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PDBsum entry 1zrd
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Gene regulation/DNA
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PDB id
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1zrd
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References listed in PDB file
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Key reference
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Title
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Indirect readout of DNA sequence at the primary-Kink site in the cap-Dna complex: recognition of pyrimidine-Purine and purine-Purine steps.
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Authors
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A.A.Napoli,
C.L.Lawson,
R.H.Ebright,
H.M.Berman.
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Ref.
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J Mol Biol, 2006,
357,
173-183.
[DOI no: ]
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PubMed id
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Abstract
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The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex,
typically introducing a sharp DNA kink, with a roll angle of approximately 40
degrees and a twist angle of approximately 20 degrees, between positions 6 and 7
of the DNA half-site, 5'-A1A2A3T4G5T6G7A8T9C10T11 -3' ("primary
kink"). In previous work, we showed that CAP recognizes the nucleotide
immediately 5' to the primary-kink site, T6, through an
"indirect-readout" mechanism involving sequence effects on energetics
of primary-kink formation. Here, to understand further this example of indirect
readout, we have determined crystal structures of CAP-DNA complexes containing
each possible nucleotide at position 6. The structures show that CAP can
introduce a DNA kink at the primary-kink site with any nucleotide at position 6.
The DNA kink is sharp with the consensus pyrimidine-purine step T6G7 and the
non-consensus pyrimidine-purine step C6G7 (roll angles of approximately 42
degrees, twist angles of approximately 16 degrees ), but is much less sharp with
the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of
approximately 20 degrees, twist angles of approximately 17 degrees). We infer
that CAP discriminates between consensus and non-consensus pyrimidine-purine
steps at positions 6-7 solely based on differences in the energetics of DNA
deformation, but that CAP discriminates between the consensus pyrimidine-purine
step and non-consensus purine-purine steps at positions 6-7 both based on
differences in the energetics of DNA deformation and based on qualitative
differences in DNA deformation. The structures further show that CAP can achieve
a similar, approximately 46 degrees per DNA half-site, overall DNA bend through
a sharp DNA kink, a less sharp DNA kink, or a smooth DNA bend. Analysis of these
and other crystal structures of CAP-DNA complexes indicates that there is a
large, approximately 28 degrees per DNA half-site, out-of-plane component of
CAP-induced DNA bending in structures not constrained by end-to-end DNA lattice
interactions and that lattice contacts involving CAP tend to involve residues in
or near biologically functional surfaces.
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Figure 2.
Figure 2. Superimposed structures of complexes of CAP with
DNA sites containing all possible base-pairs at position 6 of
the primary-kink site obtained in this study. CAP is presented
in a ribbon representation. DNA is colored as follows: cyan,
CAP-DNA; blue, CAP-[6A;17T]DNA; yellow, CAP-[6G;17C]DNA; red,
CAP-[6C;17G]DNA. The Figure was generated using PyMol
(http://pymol.sourceforge.net/) and nuccyl
(http://www.mssm.edu/students/jovinl02/research/nuccyl.html).
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Figure 5.
Figure 5. Analysis of crystal structures of wild-type
CAP-DNA complexes herein and in the literature. (a) Plot of DNA
dihedral angle versus DNA bend angle in crystal structures of
wild-type CAP-DNA complexes (squares, crystal form-A; triangles,
crystal form-B; diamonds, crystal form-C; circles, crystal
form-C'). (b) Plot of CAP residue number versus frequency of
involvement in crystal-lattice contacts in crystal structures of
wild-type CAP-DNA complexes. (c) Surface representation of CAP
showing residues involved in crystal-lattice contacts in at
least 35% of crystal structures of wild-type CAP-DNA complexes
(circles, with greater diameters indicating higher frequencies
of involvement in crystal-lattice contacts), DNA recognition
helices (magenta), and transcription activating regions 1 (AR1,
blue), 2 (AR2, dark green), and 3 (AR3, olive green).
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The above figures are
reprinted
from an Open Access publication published by Elsevier:
J Mol Biol
(2006,
357,
173-183)
copyright 2006.
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