The N-terminal is composed of six residues (NH2-Ser-Thr-Lys-Lys-Lys-Pro). At the consensus operator half-site, these residues are part of a flexible arm in solution that is able to form approximately ten essential contacts with operator DNA by wraping around the back side of the operator. The consensus binding N-terminal's arm position in the protien has been well charactorized. The N-terminal arm which binds to the non-consensus operator half-site is much more poorly charactorized. This is because it plays less of a role in recognition and binding of DNA at the non-consensus operator half-site. The poor electron density in the region during crystolography is probably due to thermal motion. These sturctural differences imply that there exist fundamentally different roles of these two N-terminal arms in DNA binding.
Different arguments exist as to the function of the two N-terminal arms. The consensus N-terminal arm is clearly extremely importent for the recognition and binding of cI-repressor. Removal of the first six residues from cI repressor greatly reduces its binding affinity for the operator. In contrast, the non-consensus arm is not significantly important for recognition or binding. Removal of the non-consensus arm does not reduce dimer affinity for the operator site. Also, mutation of base pair 8' does not have a great affect on DNA binding (mutation of bp 8, involved in contacting the consensus site does reduce repressor affinity). Another theory suggest that the N-terminal arm exist as a remnant that is present only as a consequence of the repressor being a homodimer.
Residues Important for Binding-
Lys3, Lys4 and Lys5 are important for the recognition in the consensus operator half site. Here, the interactions of each with DNA are charactorized in sequence.
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