|
Figure 3.
Fig. 3. (A) Superposition (based on the R-loop residues
184-187) of the least-bent form IV (red) and the most-bent form
I (blue), showing interdigitation of Leu-46, Thr-42, and Val-39
at the B-helix interface. Arrows indicate the antiparallel
movements of the helices during the 11° bending of the DNA
in progressing from form IV to form I. Distances between C  T42 (blue)
and C Thr-42
(red) are 3.4 Å in subunit A and 2.2 Å in subunit B.
(B) Propagation of the B-helix conformational changes to DNA
bending, with structures superimposed as in A. The B-helices and
DNA from crystal form I (blue) and crystal form IV (red) are
shown, with coupling between the Thr-37-Thy-8 ribose contact and
the B-helix translation also illustrated. Thr-37 and the ribose
sugar in form I are shown in green in thicker bonds for clarity.
These groups in form IV are shown in gold. (C) Plot of the
center-step DNA-bending angle as a function of distance between
Thr-37C  and
Thy-8-C4'. Error bars for crystal forms II and IV reported here
indicate coordinate error as calculated with the program SIGMAA.
The error bars for crystal forms I and III (9, 10) were
estimated from the resolutions of the data sets, based on
calculations from truncated penicillopepsin data, and may
represent underestimates (33). The points represent the average
Thr-37(C )-ribose(C4')
distance for the two monomer subunits of each dimer. Roman
numerals adjacent to the data points indicate the crystal form
(Tables 1 and 3). (D) Propagation of the B-helix conformational
change into the adjacent Q-loops. Residues in the active sites
Glu-45, Glu-65, and Asp-74 are shown, as is the Thr-37-Gln-69
contact in crystal form I (blue) and crystal form IV (red). The
superposition was done as in A.
|
