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PDBsum entry 3fwe
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Transcription regulator
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PDB id
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3fwe
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References listed in PDB file
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Key reference
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Title
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Structure of apo-Cap reveals that large conformational changes are necessary for DNA binding.
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Authors
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H.Sharma,
S.Yu,
J.Kong,
J.Wang,
T.A.Steitz.
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Ref.
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Proc Natl Acad Sci U S A, 2009,
106,
16604-16609.
[DOI no: ]
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PubMed id
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Abstract
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The binding of cAMP to the Escherichia coli catabolite gene activator protein
(CAP) produces a conformational change that enables it to bind specific DNA
sequences and regulate transcription, which it cannot do in the absence of the
nucleotide. The crystal structures of the unliganded CAP containing a D138L
mutation and the unliganded WT CAP were determined at 2.3 and 3.6 A resolution,
respectively, and reveal that the two DNA binding domains have dimerized into
one rigid body and their two DNA recognition helices become buried. The WT
structure shows multiple orientations of this rigid body relative to the
nucleotide binding domain supporting earlier biochemical data suggesting that
the inactive form exists in an equilibrium among different conformations.
Comparison of the structures of the liganded and unliganded CAP suggests that
cAMP stabilizes the active DNA binding conformation of CAP through the
interactions that the N(6) of the adenosine makes with the C-helices. These
interactions are associated with the reorientation and elongation of the
C-helices that precludes the formation of the inactive structure.
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Figure 2.
Comparison of the inactive (Left) and the active forms of CAP
(Right). (A) Schematic representation of CAP shows
[beta]-strands as arrows and [alpha]-helices as coils. The cAMP
is shown in ball and stick representation. DNA is shown as
transparent spheres and its bases are colored slate blue. (B)
The cAMP binding domains and DNA have been excluded to emphasize
the orientations of the DNA binding domains and the C-helices.
Residues capping the C- and D-helices and cAMP are shown as ball
and stick. In the inactive form, K130 is located at the C
termini of the C-helices, whereas in the active form, D138 is
located at the N termini of the D-helices. (C) The C terminus of
the C-helix, the N terminus of the D-helix, and the hinge
residues of one protomer of the inactive and the active form.
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Figure 4.
The cAMP induced conformational changes of CAP. The side view
of CAP is shown. Structure of the unliganded CAP (Left) and of
the liganded CAP (Right). A superposition of these two
structures along their C-helices is shown in the middle of the
figure. The unliganded structure is solid, whereas the liganded
structure is transparent. To emphasize the conformational
changes on cAMP binding, only the C-, D-, and F-helices are
shown.
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