Solution Structure and DNA-binding Mode of the Matrix Attachment Region-binding Domain of the Transcription Factor SATB1 That Regulates the T-cell Maturation

Masaru Tateno,Kazuhiko Yamasaki,Hiroshi Yamaguchi

doi:10.1074/jbc.m510933200

Abstract

SATB1 is a transcriptional regulator controlling the gene expression that is essential in the maturation of the immune T-cell. SATB1 binds to the nuclear matrix attachment regions of DNA, where it recruits histone deacetylase and represses transcription through a local chromatin remodeling. Here we determined the solution structure of the matrix attachment region-binding domain, possessing similarity to the CUT DNA-binding domain, of human SATB1 by NMR spectroscopy. The structure consists of five alpha-helices, in which the N-terminal four are arranged similarly to the four-helix structure of the CUT domain of hepatocyte nuclear factor 6alpha. By an NMR chemical shift perturbation analysis and by surface plasmon resonance analyses of SATB1 mutant proteins, an interface for DNA binding was revealed to be located at the third helix and the surrounding regions. Surface plasmon resonance experiments using groove-specific binding drugs and methylated DNAs indicated that the domain recognizes DNA from the major groove side. These observations suggested that SATB1 possesses a DNA-binding mode similar to that of the POU-specific DNA-binding domain, which is known to share structural similarity to the four-helix CUT domain.

Highlights

IntroductionSATB1 (from special AT-rich sequence-binding protein 1) was initially identified as a factor that binds to the BUR sequence, which is predominantly expressed in thymus [3]
SATB1 was initially identified as a factor that binds to the BUR sequence, which is predominantly expressed in thymus [3]
We have initially expressed and purified a fragment corresponding to this region, and we found that the fragment contained significantly unfolded region(s) by NMR analyses

Summary

Introduction

SATB1 (from special AT-rich sequence-binding protein 1) was initially identified as a factor that binds to the BUR sequence, which is predominantly expressed in thymus [3]. SATB1 is ϳ800 amino acids in length, in which a region of ϳ150 amino acids located nearly in the middle (Tyr346–Asn495) is originally reported to be relevant to binding to the MAR DNA (MAR-binding domain (MBD)) [8]. This protein contains a homeodomain located at a more C-terminal region, which alone does not show significant DNA binding activity but enhances the activity of MBD [9]. The DNA-binding mode was elucidated by NMR titration, surface plasmon resonance (SPR), and point mutation experiments and was proposed to be similar to that by POU-specific domains

Methods

Results

Conclusion