title: Altered DNA recognition and bending by insertions in the alpha 2 tail of the yeast a1/alpha 2 homeodomain heterodimer.
abstract: The yeast MAT alpha 2 and MATa1 homeodomain proteins bind cooperatively as a heterodimer to sites upstream of haploid-specific genes, repressing their transcription. In the crystal structure of alpha 2 and a1 bound to DNA, each homeodomain makes independent base-specific contacts with the DNA and the two proteins contact each other through an extended tail region of alpha 2 that tethers the two homeodomains to one another. Because this extended region may be flexible, the ability of the heterodimer to discriminate among DNA sites with altered spacing between alpha 2 and a1 binding sites was examined. Spacing between the half sites was critical for specific DNA binding and transcriptional repression by the complex. However, amino acid insertions in the tail region of alpha 2 suppressed the effect of altering an a1/alpha 2 site by increasing the spacing between the half sites. Insertions in the tail also decreased DNA bending by a1/alpha 2. Thus tethering the two homeodomains contributes to DNA bending by a1/alpha 2, but the precise nature of the resulting bend is not essential for repression.
authors.affiliation: Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08855-0759, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Jin
authors.forename: J
authors.initials: J
authors.lastname: Mead
authors.forename: T
authors.initials: T
authors.lastname: Li
authors.forename: C
authors.initials: C
authors.lastname: Wolberger
authors.forename: A K
authors.initials: AK
authors.lastname: Vershon
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D003001:Cloning, Molecular; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D005656:Fungal Proteins / Q000737:chemistry / Q000378:metabolism*; D005800:Genes, Fungal; D018398:Homeodomain Proteins / Q000737:chemistry / Q000378:metabolism*; D046911:Macromolecular Substances; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012097:Repressor Proteins / Q000737:chemistry / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000737:chemistry; D029701:Saccharomyces cerevisiae Proteins; D017384:Sequence Deletion; D014158:Transcription, Genetic
chemical_list: D004271:DNA, Fungal; D005656:Fungal Proteins; D018398:Homeodomain Proteins; C096063:MATA1 protein, S cerevisiae; C062928:MATA2 protein, S cerevisiae; D046911:Macromolecular Substances; D012097:Repressor Proteins; D029701:Saccharomyces cerevisiae Proteins