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Genes and Development
Vol. 11, No. 17,
pp. 2227-2238,
September 1, 1997
1 Center for Blood Research and Department of Pathology
and
2 Department of Biological Chemistry and Molecular
Pharmacology, Harvard Medical School,
Boston, Massachusetts 02115 USA
The SKN-1 transcription factor specifies early embryonic cell
fates in Caenorhabditis elegans. SKN-1 binds DNA at high
affinity as a monomer, by means of a basic region like those of
basic-leucine zipper (bZIP) proteins, which bind DNA only as dimers. We
have investigated how the SKN-1 DNA-binding domain (the Skn domain) promotes stable binding of a basic region monomer to DNA. A flexible arm at the Skn domain amino terminus binds in the minor groove, but a
support segment adjacent to the carboxy-terminal basic region can
independently stabilize basic region-DNA binding. Off DNA, the basic
region and arm are unfolded and, surprisingly, the support segment
forms a molten globule of four 
-helices. On binding DNA, the Skn
domain adopts a tertiary structure in which the basic region helix
extends directly from a support segment -helix, which is required
for binding. The remainder of the support segment anchors this
uninterrupted helix on DNA, but leaves the basic region exposed in the
major groove. This is similar to how the bZIP basic region extends from
the leucine zipper, indicating that positioning and cooperative
stability provided by helix extension are conserved mechanisms that
promote binding of basic regions to DNA.
[Key Words:
basic region; SKN-1; DNA binding; bZIP; molten globule; -helix]
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