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PDBsum entry 3n4m
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Gene regulation/DNA
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PDB id
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3n4m
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References listed in PDB file
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Key reference
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Title
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The RNA polymerase α subunit recognizes the DNA shape of the upstream promoter element.
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Authors
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S.Lara-Gonzalez,
A.C.Dantas machado,
S.Rao,
A.A.Napoli,
J.Birktoft,
R.Di felice,
R.Rohs,
C.L.Lawson.
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Ref.
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Biochemistry, 2020,
59,
4523-4532.
[DOI no: ]
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PubMed id
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Abstract
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We demonstrate here that the α subunit C-terminal domain of Escherichia
coli RNA polymerase (αCTD) recognizes the upstream promoter (UP) DNA
element via its characteristic minor groove shape and electrostatic potential.
In two compositionally distinct crystallized assemblies, a pair of αCTD
subunits bind in tandem to the UP element consensus A-tract that is 6 bp in
length (A6-tract), each with their arginine 265 guanidinium group
inserted into the minor groove. The A6-tract minor groove is
significantly narrowed in these crystal structures, as well as in
computationally predicted structures of free and bound DNA duplexes derived by
Monte Carlo and molecular dynamics simulations, respectively. The negative
electrostatic potential of free A6-tract DNA is substantially
enhanced compared to that of generic DNA. Shortening the A-tract by 1 bp is
shown to "knock out" binding of the second αCTD through widening of
the minor groove. Furthermore, in computationally derived structures with
arginine 265 mutated to alanine in either αCTD, either with or without the
"knockout" DNA mutation, contact with the DNA is perturbed,
highlighting the importance of arginine 265 in achieving αCTD-DNA binding.
These results demonstrate that the importance of the DNA shape in
sequence-dependent recognition of DNA by RNA polymerase is comparable to that of
certain transcription factors.
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Secondary reference #1
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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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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
reproduced from the cited reference
with permission from the AAAs
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