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).
Slide 3: Ligands
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: Noncovalent Bonds
• 6 cysteine sulfurs form a cage around the two cadmium metal ions.
Slide 7: 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 8: 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.
Top Related