E. coli Gre A Transcription Elongation Factor Project
Control of transcription occurs primarily at the initiation step, but there is also some control during elongation. Transcription elongation factors stimulate the activity of DNA-dependent RNA polymerase by increasing the overall rate of elongation and completion of RNA chains.
Analyze PDB 1GRJ and describe the following:
(1) The 2 major domains (N- and C- termini) : describe each in terms of secondary structure
and any structural motifs.
(2) For the 2 long helices, identify:
a. The hydrophobic residues at the a and d positions of the heptad repeats
b. Other interactions between the helices
c. The amino acid responsible for the bulge in the left chain
d. The amino acid responsible for the kink in the left chain
e. Estimate the angle of the kink
(3) The short helices
(4) The hydrophobic region at the C-terminal domain
(5) The surface charge distribution of the molecule: acidic, basic, neutral, hydrophobic
(6) Within the area where the helical domain interfaces the C-terminal domain, the two
helices are splayed apart, leaving a gap in its hydrophobic core. What residue fills the gap? (Hydrophobic amino acids are conserved at this position in homologous Gre factors.)
The mechanism of Gre A involves hydrolytic cleavage of the transcript within the RNA polym
erase, followed by release of the 3-terminus. The site of interaction with the 3-end is localized to a peptide segment within the right-sided helix, near the end of the coiled-coil structure. The core enzyme of RNA polymerase has an isoelectric point (calculated) of 5.34.
With this information, and from your study of the molecule thus far, suggest how Gre A interacts with an elongation transcript on a physical basis.