TBP

(Originally created as a Rasmol script by Bob Boor for BMMB 597C, who was guided by the article "Crystal structure of a yeast TBP/TATA-Box Complex", Youngchang et al. (1993) Nature 365: 512-519).

• TBP or TATA Binding Protein is involved in building the eukaryotic transcription complex.
  • Primarily through hydrophobic interactions, TBP binds to the minor groove of the DNA double helix.
  • In doing so there is a dramatic change in the structure of the helix.
  • What you are seeing now is the Carboxy terminal 180 residues of the protein.
  • Take note of its saddle shape and the location of the stirrups.

   

• <> 4 phenylalanine residues are responsible for buckling the DNA helix on either side of the TATA box

   

• <> A b-sheet making the inner face of the protein interacts with the minor groove of the DNA

   

• <> Buckling the DNA bends it over a large angle. Note the distortion of the minor groove.
  • <> Highlight the AT base pairs at either end of the TATA box that interact with the Phe residues of the protein
  • <> Add the phenylalanines (wireframe) that buckle the DNA
    • <> Rotate and zoom the view
  • <> Highlight the basepairs between the AT's that line the inner face of the protein molecule
    • <> Zoom out and rotate
  • <> Add the protein and view the DNA/Protein complex
    • <> Survey the view, and change the phe's to spacefill
  • <> Highlight the inner face of the protein that interacts with the minor groove
    • <> Survey the view

  Views from class overheads

• <> TBP / TATA complex
  • as seen in class

   

• <> TBP / TFIIA / TATA complex
  • TBP bound to TATA associates with TFIIA, a transcription factor

   

• <> TBP Dimer
  • TBP exists as a dimer in solution and in crystals.
  • By occluding the DNA binding surface, dimerization of TBP may render it incapable of initiating a transcription complex
  • The role of activators may thus be to disrupt the TBP dimer, activating its DNA binding activity.