Linker length and composition influence the flexibility of Oct-1 DNA binding

EMBO J. 1997 Apr 15;16(8):2043-53. doi: 10.1093/emboj/16.8.2043.


POU domain transcription factors have two separate helix-turn-helix DNA-binding subdomains, the POU homeodomain (POUhd) and the POU-specific domain (POUs). Each subdomain recognizes a specific subsite of 4 or 5 bp in the octamer recognition sequence. The Oct-1 POU subdomains are connected by a 23 amino acid unstructured linker region. To investigate the requirements for the linker and its role in DNA recognition, we constructed POU domains in which the subdomains are connected with linkers varying in length between 2 and 37 amino acids. Binding to the natural octamer site required a minimal linker length of between 10 and 14 amino acids. A POU domain with an eight amino acid linker, however, had a high affinity for a site in which the POUs recognition sequence was inverted. Computer modelling shows that inversion of the POUs subdomain shortens the distance between the subdomains sufficiently to enable an eight amino acid linker to bridge the distance. DNase I footprinting as well as mutation of the POUs-binding site confirms the inverted orientation of the POUs domain. Switching of the POUs and POUhd subdomains and separation by 3 bp leads to a large distance which could only be bridged effectively by a long 37 amino acid linker. In addition to linker length, mutation of a conserved glutamate residue in the linker affected binding. As shown by surface plasmon resonance measurements, this was caused by a decrease in the on-rate. Our data indicate that there are both length and sequence requirements in the linker region which allow flexibility leading to selective binding to differently spaced and oriented subsites.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • DNA Footprinting
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / genetics
  • Glutamic Acid / metabolism
  • Helix-Turn-Helix Motifs*
  • Homeodomain Proteins / chemistry*
  • Homeodomain Proteins / genetics
  • Host Cell Factor C1
  • Models, Molecular*
  • Molecular Sequence Data
  • Octamer Transcription Factor-1
  • Protein Conformation
  • Sequence Deletion
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics


  • DNA-Binding Proteins
  • Homeodomain Proteins
  • Host Cell Factor C1
  • Octamer Transcription Factor-1
  • Transcription Factors
  • Glutamic Acid