@article{Shultzaberger.Schneider-flexprom2007, author = "R. K. Shultzaberger and Zehua Chen and Karen A. Lewis and T. D. Schneider", title = "{Anatomy of \emph{Escherichia coli} $\sigma^{70}$ promoters}", journal = "Nucleic Acids Res.", volume = "35", pages = "771--788", note = "\htmladdnormallink {http://www.ccrnp.ncifcrf.gov/\~{}toms/paper/f{l}exprom/} {http://www.ccrnp.ncifcrf.gov/\~{}toms/paper/f{l}exprom/}", comment = "former name Shultzaberger.Schneider-flexprom2005", year = "2007"}
Start coordinates for sigma70 in E. coli accession U00096:
sigma70_start_coords.txt
We used this structure given by Campbell.Darst2002 to determine how the sigma 70 -35 binds to DNA.
@article{Campbell.Darst2002, author = "E. A. Campbell and O. Muzzin and M. Chlenov and J. L. Sun and C. A. Olson and O. Weinman and M. L. Trester-Zedlitz and S. A. Darst", title = "{Structure of the bacterial RNA polymerase promoter specificity $\sigma$ subunit}", journal = "Mol Cell", volume = "9", pages = "527--539", pmid = "11931761", year = "2002"}
These files show how the 4.2 part of the sigma protein binds into the -35 region of a promoter. Run them as:
rasmolscript 1KU7.pdb -script 1KU7.ras rasmolscript 1KU7-nowater.pdb -script 1KU7-nowater.ras
See also the companion paper, Anatomy of Escherichia coli Ribosome Binding Sites
The Delila Server allows you to try the model on the E. coli genome.
Other pointers:
Schneider Lab
origin: 2004 May 13
updated: 2008 Feb 22