CHIME EXERCISE

 

 

1PCZ: TATA Binding Protein

 

 

1YTB: Yeast TBP/TATA Box Complex

In the structure to the right of Yeast TBP/TATA Box Complex, identify the following:

  • pseudo-2-fold axis of symmetry for TBP

  • Orientation of the helical axis of the DNA segment with respect to the pseudo-2-fold symmetry (parallel or perpendicular?)

  • Identify DNA major and minor grooves

  • Observe how TBP splits apart the minor groove at each end of the TATA box

  • Secondary structural elements of TBP inserted into the partially unwound DNA's minor groove

  • Find the Phe residues that induce kinks in, and stabilize the DNA. Note where the links occur on the TATA element

  • Find the Asn residues that hydrogen-bond to the minor groove

  • Find the Ile and Leu residue that might be involved in DNA recognition

  • Can you see that the bound DNA is distorted into a crank-shaped structure?