 |
PDBsum entry 2kjc
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Transcription regulator
|
PDB id
|
|
|
|
2kjc
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Solution structure of a paradigm arsr family zinc sensor in the DNA-Bound state.
|
|
|
Authors
|
|
A.I.Arunkumar,
G.C.Campanello,
D.P.Giedroc.
|
|
|
Ref.
|
|
Proc Natl Acad Sci U S A, 2009,
106,
18177-18182.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
Staphylococcus aureus CzrA is a zinc-dependent transcriptional repressor from
the ubiquitous ArsR family of metal sensor proteins. Zn(II) binds to a pair of
intersubunit C-terminal alpha5-sensing sites, some 15 A distant from the
DNA-binding interface, and allosterically inhibits DNA binding. This regulation
is characterized by a large allosteric coupling free energy (DeltaGc) of
approximately +6 kcal mol(-1), the molecular origin of which is poorly
understood. Here, we report the solution quaternary structure of homodimeric
CzrA bound to a palindromic 28-bp czr operator, a structure that provides an
opportunity to compare the two allosteric "end" states of an ArsR family sensor.
Zn(II) binding drives a quaternary structural switch from a "closed" DNA-binding
state to a low affinity "open" conformation as a result of a dramatic change in
the relative orientations of the winged helical DNA binding domains within the
dimer. Zn(II) binding also effectively quenches both rapid and intermediate
timescale internal motions of apo-CzrA while stabilizing the native state
ensemble. In contrast, DNA binding significantly enhances protein motions in the
allosteric sites and reduces the stability of the alpha5 helices as measured by
H-D solvent exchange. This study reveals how changes in the global structure and
dynamics drive a long-range allosteric response in a large subfamily of
bacterial metal sensor proteins, and provides insights on how other structural
classes of ArsR sensor proteins may be regulated by metal binding.
|
|
|
|
|
|
|
|
Figure 1.
Solution structure of CzrO DNA-bound CzrA. (A) Backbone heavy
atom (N, Cα, and C') overlay of 20 lowest-energy structures of
DNA bound CzrA (see Table S2 for structure statistics;
unstructured residues 100–103 of the bundle are not shown in
this view for clarity). The ribbon diagram in the overlay
represents the mean structure of the ensemble and the two
subunits are shaded salmon and red. (B) Ribbon diagram
representation of the global overlay of DNA bound CzrA and the
crystal structure of Zn(II) CzrA (8). The subunits of DNA bound
CzrA are colored as in A and the two subunits of Zn(II) CzrA are
colored slate and blue. Zn(II) ions are colored yellow. (C)
Another view of the same overlay as in B (rotated 45°) and
the green arrows represent the direction of the quaternary
structural change.
|
|
Figure 2.
Distinct conformational states of α5 metal sensor proteins.
(A) Overlay of the apo SmtB (magenta ribbon), Zn(II)-bound CzrA
(light blue ribbon) and DNA-bound CzrA (salmon ribbon). The
“right” subunit is overlaid to better show the quaternary
structural differences. (B) Effect of binding DNA on apo CzrA
structure is mapped using a ^1H HN chemical shift perturbation
experiment. Colors on the ribbon are ramped according to Δδ
ppm as follows: gray, Δδ<0.2 ppm; magenta, 0.2<Δδ<0.8 and
red; 0.8<Δδ<1.5 ppm. (C) A comparison of the short time scale
^15N relaxation dynamics of Zn[2] CzrA vs. apo-CzrA (see Fig. S2
for primary data). Blue, increased S^2 by ≥ 0.02 on Zn(II)
binding; yellow, decreased S^2 by ≤ –0.02 on Zn(II) binding;
purple, residues in apo-CzrA that exhibit measurable R[ex] ≥ 1
s^−1 that is completely dampened upon Zn(II) binding; orange,
the single residue in Zn[2] CzrA for which there is measurable
R[ex] ≥ 1 s^−1 (L35).
|
|
|
|
|
|
|
|
|
|
