Slide 1Powerpoint Assignment for Micbio 565 • Eric Martz • Yeast Gal4 transcriptional regulator, 1d66. • X-ray crystallography, resolution 2.7 Angstroms. • 2 protein chains + 2 DNA chains (total 4)
Slide 2: PQS • The published PDB file has 4 chains. • PQS says “dimeric complex”, meaning a protein dimer complexed to DNA (still 4 chains). Published PQS
Slide 4: Hydrophobic/Polar • This protein has a mostly polar surface, consistent with it being water soluble. There are no large hydrophobic patches on its surface.
Slide 5: Charge • The DNA-binding notch in the protein has only positive charge, consistent with the need to bind the negatively-charged phosphate backbone of the DNA.
Slide 6: Conservation (ConSurf) The amino acids that contact the major groove of the DNA are highly conserved. This is where Lysine 18 (highlighted) recognizes the specific DNA sequence CGG.
Slide 7: Animation from Polyview-3D Lysine 18 in Gal4 sits in the major groove of DNA, recognizing the DNA sequence CGG. This animation was kept small to minimize the load on the Polyview-3D server. It rocks through 90 degrees in 2 degree steps, with a 5/100 second delay.
Optional Slide 8:Noncovalent Bonds • 6 cysteine sulfurs form a cage around the two cadmium metal ions.