2O4A

Crystal Structure of the N-terminal CUT Domain of SATB1 Bound to Matrix Attachment Region DNA

Summary for 2O4A

• Entry DOI: 10.2210/pdb2o4a/pdb
• Related: 1YSE 2O49
• Descriptor: DNA (5'-D(*DGP*DCP*DTP*DAP*DAP*DTP*DAP*DTP*DAP*DTP*DGP*DC)-3'), DNA (5'-D(*DGP*DCP*DAP*DTP*DAP*DTP*DAP*DTP*DTP*DAP*DGP*DC)-3'), DNA-binding protein SATB1, ... (4 entities in total)
• Functional Keywords: protein-dna complex, transcription, transcription-dna complex, transcription/dna
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus matrix: Q01826
• Total number of polymer chains: 3
• Total formula weight: 18275.21

Authors

Yamasaki, K.,Akiba, T.,Harata, K. (deposition date: 2006-12-04, release date: 2007-08-14, Last modification date: 2023-10-25)

Primary citation

Yamasaki, K.,Akiba, T.,Yamasaki, T.,Harata, K.
Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1.
Nucleic Acids Res., 35:5073-5084, 2007

PubMed Abstract: 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.

PubMed: 17652321
DOI: 10.1093/nar/gkm504

Experimental method

X-RAY DIFFRACTION (1.75 Å)