2007 Fiscal Year Final Research Report Summary
Basic research on double-stranded DNA-binding proteins
| Project/Area Number |
17370058
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Yokohama City University |
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Principal Investigator |
NISHIMURA Yoshifumi Yokohama City University, Division of Structural Biology, International Graduate School of Arts and Sciences, Professor (70107390)
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| Co-Investigator(Kenkyū-buntansha) |
AKASHI Satoko Yokohama City University, Division of Structural Biology, International Graduate School of Arts and Sciences, Associate Professor (10280728)
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| Project Period (FY) |
2005 – 2007
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| Keywords | Nucleic acid / Genome / Protein / Regulation of gene expression / Aging / NMR / General transcription factor / Structural biology |
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| Research Abstract |
We determined the structures of both free hTFIIEalpha C-tearminal acidic domain (AC-D) and its form bound to the N-terminal pleckstrin homology domain (PH-D) of the p62 subunit of hTFIIH. Intriguingly, hTFIIEalpha AC-D was found to share its binding surface on p62 PH-D with the acidic transactivation peptide fragment of the human tumor supressor protein p53. However, hTFIIEalpha AC-D employs an entirely novel binding mode, which differs from the amphipathic helix method used by many transcriptional activators. The binding surface between p62 PH-D and hTFIIEalpha AC-D is much broader than the specific binding surface between p62 PH-D and the p53 peptide fragment. Given the recent demonstration of TFIIE and TFIIH functions in post initiation events (i.e. promoter clearance) these data are of special relevance to the regulatory mechanisms involved.
Essential Sas-related acetyltransferase 1 (Esa1) contains a presumed chromodomain in addition to a histone acetyltransferase (HAT) domain. We initially determined the solution structure of the Esa1 presumed chromodomain, and showed it to consist of a well folded structure similar to the tudor domain. The domain showed no RNA/DNA binding ability. Since the N-terminus of the protein forms a helical turn, we prepared an N-terminally extended construct, which was surprisingly found to bind to RNA and to be critical for in vivo function. This extended protein contains an additional β-sheet which acts as a knot for the tudor domain. The knot does not cause a global change in the core structure but induces a well defined loop in the tudor domain itself, which is responsible for RNA binding. We made point mutants in an esa1 mutant gene in yeast and their functional abilities examined. The knotted tudor domain mutations which were lethal to the yeast lost RNA binding ability.
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[Journal Article] Novel structural and functional mode of a knot essential for RNA binding activity of the Esal presumed chromodomain.2008
Author(s)
Shimojo, H., Sano, N., Moriwaki, Y., Okuda, M., Horikoshi, M., and Nishimura, Y
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Journal Title
J. Mol. Biol. 378
Pages: 987-1001
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Stmctural insight into the TFIIE/TFIIH interaction: TFIIEand p53 share the binding region on TFIIH.2008
Author(s)
Okuda, M., Tanaka, A., Satoh, M., Mizuta, S., Takazawa, M., Ohkuma, Y., and Nishimura, Y.
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Journal Title
EMBO J. 27
Pages: 1161-1171
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] A Mass Spectrometric Approach to the Study of DNA-Binding Proteins: The Interaction of Human TRF2 with Telomeric DNA.2008
Author(s)
Sperry, J.B. Shi, X., Rempel, D.L., Nishimura, Y., Akashi, S., Gross, M.L.
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Journal Title
Biochemsitry 47
Pages: 1797-1807
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Water-mediated interactions between DNA and PhoB DNA-binding/ transctivation domain: NMR-restrained molecular dynamics in explicit water en vironment.2008
Author(s)
Yamane, T., Okamura, H., Ikeguchi, M., Nishimura, Y., Kidera, A.
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Journal Title
PROTEINS: Structure, Function, and Bioinformatics 71
Pages: 1970-1983
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
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[Journal Article] Structural characterization of human general transcription factor TFIIF in solution.2008
Author(s)
Akashi, S., Nagakura, S., Yamamoto, S., Okuda, M., Ohkuma, Y., Nishimura Y.
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Journal Title
Protein Sci. 17
Pages: 389-400
Description
「研究成果報告書概要(和文)」より
Peer Reviewed
-
[Journal Article] Novel structural and functional mode of a knot essential for RNA binding activity of the Esal presumed chromodomain2008
Author(s)
Shimojo, H., Sano, N., Moriwaki, Y, Okuda, M., Horikoshi, M., Nishimura, Y
-
Journal Title
J. Mol. Biol 378
Pages: 987-1001
Description
「研究成果報告書概要(欧文)」より
-
[Journal Article] Structural insight into the TFIIE/TFIIH interaction: TFIIE and p53 share the binding region on TFIIH2008
Author(s)
Okuda, M., Tanaka, A., Satoh, M., Mizuta, S., Takazawa, M., Ohkuma, Y., Nishimura. Y
-
Journal Title
EMBO J 27
Pages: 1161-1171
Description
「研究成果報告書概要(欧文)」より
-
-
[Journal Article] Water-mediated interactions between DNA and PhoB DNA-binding/ transctivation domain: NMR-restrained molecular dynamics in explicit water environment.2008
Author(s)
Yamane, T., Okamura, H., Ikeguchi, M., Nishimura. Y., Kidera, A
-
Journal Title
PROTEINS: Structure, Function, and Bioinformatics 71
Pages: 1970-1983
Description
「研究成果報告書概要(欧文)」より
-
[Journal Article] Structural characterization of human general transcription factor TFIIF in solution.2008
Author(s)
Akashi, S., Nagakura, S., Yamamoto, S., Okuda, M., Ohkuma, Y., Nishimura Y
-
Journal Title
Protein Sci 17
Pages: 389-400
Description
「研究成果報告書概要(欧文)」より
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