2006 Fiscal Year Final Research Report Summary
Structural biology of transcriptional regulation by SATB1 that binds to matrix attachment region of DNA
| Project/Area Number |
17570103
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Structural biochemistry
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| Research Institution | National Institute of Advanced Industrial Science and Technology (AIST) |
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Principal Investigator |
YAMASAKI Kazuhiko National Institute of Advanced Industrial Science and Technology, Age Dimension Research Center, Team Leader, 年齢軸生命工学研究センター, 研究チーム長 (00358243)
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| Project Period (FY) |
2005 – 2006
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| Keywords | protein-DNA interaction / transcription regulation / immune T-cell / NMR / X-ray crystallography / surface plasmon resonance / CUT domain |
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| Research Abstract |
SATB1 (special AT-rich sequence binding protein 1) is a transcription factor that regulates maturation of immune T-cells in thymus. It represses transcription of several genes including interleukin 2 receptor by binding to the matrix attachment region (MAR) of DNA of the target gene promoters and by recruiting histone deacetylase to the binding site. In this study we revealed the mechanism of recognition of MAR-DNA by SATB1 by means of structural biology.
We first determined the structure of MAR binding domain (MBD) of SATB1 by NMR spectroscopy. The structure possesses five a-helices arranged in a novel topology. By NMR titration experiments and surface plasmon resonance analyses of DNA binding of mutant proteins, the region of the protein relevant to DNA binding was identified. Also, by surface plasmon resonance experiments with DNA including modified bases and groove-specific binding drugs, it was revealed that SATB1-MBD binds to DNA from the major groove side, which is different from what was expected previously.
Next, we crystallized the complex of SATB1-MBD and MAR-DNA reflecting up to 2.0 Å in the laboratory diffractometer or 1.75 Å at synchrotron. Data revealed a structure of the complex in which SATB1-MBD binds to the major groove of DNA. Between the molecules direct hydrogen bonds are observed between a single amino acid and a single base, and water-mediated hydrogen bonds and hydrophobic interactions play a major role in the sequence-specific recognition. SATB1-MBD belongs to CUT domain and this is the first report on the mechanism of DNA recognition by CUT domains.
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