 |
PDBsum entry 2ro4
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Transcription
|
PDB id
|
|
|
|
2ro4
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Insights into the nature of DNA binding of abrb-Like transcription factors.
|
|
|
Authors
|
|
D.M.Sullivan,
B.G.Bobay,
D.J.Kojetin,
R.J.Thompson,
M.Rance,
M.A.Strauch,
J.Cavanagh.
|
|
|
Ref.
|
|
Structure, 2008,
16,
1702-1713.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
perfect match.
|
|
|
|
Abstract
|
|
|
Understanding the DNA recognition and binding by the AbrB-like family of
transcriptional regulators is of significant interest since these proteins
enable bacteria to elicit the appropriate response to diverse environmental
stimuli. Although these "transition-state regulator" proteins have been well
characterized at the genetic level, the general and specific mechanisms of DNA
binding remain elusive. We present RDC-refined NMR solution structures and
dynamic properties of the DNA-binding domains of three Bacillus subtilis
transition-state regulators: AbrB, Abh, and SpoVT. We combined previously
investigated DNase I footprinting, DNA methylation, gel-shift assays, and
mutagenic and NMR studies to generate a structural model of the complex between
AbrBN(55) and its cognate promoter, abrB8. These investigations have enabled us
to generate a model for the specific nature of the transition-state
regulator-DNA interaction, a structure that has remained elusive thus far.
|
|
|
|
|
|
|
|
Figure 2.
Figure 2. Structural Similarities and Differences among
AbrBN^53, AbhN, and SpoVTN
(A–F) Critical arginine
residues involved in DNA binding orientations for (A) R8; (B)
R15; and (C) R23 and R24 from AbrBN^53 (red), AbhN (gold), and
SpoVTN (green). Comparison of the electrostatic surface
potential between (D) AbrBN^53, (E) AbhN, and (F) SpoVTN. Blue
regions indicate positive charge, whereas red regions indicate
negative charge. Proteins are oriented as depicted in Figure 1.
|
|
Figure 4.
Figure 4. Lowest-Energy DNA-Bound AbrBN^55 Model from
Semi-Flexible Docking and Comparison to Unbound AbrBN^53
(A) Two views of the lowest-energy HADDOCK structure from the
semi-flexible docking studies. Disulfide linkages are shown as
spheres in the image. Insets show a detailed look at the
positioning of the arginine residues involved in binding.
(B) Overlay of unbound AbrBN^53 (red) and the lowest HADDOCK
score model of AbrBN^55 bound to abrB8 (blue). One monomer is
highlighted for clarity.
(C) The degree of structural
variation between the unbound AbrBN^53 NMR structure and the
modeled AbrBN^55 bound to abrB8, colored from white (little
variation) to red (large variation), as calculated in the Cα
alignment by THESEUS plotted on the refined AbrBN^53 solution
structure. The unbound and bound AbrBN^53 dimer structures
overlay with a Cα rmsd of 2.84 Å. LP1 and LP2 (chain A)
and LP1′ and LP2′ (chain B) are noted. Proteins are oriented
as depicted in Figure 1 on structures most similar to the
average structure in the ensemble reported by THESEUS.
|
|
|
|
|
|
The above figures are
reprinted
from an Open Access publication published by Cell Press:
Structure
(2008,
16,
1702-1713)
copyright 2008.
|
|
|
|
|
|
|
