Protein-DNA binding motifs


Type of Interaction*
Example proteins
- helices __
AK(P)not sequence selective

contacts with sugar-phosphate backbone.

Histone H1
Helix-turn-helixMajor groove, orientation within groove is variable E.coli CAP (440 kb), tet repressor
HomeodomainMajor groove + a few minor groove contacts homeobox proteins
Anfingers (TFIIIA type) Major grooveTFIIIA
Zn fingers (steroid receptor type) Major grooveglucocorticoid receptor
Zn fingers (GAL4 type) Major grooveGAL4
Bzip (leucine zipper) Major grooveGCN4, Fos, Jun (293 kb)
Parallel - helices Major grooveEcoR I (208 kb monomer)
- structures __
Anti-parallel strands +/- sequence selective. Major groove / minor groove contacts E.coli HU protein
GR(P) and SPKKMinor groove nucleolin
Other_ _
Helix-loop-helix-helical dimerisation, recognition assumed-helical. scute
HMG-boxsequence and structure selective, minor groove contacts. HMG-1
Y-box_ FRY-1

* sequence selective unless otherwise noted.

Adapted from P.54 of DNA-Protein interactions, Andrew Travers (1993)