Transcript Sample completed assignment

Slide 1
Powerpoint 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 negativelycharged 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.