Abstract
The nuclear matrix attachment DNA (MAR) binding protein SATB1 is a
sequence context-specific binding protein that binds in the minor
groove, making virtually no contact with the DNA bases. The SATB1
binding sites consist of a special AT-rich sequence context in which
one strand is well-mixed A's, T's, and C's, excluding G's
(ATC sequences), which is typically found in clusters within different
MARs. To determine the extent of conservation of the SATB1 gene among
different species, we cloned a mouse homolog of the human STAB1 cDNA
from a cDNA expression library of the mouse thymus, the tissue in
which this protein is predominantly expressed. This mouse cDNA encodes
a 764-amino-acid protein with a 98% homology in amino acid sequence
to the human SATB1 originally cloned from testis. To characterize
the DNA binding domain of this novel class of protein, we used the
mouse SATB1 cDNA and delineated a 150-amino-acid polypeptide as the
binding domain. This region confers full DNA binding activity, recognizes
the specific sequence context, and makes direct contact with DNA
at the same nucleotides as the whole protein. This DNA binding domain
contains a novel DNA binding motif: when no more than 21 amino acids
at either the N- or C-terminal end of the binding domain are deleted,
the majority of the DNA binding activity is lost. The concomitant
presence of both terminal sequences is mandatory for binding. These
two terminal regions consist of hydrophilic amino acids and share
homologous sequences that are different from those of any known DNA
binding motifs. We propose that the DNA binding region of SATB1 extends
its two terminal regions toward DNA to make direct contact with DNA.
- acid
- acid;
- alignment;
- amino
- amino_acid_sequence
- analysis;
- animals
- animals;
- antigens,
- antigens,_nuclear
- attachment
- binding
- binding_sites
- chemistry
- chemistry/metabolism;
- chemistry;
- cloning,
- cloning,_molecular
- complementary,
- data;
- deletion;
- deoxyribonucleoproteins,
- deoxyribonucleoproteins,_chemistry
- dna
- dna,
- dna,_complementary,_genetics
- dna-binding
- dna-binding_proteins,_chemistry/metabolism
- dna_mutational_analysis
- factors,
- genes
- genes;
- genetics;
- gland,
- homology,
- matrix
- matrix,
- matrix_attachment_region_binding_proteins
- metabolism;
- mice
- mice;
- molecular
- molecular;
- molecular_sequence_data
- mutational
- nuclear
- nuclear;
- nuclear_matrix,_metabolism
- nuclear_proteins,_chemistry
- oligodeoxyribonucleotides,
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