title: Structural basis for the cooperative DNA recognition by Smad4 MH1 dimers.
abstract: Smad proteins form multimeric complexes consisting of the 'common partner' Smad4 and receptor regulated R-Smads on clustered DNA binding sites. Deciphering how pathway specific Smad complexes multimerize on DNA to regulate gene expression is critical for a better understanding of the cis-regulatory logic of TGF-β and BMP signaling. To this end, we solved the crystal structure of the dimeric Smad4 MH1 domain bound to a palindromic Smad binding element. Surprisingly, the Smad4 MH1 forms a constitutive dimer on the SBE DNA without exhibiting any direct protein-protein interactions suggesting a DNA mediated indirect readout mechanism. However, the R-Smads Smad1, Smad2 and Smad3 homodimerize with substantially decreased efficiency despite pronounced structural similarities to Smad4. Therefore, intricate variations in the DNA structure induced by different Smads and/or variant energetic profiles likely contribute to their propensity to dimerize on DNA. Indeed, competitive binding assays revealed that the Smad4/R-Smad heterodimers predominate under equilibrium conditions while R-Smad homodimers are least favored. Together, we present the structural basis for DNA recognition by Smad4 and demonstrate that Smad4 constitutively homo- and heterodimerizes on DNA in contrast to its R-Smad partner proteins by a mechanism independent of direct protein contacts.
authors: Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore-138672.
authors: Nithya
authors: N
authors: Baburajendran
authors: Ralf
authors: R
authors: Jauch
authors: Clara Yueh Zhen
authors: CY
authors: Tan
authors: Kamesh
authors: K
authors: Narasimhan
authors: Prasanna R
authors: PR
authors: Kolatkar
mesh_terms: D000818:Animals; D001665:Binding Sites; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D019281:Dimerization; D051379:Mice; D011485:Protein Binding; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D050436:Regulatory Elements, Transcriptional; D051896:Smad Proteins, Receptor-Regulated / Q000378:metabolism; D051901:Smad4 Protein / Q000737:chemistry* / Q000378:metabolism
chemical_list: D051896:Smad Proteins, Receptor-Regulated; D051901:Smad4 Protein; C490810:Smad4 protein, mouse; D004247:DNA