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PDBsum entry 1lb2
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Gene regulation/DNA
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PDB id
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1lb2
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural basis of transcription activation: the cap-Alpha ctd-Dna complex.
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Authors
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B.Benoff,
H.Yang,
C.L.Lawson,
G.Parkinson,
J.Liu,
E.Blatter,
Y.W.Ebright,
H.M.Berman,
R.H.Ebright.
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Ref.
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Science, 2002,
297,
1562-1566.
[DOI no: ]
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PubMed id
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Abstract
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The Escherichia coli catabolite activator protein (CAP) activates transcription
at P(lac), P(gal), and other promoters through interactions with the RNA
polymerase alpha subunit carboxyl-terminal domain (alphaCTD). We determined the
crystal structure of the CAP-alphaCTD-DNA complex at a resolution of 3.1
angstroms. CAP makes direct protein-protein interactions with alphaCTD, and
alphaCTD makes direct protein-DNA interactions with the DNA segment adjacent to
the DNA site for CAP. There are no large-scale conformational changes in CAP and
alphaCTD, and the interface between CAP and alphaCTD is small. These findings
are consistent with the proposal that activation involves a simple
"recruitment" mechanism.
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Figure 2.
Fig. 2. CAP-  CTD^CAP,DNA-DNA(interactions
representative of those at a class I or class II CAP-dependent
promoter). (A) Stereo view of interactions among CAP, CTD^CAP,DNA,
and DNA (two orthogonal views). AR1 of CAP is in blue; the 287
determinant (CAP contact), 265 determinant (DNA contact), and
the 261 determinant (proposed  70
contact) of CTD^CAP,DNA
are in yellow, red, and gray-white, respectively. (B)
Interactions between AR1 of CAP and residues 285 to 288 of the
287 determinant of CTD^CAP,DNA.
Hydrogen bonds are in magenta. (C) Interactions between the
COOH-terminal residue of CAP (Arg209) and residues 315 and 317
of the 287 determinant of CTD^CAP,DNA.
Hydrogen bonds are in magenta. C-TER, COOH-terminus. (D)
Interactions between CTD^CAP,DNA
and DNA (view along DNA minor-groove axis). Water-mediated
hydrogen bonds involving the Arg265 side-chain guanidinium, DNA
bases, and an experimentally defined water molecule (sphere near
center) are in cyan. The network of hydrogen bonds buttressing
the Arg265 side-chain guanidinium relative to the phosphate
backbones of the two DNA strands is in yellow. Other hydrogen
bonds are in magenta. (E) Summary of interactions between CTD^CAP,DNA
and DNA. Colors are as in (D). G, Gly; K, Lys; N, Asn; R, Arg;
S, Ser; and V, Val.
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Figure 3.
Fig. 3. CTD^DNA-DNA
(interactions representative of those at an UP element
subsite-dependent promoter). (A) Stereo view comparing
interactions between CTD^DNA
and DNA (dark green and gray) and interactions between CTD^CAP-DNA
and DNA (light green and gray) (RMSD = 0.74 Å for 72 C
and 10 P
atoms). (B) Interactions between CTD^DNA
and DNA. View and colors are as in Fig. 2D. No water molecules
were observed in the CTD^DNA-DNA
interface in this structure at 3.1 Å. However, the
positions of the Arg265 side-chain guanidinium and DNA bases are
compatible with the establishment of water-mediated hydrogen
bonds identical to those at the CTD^CAP,DNA-DNA
interface (Fig. 2D) (39). (C) Summary of interactions between
CTD^DNA
and DNA. Colors are as in Fig. 2, D and E.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2002,
297,
1562-1566)
copyright 2002.
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