NF-Y histone fold alpha1 helices help impart CCAAT specificity

J Mol Biol. 1999 Feb 19;286(2):327-37. doi: 10.1006/jmbi.1998.2496.


NF-Y is a conserved trimeric transcriptional activator with an extremely high specificity for CCAAT boxes. The NF-YB and NF-YC subunits have histone fold motifs with a high degree of homology to NC2alpha/beta, a TBP-binding repressor. The histone fold is composed of three alpha helices, alpha1, alpha2, alpha3, separated by short loops. Structural data on core histones showed that alpha1 are involved in DNA-binding. To understand the molecular basis of NF-Y sequence-specificity, we constructed deletion and swapping mutants, in which the alpha1 of NC2 and archeal HMfB, a bona fide histonic protein, was placed in NF-YB and NF-YC. Our analysis indicates that (i) subunit interactions are normal; (ii) NF-YB-NF-YC and NC2alpha/beta do not form heterodimers and NC2 cannot associate NF-YA. (iii) None of the NF-Y swaps can complex with TBP on a TATA box. (iv) Specific residues, R47 and K49 in NF-YC and N61 in NF-YB, are crucial for CCAAT-binding. We conclude that specificity of the NF-Y trimer is not due to NF-YA only, but stems in part from the contribution of the histone fold alpha1, particularly that of NF-YB.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Archaea / genetics
  • Bacterial Proteins / chemistry*
  • Binding Sites
  • CCAAT-Enhancer-Binding Proteins
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Dimerization
  • Histones / chemistry*
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Phosphoproteins / metabolism
  • Protein Binding
  • Protein Structure, Secondary*
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / metabolism
  • Regulatory Sequences, Nucleic Acid*
  • Sequence Deletion
  • Substrate Specificity
  • Transcription Factors / metabolism


  • Bacterial Proteins
  • CCAAT-Enhancer-Binding Proteins
  • DNA-Binding Proteins
  • Histones
  • Phosphoproteins
  • Recombinant Fusion Proteins
  • Transcription Factors
  • down-regulator of transcription 1
  • histone HMf
  • DNA