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.