substrates
    Saki Maegawa
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Mol Microbiol 64:435-47. 2007
  9. ncbi request reprint DsbB elicits a red-shift of bound ubiquinone during the catalysis of DsbA oxidation
    Kenji Inaba
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    J Biol Chem 279:6761-8. 2004
  10. ncbi request reprint Nearest neighbor analysis of the SecYEG complex. 2. Identification of a SecY-SecE cytosolic interface
    Yasunari Satoh
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Biochemistry 42:7442-7. 2003

Collaborators

Detail Information

Publications56

  1. pmc YaeL (EcfE) activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA
    Kazue Kanehara
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Genes Dev 16:2147-55. 2002
    ..Thus, YaeL is positively required for the sigma(E) extracytoplasmic stress response...
  2. pmc Mutational analysis of transmembrane regions 3 and 4 of SecY, a central component of protein translocase
    Hiroyuki Mori
    Institute for Virus Research, Kyoto University, Sakyo ku, Kyoto 606 8507, Japan
    J Bacteriol 186:3960-9. 2004
    ..These results are discussed in light of the structural information available for the SecY complex...
  3. pmc Conformational transition of Sec machinery inferred from bacterial SecYE structures
    Tomoya Tsukazaki
    Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta cho, Midori ku, Yokohama shi, Kanagawa 226 8501, Japan
    Nature 455:988-91. 2008
    ....
  4. ncbi request reprint Ribosome-based protein folding systems are structurally divergent but functionally universal across biological kingdoms
    Koreaki Ito
    Institute for Virus Research, and CREST of Japan Science and Technology Agency, Kyoto University, Kyoto 606 8507, Japan
    Mol Microbiol 57:313-7. 2005
    ....
  5. ncbi request reprint Cellular functions, mechanism of action, and regulation of FtsH protease
    Koreaki Ito
    Institute for Virus Research, Kyoto University, Sakyo ku, Kyoto 606 8507, Japan
    Annu Rev Microbiol 59:211-31. 2005
    ....
  6. ncbi request reprint Reactivities of quinone-free DsbB from Escherichia coli
    Kenji Inaba
    Institute for Virus Research, Kyoto University, and CREST of Japan Science and Technology Agency, Kyoto 606 8507, Japan
    J Biol Chem 280:33035-44. 2005
    ..We discuss the significance of having such multiple reaction pathways for the DsbB-dependent DsbA oxidation...
  7. ncbi request reprint Reconstitution of membrane proteolysis by FtsH
    Yoshinori Akiyama
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    J Biol Chem 278:18146-53. 2003
    ..Addition of ATP then resulted in degradation of the substrate. It was shown that FtsH can function in the process of membrane proteins degradation without aid from any other cellular factors...
  8. ncbi request reprint The intramembrane active site of GlpG, an E. coli rhomboid protease, is accessible to water and hydrolyses an extramembrane peptide bond of substrates
    Saki Maegawa
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Mol Microbiol 64:435-47. 2007
    ....
  9. ncbi request reprint DsbB elicits a red-shift of bound ubiquinone during the catalysis of DsbA oxidation
    Kenji Inaba
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    J Biol Chem 279:6761-8. 2004
    ..We propose that the Cys44-induced anomaly in ubiquinone represents its activated state, which drives the DsbB-mediated electron transfer...
  10. ncbi request reprint Nearest neighbor analysis of the SecYEG complex. 2. Identification of a SecY-SecE cytosolic interface
    Yasunari Satoh
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Biochemistry 42:7442-7. 2003
    ..We suggest that the cytosolic and intramembrane interactions bring these two subunits together, forming a functionally crucial SecYE interface involving the SecY C5 region and the conserved cytosolic segment of SecE...
  11. doi request reprint Substrate recognition and binding by RseP, an Escherichia coli intramembrane protease
    Kayo Koide
    Institute for Virus Research, Kyoto University, Kawara chu, Shogoin, Kyoto 606 8507, Japan
    J Biol Chem 283:9562-70. 2008
    ..These results provide insights into the mechanism of membrane protein proteolysis by RseP...
  12. ncbi request reprint Role of the cytosolic loop of DsbB in catalytic turnover of the ubiquinone-DsbB complex
    Yoh hei Takahashi
    Institute for Virus Research, Kyoto University and CREST, Japan Science and Technology Agency, Kyoto, Japan
    Antioxid Redox Signal 8:743-52. 2006
    ..These observations suggest that the cytosolic loop is important to coordinate the active-site residues of DsbB and ubiquinone to allow their proper reaction cycles...
  13. ncbi request reprint Characterization of the menaquinone-dependent disulfide bond formation pathway of Escherichia coli
    Yoh hei Takahashi
    Institute for Virus Research, Kyoto University, Sakyo ku, Kyoto 606 8507, Japan
    J Biol Chem 279:47057-65. 2004
    ..The MK-dependent pathway provides opportunities to further dissect the quinone-dependent DsbA-DsbB redox reactions...
  14. pmc YaeL proteolysis of RseA is controlled by the PDZ domain of YaeL and a Gln-rich region of RseA
    Kazue Kanehara
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    EMBO J 22:6389-98. 2003
    ..These results indicate that multiple negative elements both in the enzyme (PDZ domain) and in the substrate (glutamine-rich region) determine the strict dependence of the site-2 proteolysis on the site-1 cleavage...
  15. ncbi request reprint Crystal structure of the DsbB-DsbA complex reveals a mechanism of disulfide bond generation
    Kenji Inaba
    Institute for Virus Research, Kyoto University and CREST, Japan Science and Technology Agency, Kyoto 606 8507, Japan
    Cell 127:789-801. 2006
    ..We propose that DsbB is converted by its specific substrate, DsbA, to a superoxidizing enzyme, capable of oxidizing this extremely oxidizing oxidase...
  16. ncbi request reprint The Escherichia coli plasma membrane contains two PHB (prohibitin homology) domain protein complexes of opposite orientations
    Shinobu Chiba
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Mol Microbiol 60:448-57. 2006
    ..We discuss possible significance of having PHB domains on both sides of the membrane...
  17. ncbi request reprint Nearest neighbor analysis of the SecYEG complex. 1. Identification of a SecY-SecG interface
    Yasunari Satoh
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Biochemistry 42:7434-41. 2003
    ..These results collectively suggest that a C2-TM3-P2-TM4-C3 region of SecY serves as an interface with SecG...
  18. ncbi request reprint Proteolytic activity of HtpX, a membrane-bound and stress-controlled protease from Escherichia coli
    Machiko Sakoh
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    J Biol Chem 280:33305-10. 2005
    ..We verified its ability to cleave SecY in vivo by overproducing both HtpX and SecY. These results showed that HtpX is a zinc-dependent endoprotease member of the membrane-localized proteolytic system in E. coli...
  19. pmc RseP (YaeL), an Escherichia coli RIP protease, cleaves transmembrane sequences
    Yoshinori Akiyama
    Institute for Virus Research, Kyoto University, Kyoto, Japan
    EMBO J 23:4434-42. 2004
    ..These results show that RseP has potential ability to cut a broad range of membrane protein sequences. Intriguingly, it is nevertheless recruited to the sigma(E) stress-response cascade as a specific player of RIP...
  20. pmc SecM facilitates translocase function of SecA by localizing its biosynthesis
    Hitoshi Nakatogawa
    Institute for Virus Research and CREST, Japan Science and Technology Corporation, Kyoto University, Kyoto 606 8507, Japan
    Genes Dev 19:436-44. 2005
    ..Biosynthesis in the vicinity of the membrane and the Sec translocon will be beneficial for this multiconformation ATPase to adopt ready-to-function conformations...
  21. pmc Translation arrest of SecM is essential for the basal and regulated expression of SecA
    Akiko Murakami
    Institute for Virus Research and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto University, Kyoto 606 8507, Japan
    Proc Natl Acad Sci U S A 101:12330-5. 2004
    ..Second, the prolonged SecM elongation arrest under conditions of unfavorable protein secretion is required for the enhanced expression of SecA to cope with such conditions...
  22. pmc Critical role of a thiolate-quinone charge transfer complex and its adduct form in de novo disulfide bond generation by DsbB
    Kenji Inaba
    Institute for Virus Research, Kyoto University and Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kyoto 606 8507, Japan
    Proc Natl Acad Sci U S A 103:287-92. 2006
    ..A similar mechanism is conceivable for a class of eukaryotic dithiol oxidases having a FAD cofactor...
  23. pmc Peculiar properties of DsbA in its export across the Escherichia coli cytoplasmic membrane
    Nobuyuki Shimohata
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    J Bacteriol 187:3997-4004. 2005
    ..These results suggest that DsbA uses not only the signal recognition particle targeting pathway but also a special route of translocation through the translocon, which is hence suggested to actively discriminate pre-proteins...
  24. pmc SecY alterations that impair membrane protein folding and generate a membrane stress
    Nobuyuki Shimohata
    Institute for Virus Research, Kyoto University, Sakyo ku, Kyoto 606 8507, Japan
    J Cell Biol 176:307-17. 2007
    ..The results demonstrate that normal SecY function is required for the folding of membrane proteins after their insertion into the translocon...
  25. ncbi request reprint The long alpha-helix of SecA is important for the ATPase coupling of translocation
    Hiroyuki Mori
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    J Biol Chem 281:36249-56. 2006
    ..Based on these results, we propose that the motor function of SecA is realized by ligand-activated ATPase engine and its HSD-mediated conversion into the mechanical work of preprotein translocation...
  26. ncbi request reprint The Cpx stress response system of Escherichia coli senses plasma membrane proteins and controls HtpX, a membrane protease with a cytosolic active site
    Nobuyuki Shimohata
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Genes Cells 7:653-62. 2002
    ..The pathway for this transmembrane signalling is mediated by the CpxR-CpxA two-component phospho-relay mechanism...
  27. ncbi request reprint Environment of the active site region of RseP, an Escherichia coli regulated intramembrane proteolysis protease, assessed by site-directed cysteine alkylation
    Kayo Koide
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    J Biol Chem 282:4553-60. 2007
    ..These results suggest that the active site of RseP is not totally embedded in the lipid phase but located within a proteinaceous structure that is partially exposed to the aqueous milieu...
  28. pmc Post-liberation cleavage of signal peptides is catalyzed by the site-2 protease (S2P) in bacteria
    Akira Saito
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Proc Natl Acad Sci U S A 108:13740-5. 2011
    ..These results uncover a physiological role of bacterial S2P proteases and update the basic knowledge about the fate of signal peptides in bacterial cells...
  29. ncbi request reprint FtsH exists as an exceptionally large complex containing HflKC in the plasma membrane of Escherichia coli
    Naoya Saikawa
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    J Struct Biol 146:123-9. 2004
    ..This complex appears to have molecular mass of around 1000 kDa. A tentative model is presented that it is composed of hexamers of FtsH and of HflKC, with an ability to bind one or a few substrate molecules...
  30. ncbi request reprint Genetically encoded but nonpolypeptide prolyl-tRNA functions in the A site for SecM-mediated ribosomal stall
    Hiroki Muto
    Institute for Virus Research, Kyoto University, Japan
    Mol Cell 22:545-52. 2006
    ..These results reveal that secM-encoded Pro166-tRNA functions as a nonpolypeptide element in fulfilling SecM's role as a secretion monitor...
  31. doi request reprint The disulfide bond formation (Dsb) system
    Koreaki Ito
    Institute for Virus Research, Kyoto University, Kyoto, Japan
    Curr Opin Struct Biol 18:450-8. 2008
    ..Molecular details of these remarkable biochemical cascades are being rapidly unraveled by genetic, biochemical, and structural analyses in recent years...
  32. pmc Biochemical characterization of a mutationally altered protein translocase: proton motive force stimulation of the initiation phase of translocation
    Hiroyuki Mori
    Institute for Virus Research, Kyoto University, Sakyo ku, Japan
    J Bacteriol 185:405-12. 2003
    ..The proton motive force-dependent step proved to lie before signal peptide cleavage. We suggest that the proton motive force assists in the initiation phase of protein translocation...
  33. pmc Membrane protein degradation by FtsH can be initiated from either end
    Shinobu Chiba
    Institute for Virus Research, Kyoto University, Sakyo ku, Kyoto 606 8507, Japan
    J Bacteriol 184:4775-82. 2002
    ..Our results also suggest that some membrane proteins receive bidirectional degradation simultaneously. These results raise intriguing questions about the molecular directionality of the dislocation and proteolysis catalyzed by FtsH...
  34. ncbi request reprint Intraribosomal regulation of expression and fate of proteins
    Hitoshi Nakatogawa
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Chembiochem 5:48-51. 2004
    ..These properties of nascent proteins can in turn provide regulatory mechanisms by which the expression of genetic information at different levels is regulated...
  35. ncbi request reprint Peptidyl-prolyl-tRNA at the ribosomal P-site reacts poorly with puromycin
    Hiroki Muto
    Institute for Virus Research, Kyoto University, Sakyo ku, Kyoto 606 8507, Japan
    Biochem Biophys Res Commun 366:1043-7. 2008
    ..These results raise a possibility that the peptidyl transferase activity of the ribosome may have some specificity with regard to the P-site amino acids...
  36. pmc Different modes of SecY-SecA interactions revealed by site-directed in vivo photo-cross-linking
    Hiroyuki Mori
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Proc Natl Acad Sci U S A 103:16159-64. 2006
    ..On the basis of these findings, we propose that the C6 tail of SecY interacts with the working form of SecA, whereas C4-C5 loops may offer constitutive SecA-binding sites...
  37. ncbi request reprint Control of SecA and SecM translation by protein secretion
    Hitoshi Nakatogawa
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Curr Opin Microbiol 7:145-50. 2004
    ..These results are discussed in relation to the versatile nature of SecA in its localization and structure...
  38. ncbi request reprint Fluorescence resonance energy transfer analysis of protein translocase. SecYE from Thermus thermophilus HB8 forms a constitutive oligomer in membranes
    Hiroyuki Mori
    Institute for Virus Research, Kyoto University, Japan
    J Biol Chem 278:14257-64. 2003
    ....
  39. pmc A SecE mutation that modulates SecY-SecE translocase assembly, identified as a specific suppressor of SecY defects
    Hiroyuki Mori
    Institute for Virus Research, Kyoto University, Sakyo ku, Kyoto 606 8507, Japan
    J Bacteriol 185:948-56. 2003
    ..It is suggested that the S105P alteration affects the SecYEG channel such that it is more prone to open and to accept the translocation initiation domain of a preprotein molecule...
  40. pmc Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus
    Tomoya Tsukazaki
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:376-80. 2006
    ..These results provide information that is essential for the determination of the three-dimensional structure of this important membrane component of the protein-translocation machinery...
  41. ncbi request reprint Proteolytic action of GlpG, a rhomboid protease in the Escherichia coli cytoplasmic membrane
    Saki Maegawa
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Biochemistry 44:13543-52. 2005
    ..These results point to a detailed molecular mechanism and cellular analysis of this interesting class of membrane-embedded proteases...
  42. ncbi request reprint Identification of glutamic acid 479 as the gluzincin coordinator of zinc in FtsH (HflB)
    Naoya Saikawa
    Institute for Virus Research, Kyoto University, Sakyo ku, Kyoto 606 8507, Japan
    Biochemistry 41:1861-8. 2002
    ..They exhibited reduced zinc contents upon purification. From these results, we conclude that Glu(479) is a zinc-coordinating residue...
  43. pmc Paradoxical redox properties of DsbB and DsbA in the protein disulfide-introducing reaction cascade
    Kenji Inaba
    Institute for Virus Research, Japan Science and Technology Corporation, Kyoto University, Kyoto 606 8507, Japan
    EMBO J 21:2646-54. 2002
    ..Thus, DsbB can mediate electron flow from DsbA to ubiquinone irrespective of the intrinsic redox potential of the Cys residues involved...
  44. ncbi request reprint [The functions of the ribosomal tunnel in a birth of proteins]
    Hitoshi Nakatogawa
    Tanpakushitsu Kakusan Koso 49:829-33. 2004
  45. ncbi request reprint [New concepts gained from the study of SecM, a secretion monitor protein]
    Hiroki Muto
    Tanpakushitsu Kakusan Koso 51:2583-9. 2006
  46. ncbi request reprint [Translation arrest and its involvement in protein translocation across membranes]
    Hitoshi Nakatogawa
    Tanpakushitsu Kakusan Koso 48:338-45. 2003
  47. pmc Roles of the C-terminal end of SecY in protein translocation and viability of Escherichia coli
    Kazuhiko Chiba
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    J Bacteriol 184:2243-50. 2002
    ..SecA binding was normal, but SecA insertion in response to ATP and a preprotein was impaired. It is suggested that the C-terminal SecY residues are required for SecA-dependent translocation initiation...
  48. ncbi request reprint Superactive SecY variants that fulfill the essential translocation function with a reduced cellular quantity
    Hiroyuki Mori
    Institute for Virus Research, Kyoto University, Sakyo ku, Japan
    J Biol Chem 277:48550-7. 2002
    ..These results have been interpreted in terms of balance shifts between channel closing and channel opening alterations in the SecYEG translocase...
  49. ncbi request reprint The ribosomal exit tunnel functions as a discriminating gate
    Hitoshi Nakatogawa
    Institute for Virus Research and CREST, Japan Science and Technology Corporation, Kyoto University, Japan
    Cell 108:629-36. 2002
    ..Thus, we suggest that this region of the exit tunnel interacts with nascent translation products and functions as a discriminating gate...
  50. ncbi request reprint Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer
    Dmitry G Vassylyev
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 434 Kaul Genetics Building, 720 20 th Street South, Birmingham, AL 35294, USA
    J Mol Biol 364:248-58. 2006
    ....
  51. ncbi request reprint Structure and mechanisms of the DsbB-DsbA disulfide bond generation machine
    Kenji Inaba
    Division of Protein Chemistry, Post Genome Science Center, Medical Institute of Bioregulation, Kyushu University, 3 1 1 Maidashi, Higashi ku, Fukuoka 812 8582, Japan
    Biochim Biophys Acta 1783:520-9. 2008
    ..One of the DsbB cysteines that are now reduced then interacts with ubiquinone to form a charge transfer complex, leading to the regeneration of a disulfide at the DsbB active site, and the cycle can begin anew...
  52. ncbi request reprint [Structural basis for disulfide bond generation in the cell]
    Kenji Inaba
    Tanpakushitsu Kakusan Koso 52:853-61. 2007
  53. ncbi request reprint Characterization of mutations in the GTP-binding domain of IF2 resulting in cold-sensitive growth of Escherichia coli
    Brian Søgaard Laursen
    Department of Molecular Biology, Aarhus University, DK 8000 C Aarhus, Denmark
    J Mol Biol 326:543-51. 2003
    ..The results indicate that the amino acid residues, Asp409 and Gly422, are located in important regions of the IF2 G-domain and demonstrate the importance of GTP hydrolysis in translation initiation for optimal cell growth...
  54. ncbi request reprint [Finding of translocon]
    Koreaki Ito
    Tanpakushitsu Kakusan Koso 52:1480-31. 2007
  55. ncbi request reprint Redox control of protein processing: from electrons to cells
    Koreaki Ito
    Antioxid Redox Signal 8:729-30. 2006
  56. pmc Cloning, expression, purification, crystallization and initial crystallographic analysis of the preprotein translocation ATPase SecA from Thermus thermophilus
    Marina N Vassylyeva
    Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, 402B Kaul Genetics Building, 720 20th Street South, Birmingham, AL 35294, USA
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:909-12. 2006
    ..The crystals, improved by macroseeding, diffracted to beyond 2.8 and 3.5 A resolution for the trigonal and hexagonal crystal forms, respectively. Structure determination using the multiple isomorphous replacement method is in progress...