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Nucleic Acids Research Advance Access published online on July 25, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm504
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© 2007
The Author(s) This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1

Kazuhiko Yamasaki1,*, Toshihiko Akiba2, Tomoko Yamasaki1 and Kazuaki Harata2

1Age Dimension Research Center and 2Biological Information Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan

*To whom correspondence should be addressed: Tel: +81 29 8619473; Fax: +81 29 8612706; Email: k-yamasaki{at}aist.go.jp

Received March 16, 2007. Revised June 11, 2007. Accepted June 11, 2007.

Special AT-rich sequence binding protein 1 (SATB1) regulates gene expression essential in immune T-cell maturation and switching of fetal globin species, by binding to matrix attachment regions (MARs) of DNA and inducing a local chromatin remodeling. Previously we have revealed a five-helix structure of the N-terminal CUT domain, which is essentially the folded region in the MAR-binding domain, of human SATB1 by NMR. Here we determined crystal structure of the complex of the CUT domain and a MAR DNA, in which the third helix of the CUT domain deeply enters the major groove of DNA in the B-form. Bases of 5'-CTAATA-3' sequence are contacted by this helix, through direct and water-mediated hydrogen bonds and apolar and van der Waals contacts. Mutations at conserved base-contacting residues, Gln402 and Gly403, reduced the DNA-binding activity, which confirmed the importance of the observed interactions involving these residues. A significant number of equivalent contacts are observed also for typically four-helix POU-specific domains of POU-homologous proteins, indicating that these domains share a common framework of the DNA-binding mode, recognizing partially similar DNA sequences.


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