NMR structure of transcription factor Sp1 DNA binding domain

Biochemistry. 2004 Dec 28;43(51):16027-35. doi: 10.1021/bi048438p.


To understand the DNA recognition mechanism of zinc finger motifs of transcription factor Sp1, we have determined the solution structure of DNA-binding domain of the Sp1 by solution NMR techniques. The DNA-binding domain of Sp1 consists of three Cys(2)His(2)-type zinc finger motifs. They have typical betabetaalpha zinc finger folds and relatively random orientations. From DNA-binding analysis performed by NMR and comparison between structures determined here and previously reported structures of other zinc fingers, it was assumed that DNA recognition modes of fingers 2 and 3 would be similar to those of fingers of Zif268, in which each finger recognizes four base pairs strictly by using residues at positions -1, 2, 3, and 6 of the recognition helix. On the contrary, finger 1 can use only two residues for DNA recognition, Lys550 and His553 at positions -1 and 3 of the helix, and has more relaxed sequence and site specificity than other Cys(2)His(2) zinc fingers. It is proposed that this relaxed property of finger 1 allows transcription factor Sp1 to bind various DNA sequences with high affinity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Crystallography, X-Ray
  • DNA / metabolism*
  • Magnetic Resonance Spectroscopy
  • Molecular Sequence Data
  • Nitrogen Isotopes
  • Sequence Alignment
  • Sp1 Transcription Factor / chemistry*
  • Sp1 Transcription Factor / metabolism


  • Nitrogen Isotopes
  • Sp1 Transcription Factor
  • DNA

Associated data

  • PDB/1TF3
  • PDB/1VA1
  • PDB/1VA2
  • PDB/1VA3