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PDBsum entry 1zh2
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Transcription
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PDB id
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1zh2
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References listed in PDB file
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Key reference
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Title
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A common dimerization interface in bacterial response regulators kdpe and torr.
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Authors
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A.Toro-Roman,
T.Wu,
A.M.Stock.
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Ref.
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Protein Sci, 2005,
14,
3077-3088.
[DOI no: ]
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PubMed id
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Abstract
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Bacterial response regulators are key regulatory proteins that function as the
final elements of so-called two-component signaling systems. The activities of
response regulators in vivo are modulated by phosphorylation that results from
interactions between the response regulator and its cognate histidine protein
kinase. The level of response regulator phosphorylation, which is regulated by
intra-or extracellular signals sensed by the histidine protein kinase,
ultimately determines the output response that is initiated or carried out by
the response regulator. We have recently hypothesized that in the OmpR/PhoB
subfamily of response regulator transcription factors, this activation involves
a common mechanism of dimerization using a set of highly conserved residues in
the alpha4-beta5-alpha5 face. Here we report the X-ray crystal structures of the
regulatory domains of response regulators TorR (1.8 A), Ca(2+)-bound KdpE (2.0
A), and Mg(2+)/BeF(3)(-)-bound KdpE (2.2 A), both members of the OmpR/ PhoB
subfamily from Escherichia coli. Both regulatory domains form symmetric dimers
in the asymmetric unit that involve the alpha4-beta5-alpha5 face. As observed
previously in other OmpR/PhoB response regulators, the dimer interfaces are
mediated by highly conserved residues within this subfamily. These results
provide further evidence that most all response regulators of the OmpR/ PhoB
subfamily share a common mechanism of activation by dimerization.
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Figure 1.
Figure 1. (A,B) Ribbon diagrams of the regulatory domains
of KdpE[N]-BeF[3]^- (gold) and TorR[N] (protomers A and B,
teal). The two proteins form symmetric dimers mediated by the
 4-  5- 5 faces. In
KdpE[N]-BeF[3]^- the side chains of Asp53, Ser79, and Tyr98
(gray and red), and BeF[3]^- (magenta and salmon) are shown as
stick models, and the Mg2+ ion (orange) is shown in sphere
representation. BeF[3]^- is noncovalently bound to the site of
phosphorylation, Asp52, and serves as one of the ligands for the
catalytic Mg2+. Ser79 and Tyr98 are conserved residues involved
in the "switch" mechanism of activation associated with
phosphorylation of the conserved Asp52. The equivalent residues
Asp53, Thr80, and Tyr99 are shown for TorR[N]. (C) Alignment of
KdpE[N]-Ca2+ (protomer B, green) vs. KdpE[N]-BeF[3]^- (protomer
B, gold) showing the conserved residues involved in propagation
of the activation signal from the active site aspartate to the
4- 5- 5 face. The
side chains of Asp52, Ser79, and Tyr98 (oxygens in red), and
BeF[3]^- (magenta and salmon) are shown in stick representation,
with the Mg2+ (orange) and Ca^2+ (green) ions shown as spheres.
The 4- 4 loops are
further stabilized into a fixed conformation by interacting with
Tyr98. Minimal differences are seen between the two structures.
(D) Alignment of the four protomers found in the asymmetric unit
of the TorR[N] crystals. Side chains of Asp53, Thr80, and Tyr99
(oxygens in red) are shown as sticks. Two dimers are formed
between protomers A-B and C-D. Protomers A and D (teal) have the
switch residues Thr80 and Tyr99 in an inward active
conformation, while in protomers B and C (brown) they adopt an
outward conformation associated with the inactive state. The
conformation of the 4- 4 loops in
protomers B and C differs from that of protomers A and D because
side chains of residues in these loops are used for crystal
contacts.
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Figure 3.
Figure 3. Conserved intermolecular interactions of
KdpE[N]-BeF[3]^- (A,B) and TorR[N] (C,D) at the dimer interface.
KdpE[N]-BeF[3]^- protomers are distinguished by the colors gold
and green, and TorR[N], by the colors teal and brown.
Hydrophobic and electrostatic interactions are represented by
sphere and stick models, respectively. (A,C) In both
KdpE[N]-BeF[3]^- and TorR[N], the 4 and 5 helices are
packed together through a conserved hydrophobic patch formed in
KdpE[N]-BeF[3]^- by Ile88 ( 4), Leu91 (
4), Ala110 (
5), and Val114
( 5). Analogous
conserved interactions are seen in TorR[N] except for an
additional nonconserved hydrophobic residue in KdpE[N]-BeF[3]^-
(Val114) that further extends the hydrophobic patch down the
path of the helices. (B,D) The interface of these dimers is
further stabilized by a network of inter- and intramolecular
salt bridges formed in KdpE[N]-BeF[3]- by Glu107 ( 5) and Arg111 (
5), Asp97 (
5) and Arg111
( 5), Asp96 (
4- 5 loop) and
Arg118 ( 5), Asp92 (
4) and Arg113 (
5), and Ala95 (
4- 5 loop)/Leu91
( 4) and Arg117 (
5). In TorR[N]
the interactions are formed between Glu108 ( 5) and Arg88 (
4), Glu108 (
5) and Arg112 (
5), Asp98 (
5) and Arg112
( 5), Asp97 (
4- 5 loop) and
Arg119 ( 5), and Ala96 (
4- 5 loop)/Leu92
( 4) and Asn115 (
5). On the
right side of the TorR[N] interface the Glu108-Arg88 interaction
is bridged by the side-chain oxygen of Tyr99, which is found in
an outward conformation in protomers B and C (see Fig. 1D
Go- ). The side
chains of Glu93 and Lys114 are involved in crystal contacts, and
thus do not form the analogous salt bridge seen in
KdpE[N]-BeF[3]^-.
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The above figures are
reprinted
by permission from the Protein Society:
Protein Sci
(2005,
14,
3077-3088)
copyright 2005.
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