Software needed for this tutorial
In this tutorial, you will be examining the lambda repressor/lambda operator complex, the lac repressor/lac operator complex, and the lac repressor/inducer complex using RasMol. If RasMol is not already available on this computer, click here , to learn how to install and configure this software. A complete RasMol instruction manual is available on-line.
PDB coordinate file headers
The structures you will be viewing were generated using three
Protein Data Base (PDB) coordinate files. The headers of these
coordinate files contain lots of useful information such as alpha
helix and beta sheet assignments, polypeptide and nucleic acid
chain number assignments, references, etc. Click on the following
links to view the coordinate file headers. When you are finished
looking at a header, click on the Netscape "back" button
to return to this page.
Most promoter selective prokaryotic transcription factors bind
DNA via a helix-turn-helix (HTH) motif. One of the best characterized
such motifs is found in the lambda repressor.
Like all prokaryotic HTH proteins, lambda repressor binds to DNA
as a homodimer. The subunit folds into two independent globular
domains. The C-terminal domain is required for cooperative binding
and is not present in this crystal structure. The N-terminal domain,
which you are viewing here, contains five alpha helices. Alpha
helices 2 and 3, which are colored yellow in each subunit constitute
the HTH motif. Helix 5 constitutes provides the dimerization interface.
The HTH motif is sometimes referred to as the reading head or headpiece. Explore this structure
using the various menu commands and the Rasmol command line window
to alter the view. In particular, try to gain an appreciation
for the complementary shapes of the recognition helix and the
major groove. See if you can rotate and magnify the molecule in
such a way as to allow you to view specific amino acid-basepair
contacts. Of particular interest is the
bidentate H-bond contact between gln44 and the A24:T18 basepair.
The lac repressor tetramer can be thought
of as a dimer of dimers. Each dimer contacts one complete operator,
thereby making it possible for a single tetramer to bind two distant
operators simultaneously. The resulting loop in the DNA appears
to play a role in transcriptional repression. Zoom in on and rotate
various portions of the molecule including the tetramerization
domain and the hinge helix to gain familiarity with the structure.
It is impossible to deduce a code relating recognition helix sequence
to operator sequence, since each recognition helix is positioned
differently in the major groove. The variability in recognition
helix positioning is especially apparent upon comparison of the
lac repressor headpiece and
lambda repressor headpiece structures.
Thirty-five years after Jacob and Monod used the approaches of microbial genetics to learn about the induction of the lac operon, we finally have a structural understanding of this process! The crystal structure of the lac repressor/inducer complex reveals that the inducer binds at the junction between the C-terminal and N-terminal globular domains of lac repressor. The resulting change in the angle between the two domains moves the hinge helices apart thereby greatly lowering the affinity for the repressor for the operator.