The functional regions predicted by PatchFinder for TBP1_ARATH. PDB entry 1qn7 represents the structure of TATA-box-binding protein 1 (TBP1) from Arabidopsis thaliana (Patikoglou, et al., 1999). The protein (here in surface representation) was crystallized bound to its target DNA sequence (yellow). The primary functional region (patch) predicted by PatchFinder is colored red while the secondary patch is colored blue. Even though the DNA-binding site is apparently symmetric, the primary patch does not cover the whole binding site. Examining this asymmetry, it turns out that the transcription initiation efficiency is much more dependent on the identity of the nucleotides which bind this region, than the nucleotides which bind the secondary patch (Patikoglou, et al., 1999).
Patikoglou, G.A., Kim, J.L., Sun, L., Yang, S.H., Kodadek, T. and Burley, S.K. (1999) TATA element recognition by the TATA box-binding protein has been conserved throughout evolution, Genes Dev., 13, 3217-3230.