Structure of Pit-1 POU domain bound to DNA as a dimer: unexpected arrangement and flexibility.
Pit-1, a member of the POU domain family of transcription factors, characterized by a bipartite DNA-binding domain, serves critical developmental functions based on binding to diverse DNA elements in its target genes. Here we report a high resolution X-ray analysis of the Pit-1 POU domain bound to a DNA element as a homodimer. This analysis reveals that Pit-1 subdomains bind to perpendicular faces of the DNA, rather than opposite faces of the DNA as in Oct-1. This is accomplished by different spacing and orientation of the POU-specific domain. Contrary to previous predictions, the dimerization interface involves the carboxyl terminus of the DNA recognition helix of the homeodomain, which in an extended conformation interacts with specific residues at the amino terminus of helix alpha1 and in the loop between helices alpha3 and alpha4 of the POU-specific domain of the symmetry related monomer. These features suggest the molecular basis of disease-causing mutations in Pit-1 and provide potential basis for the flexible allostery between protein domains and DNA sites in the activation of target genes.
Jacobson
E M
EM
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.
Li
P
P
Leon-del-Rio
A
A
Rosenfeld
M G
MG
Aggarwal
A K
AK
D000595:Amino Acid Sequence; D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D019281:Dimerization; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000235:genetics; D051863:Host Cell Factor C1; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D050811:Octamer Transcription Factor-1; D050809:POU Domain Factors; D010907:Pituitary Hormones / Q000172:deficiency; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D051381:Rats; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D050817:Transcription Factor Pit-1; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
D004268:DNA-Binding Proteins; C497692:HCFC1 protein, human; D018398:Homeodomain Proteins; D051863:Host Cell Factor C1; D050811:Octamer Transcription Factor-1; D050809:POU Domain Factors; C494187:POU1F1 protein, human; C494165:POU2F1 protein, human; D010907:Pituitary Hormones; C494186:Pou1f1 protein, rat; C494168:Pou2f1 protein, rat; D011994:Recombinant Proteins; D050817:Transcription Factor Pit-1; D014157:Transcription Factors; D004247:DNA