Slide 1 Powerpoint Assignment for Micbio 565

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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)

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Slide 2 PQS

• The published PDB file has 4 chains.
• PQS says dimeric complex, meaning a protein
  dimer complexed to DNA (still 4 chains).

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Slide 3 Ligands
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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.

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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.

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Slide 6 Noncovalent Bonds

• 6 cysteine sulfurs form a cage around the two
  cadmium metal ions.

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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.
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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.