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Bacterial chemotaxis
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PDB id
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1a2o
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.3.1.1.61
- Protein-glutamate methylesterase.
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Reaction:
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Protein L-glutamate O5-methyl ester + H2O = protein L-glutamate + methanol
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Protein L-glutamate O(5)-methyl ester
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+
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H(2)O
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=
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protein L-glutamate
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+
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methanol
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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cytoplasm
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1 term
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Biological process
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intracellular signal transduction
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4 terms
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Biochemical function
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hydrolase activity
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3 terms
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DOI no:
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Proc Natl Acad Sci U S A
95:1381-1386
(1998)
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PubMed id:
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Structural basis for methylesterase CheB regulation by a phosphorylation-activated domain.
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S.Djordjevic,
P.N.Goudreau,
Q.Xu,
A.M.Stock,
A.H.West.
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ABSTRACT
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We report the x-ray crystal structure of the methylesterase CheB, a
phosphorylation-activated response regulator involved in reversible modification
of bacterial chemotaxis receptors. Methylesterase CheB and methyltransferase
CheR modulate signaling output of the chemotaxis receptors by controlling the
level of receptor methylation. The structure of CheB, which consists of an
N-terminal regulatory domain and a C-terminal catalytic domain joined by a
linker, was solved by molecular replacement methods using independent search
models for the two domains. In unphosphorylated CheB, the N-terminal domain
packs against the active site of the C-terminal domain and thus inhibits
methylesterase activity by directly restricting access to the active site. We
propose that phosphorylation of CheB induces a conformational change in the
regulatory domain that disrupts the domain interface, resulting in a
repositioning of the domains and allowing access to the active site. Structural
similarity between the two companion receptor modification enzymes, CheB and
CheR, suggests an evolutionary and/or functional relationship. Specifically, the
phosphorylated N-terminal domain of CheB may facilitate interaction with the
receptors, similar to the postulated role of the N-terminal domain of CheR.
Examination of surfaces in the N-terminal regulatory domain of CheB suggests
that despite a common fold throughout the response regulator family, surfaces
used for protein-protein interactions differ significantly. Comparison between
CheB and other response regulators indicates that analogous surfaces are used
for different functions and conversely, similar functions are mediated by
different molecular surfaces.
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Selected figure(s)
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Figure 4.
Fig. 4. Structural comparison of the chemoreceptor
modification enzymes. Structures of the methyltransferase CheR
and the methylesterase^ CheB were aligned on the basis of
similarity of their C-terminal domains by using a structural
homology search in DALI (34). For both molecules, ribbon
diagrams depict the N-terminal domains in blue, linker regions
in gold, and C-terminal domains in green. The molecule of
S-adenosylhomocysteine (SAH) in CheR and the methylesterase^
active site residues [Ser-164 (S), His-190 (H), and Asp-286(D)]
in CheB are shown as CPK models. The double-headed arrow points
toward the active sites and the receptor interaction openings.
Functionally antagonistic CheB and CheR contain active sites on
opposite faces of the structurally homologous central -sheets.
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Figure 5.
Fig. 5. CPK model of the N-terminal domain of CheB,
showing surfaces that are involved in protein-protein
interactions among the response^ regulators CheB, CheY, and
NarL. Residues involved in interaction with the C-terminal
domain of CheB are colored yellow. Residues that have been
implicated in protein-protein interactions in other response
regulators are shown with colored mesh: red for corresponding
residues in CheY that are thought to be involved in interaction
with the P2 domain of the histidine kinase CheA (39); green for
corresponding residues in NarL that interact with its C-terminal
DNA-binding domain (25).
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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G.Lan,
S.Schulmeister,
V.Sourjik,
and
Y.Tu
(2011).
Adapt locally and act globally: strategy to maintain high chemoreceptor sensitivity in complex environments.
|
| |
Mol Syst Biol, 7,
475.
|
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|
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A.A.Wise,
F.Fang,
Y.H.Lin,
F.He,
D.G.Lynn,
and
A.N.Binns
(2010).
The receiver domain of hybrid histidine kinase VirA: an enhancing factor for vir gene expression in Agrobacterium tumefaciens.
|
| |
J Bacteriol, 192,
1534-1542.
|
 |
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|
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C.H.Hansen,
V.Sourjik,
and
N.S.Wingreen
(2010).
A dynamic-signaling-team model for chemotaxis receptors in Escherichia coli.
|
| |
Proc Natl Acad Sci U S A, 107,
17170-17175.
|
 |
|
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|
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J.Herrou,
R.Foreman,
A.Fiebig,
and
S.Crosson
(2010).
A structural model of anti-anti-σ inhibition by a two-component receiver domain: the PhyR stress response regulator.
|
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Mol Microbiol, 78,
290-304.
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PDB code:
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K.Dong,
Q.Li,
C.Liu,
Y.Zhang,
G.Zhao,
and
X.Guo
(2010).
Cloning and characterization of three cheB genes in Leptospira interrogans.
|
| |
Acta Biochim Biophys Sin (Shanghai), 42,
216-223.
|
 |
|
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|
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M.Y.Galperin
(2010).
Diversity of structure and function of response regulator output domains.
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Curr Opin Microbiol, 13,
150-159.
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|
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B.Harighi
(2009).
Genetic evidence for CheB- and CheR-dependent chemotaxis system in A. tumefaciens toward acetosyringone.
|
| |
Microbiol Res, 164,
634-641.
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|
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D.Kentner,
and
V.Sourjik
(2009).
Dynamic map of protein interactions in the Escherichia coli chemotaxis pathway.
|
| |
Mol Syst Biol, 5,
238.
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|
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U.Jenal,
and
M.Y.Galperin
(2009).
Single domain response regulators: molecular switches with emerging roles in cell organization and dynamics.
|
| |
Curr Opin Microbiol, 12,
152-160.
|
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|
|
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|
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A.Briegel,
H.J.Ding,
Z.Li,
J.Werner,
Z.Gitai,
D.P.Dias,
R.B.Jensen,
and
G.J.Jensen
(2008).
Location and architecture of the Caulobacter crescentus chemoreceptor array.
|
| |
Mol Microbiol, 69,
30-41.
|
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|
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|
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B.Harighi
(2008).
Role of CheY1 and CheY2 in the chemotaxis of A. tumefaciens toward acetosyringone.
|
| |
Curr Microbiol, 56,
547-552.
|
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|
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C.H.Hansen,
R.G.Endres,
and
N.S.Wingreen
(2008).
Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation.
|
| |
PLoS Comput Biol, 4,
e1.
|
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|
|
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|
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E.Bantinaki,
R.Kassen,
C.G.Knight,
Z.Robinson,
A.J.Spiers,
and
P.B.Rainey
(2007).
Adaptive divergence in experimental populations of Pseudomonas fluorescens. III. Mutational origins of wrinkly spreader diversity.
|
| |
Genetics, 176,
441-453.
|
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|
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|
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N.Friedland,
T.R.Mack,
M.Yu,
L.W.Hung,
T.C.Terwilliger,
G.S.Waldo,
and
A.M.Stock
(2007).
Domain orientation in the inactive response regulator Mycobacterium tuberculosis MtrA provides a barrier to activation.
|
| |
Biochemistry, 46,
6733-6743.
|
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PDB code:
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|
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P.Wassmann,
C.Chan,
R.Paul,
A.Beck,
H.Heerklotz,
U.Jenal,
and
T.Schirmer
(2007).
Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition.
|
| |
Structure, 15,
915-927.
|
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PDB code:
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|
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R.Gao,
T.R.Mack,
and
A.M.Stock
(2007).
Bacterial response regulators: versatile regulatory strategies from common domains.
|
| |
Trends Biochem Sci, 32,
225-234.
|
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|
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|
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T.Gao,
X.Zhang,
N.B.Ivleva,
S.S.Golden,
and
A.LiWang
(2007).
NMR structure of the pseudo-receiver domain of CikA.
|
| |
Protein Sci, 16,
465-475.
|
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PDB code:
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|
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C.Laguri,
R.A.Stenzel,
T.J.Donohue,
M.K.Phillips-Jones,
and
M.P.Williamson
(2006).
Activation of the global gene regulator PrrA (RegA) from Rhodobacter sphaeroides.
|
| |
Biochemistry, 45,
7872-7881.
|
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|
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M.A.Laskowski,
and
B.I.Kazmierczak
(2006).
Mutational analysis of RetS, an unusual sensor kinase-response regulator hybrid required for Pseudomonas aeruginosa virulence.
|
| |
Infect Immun, 74,
4462-4473.
|
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|
|
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|
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M.Solà,
D.L.Drew,
A.G.Blanco,
F.X.Gomis-Rüth,
and
M.Coll
(2006).
The cofactor-induced pre-active conformation in PhoB.
|
| |
Acta Crystallogr D Biol Crystallogr, 62,
1046-1057.
|
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PDB code:
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|
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M.Y.Galperin
(2006).
Structural classification of bacterial response regulators: diversity of output domains and domain combinations.
|
| |
J Bacteriol, 188,
4169-4182.
|
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|
|
|
|
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M.Milani,
L.Leoni,
G.Rampioni,
E.Zennaro,
P.Ascenzi,
and
M.Bolognesi
(2005).
An active-like structure in the unphosphorylated StyR response regulator suggests a phosphorylation- dependent allosteric activation mechanism.
|
| |
Structure, 13,
1289-1297.
|
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PDB codes:
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|
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P.Bachhawat,
G.V.Swapna,
G.T.Montelione,
and
A.M.Stock
(2005).
Mechanism of activation for transcription factor PhoB suggested by different modes of dimerization in the inactive and active states.
|
| |
Structure, 13,
1353-1363.
|
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|
PDB code:
|
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|
 |
W.C.Lai,
and
G.L.Hazelbauer
(2005).
Carboxyl-terminal extensions beyond the conserved pentapeptide reduce rates of chemoreceptor adaptational modification.
|
| |
J Bacteriol, 187,
5115-5121.
|
 |
|
|
|
|
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C.Chan,
R.Paul,
D.Samoray,
N.C.Amiot,
B.Giese,
U.Jenal,
and
T.Schirmer
(2004).
Structural basis of activity and allosteric control of diguanylate cyclase.
|
| |
Proc Natl Acad Sci U S A, 101,
17084-17089.
|
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|
PDB code:
|
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|
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G.H.Wadhams,
and
J.P.Armitage
(2004).
Making sense of it all: bacterial chemotaxis.
|
| |
Nat Rev Mol Cell Biol, 5,
1024-1037.
|
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|
|
|
|
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H.Szurmant,
and
G.W.Ordal
(2004).
Diversity in chemotaxis mechanisms among the bacteria and archaea.
|
| |
Microbiol Mol Biol Rev, 68,
301-319.
|
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|
|
|
|
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J.G.Smith,
J.A.Latiolais,
G.P.Guanga,
J.D.Pennington,
R.E.Silversmith,
and
R.B.Bourret
(2004).
A search for amino acid substitutions that universally activate response regulators.
|
| |
Mol Microbiol, 51,
887-901.
|
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|
|
|
|
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K.Muchová,
R.J.Lewis,
D.Perecko,
J.A.Brannigan,
J.C.Ladds,
A.Leech,
A.J.Wilkinson,
and
I.Barák
(2004).
Dimer-induced signal propagation in Spo0A.
|
| |
Mol Microbiol, 53,
829-842.
|
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|
|
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|
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S.Banno,
D.Shiomi,
M.Homma,
and
I.Kawagishi
(2004).
Targeting of the chemotaxis methylesterase/deamidase CheB to the polar receptor-kinase cluster in an Escherichia coli cell.
|
| |
Mol Microbiol, 53,
1051-1063.
|
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|
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|
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S.Y.Park,
B.D.Beel,
M.I.Simon,
A.M.Bilwes,
and
B.R.Crane
(2004).
In different organisms, the mode of interaction between two signaling proteins is not necessarily conserved.
|
| |
Proc Natl Acad Sci U S A, 101,
11646-11651.
|
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PDB code:
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X.Feng,
D.Walthers,
R.Oropeza,
and
L.J.Kenney
(2004).
The response regulator SsrB activates transcription and binds to a region overlapping OmpR binding sites at Salmonella pathogenicity island 2.
|
| |
Mol Microbiol, 54,
823-835.
|
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|
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|
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Y.Chen,
W.R.Abdel-Fattah,
and
F.M.Hulett
(2004).
Residues required for Bacillus subtilis PhoP DNA binding or RNA polymerase interaction: alanine scanning of PhoP effector domain transactivation loop and alpha helix 3.
|
| |
J Bacteriol, 186,
1493-1502.
|
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|
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|
|
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B.A.Mello,
and
Y.Tu
(2003).
Perfect and near-perfect adaptation in a model of bacterial chemotaxis.
|
| |
Biophys J, 84,
2943-2956.
|
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|
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|
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C.Birck,
Y.Chen,
F.M.Hulett,
and
J.P.Samama
(2003).
The crystal structure of the phosphorylation domain in PhoP reveals a functional tandem association mediated by an asymmetric interface.
|
| |
J Bacteriol, 185,
254-261.
|
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PDB code:
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|
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J.H.Zhang,
G.Xiao,
R.P.Gunsalus,
and
W.L.Hubbell
(2003).
Phosphorylation triggers domain separation in the DNA binding response regulator NarL.
|
| |
Biochemistry, 42,
2552-2559.
|
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|
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V.L.Robinson,
T.Wu,
and
A.M.Stock
(2003).
Structural analysis of the domain interface in DrrB, a response regulator of the OmpR/PhoB subfamily.
|
| |
J Bacteriol, 185,
4186-4194.
|
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PDB code:
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|
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A.E.Maris,
M.R.Sawaya,
M.Kaczor-Grzeskowiak,
M.R.Jarvis,
S.M.Bearson,
M.L.Kopka,
I.Schröder,
R.P.Gunsalus,
and
R.E.Dickerson
(2002).
Dimerization allows DNA target site recognition by the NarL response regulator.
|
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Nat Struct Biol, 9,
771-778.
|
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PDB code:
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|
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G.S.Anand,
and
A.M.Stock
(2002).
Kinetic basis for the stimulatory effect of phosphorylation on the methylesterase activity of CheB.
|
| |
Biochemistry, 41,
6752-6760.
|
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|
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|
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J.Marchant,
B.Wren,
and
J.Ketley
(2002).
Exploiting genome sequence: predictions for mechanisms of Campylobacter chemotaxis.
|
| |
Trends Microbiol, 10,
155-159.
|
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|
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|
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P.Roche,
L.Mouawad,
D.Perahia,
J.P.Samama,
and
D.Kahn
(2002).
Molecular dynamics of the FixJ receiver domain: movement of the beta4-alpha4 loop correlates with the in and out flip of Phe101.
|
| |
Protein Sci, 11,
2622-2630.
|
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|
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|
|
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R.Hengge-Aronis
(2002).
Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase.
|
| |
Microbiol Mol Biol Rev, 66,
373.
|
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|
|
|
|
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A.H.West,
and
A.M.Stock
(2001).
Histidine kinases and response regulator proteins in two-component signaling systems.
|
| |
Trends Biochem Sci, 26,
369-376.
|
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|
|
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|
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E.Klauck,
M.Lingnau,
and
R.Hengge-Aronis
(2001).
Role of the response regulator RssB in sigma recognition and initiation of sigma proteolysis in Escherichia coli.
|
| |
Mol Microbiol, 40,
1381-1390.
|
 |
|
|
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|
 |
M.P.Allen,
K.B.Zumbrennen,
and
W.R.McCleary
(2001).
Genetic evidence that the alpha5 helix of the receiver domain of PhoB is involved in interdomain interactions.
|
| |
J Bacteriol, 183,
2204-2211.
|
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|
|
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|
 |
R.L.Saxl,
G.S.Anand,
and
A.M.Stock
(2001).
Synthesis and biochemical characterization of a phosphorylated analogue of the response regulator CheB.
|
| |
Biochemistry, 40,
12896-12903.
|
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|
|
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|
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W.Wang,
R.Kim,
J.Jancarik,
H.Yokota,
and
S.H.Kim
(2001).
Crystal structure of phosphoserine phosphatase from Methanococcus jannaschii, a hyperthermophile, at 1.8 A resolution.
|
| |
Structure, 9,
65-71.
|
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|
PDB code:
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|
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A.Bren,
and
M.Eisenbach
(2000).
How signals are heard during bacterial chemotaxis: protein-protein interactions in sensory signal propagation.
|
| |
J Bacteriol, 182,
6865-6873.
|
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|
|
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|
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A.M.Stock,
V.L.Robinson,
and
P.N.Goudreau
(2000).
Two-component signal transduction.
|
| |
Annu Rev Biochem, 69,
183-215.
|
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|
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|
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D.R.Buckler,
G.S.Anand,
and
A.M.Stock
(2000).
Response-regulator phosphorylation and activation: a two-way street?
|
| |
Trends Microbiol, 8,
153-156.
|
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|
|
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|
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G.S.Anand,
P.N.Goudreau,
J.K.Lewis,
and
A.M.Stoc
(2000).
Evidence for phosphorylation-dependent conformational changes in methylesterase CheB.
|
| |
Protein Sci, 9,
898-906.
|
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|
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|
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J.A.Bornhorst,
and
J.J.Falke
(2000).
Attractant regulation of the aspartate receptor-kinase complex: limited cooperative interactions between receptors and effects of the receptor modification state.
|
| |
Biochemistry, 39,
9486-9493.
|
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|
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|
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J.Lee,
J.T.Owens,
I.Hwang,
C.Meares,
and
S.Kustu
(2000).
Phosphorylation-induced signal propagation in the response regulator ntrC.
|
| |
J Bacteriol, 182,
5188-5195.
|
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|
|
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|
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J.Stock,
and
M.Levit
(2000).
Signal transduction: hair brains in bacterial chemotaxis.
|
| |
Curr Biol, 10,
R11-R14.
|
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|
|
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|
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J.Zapf,
U.Sen,
Madhusudan,
J.A.Hoch,
and
K.I.Varughese
(2000).
A transient interaction between two phosphorelay proteins trapped in a crystal lattice reveals the mechanism of molecular recognition and phosphotransfer in signal transduction.
|
| |
Structure, 8,
851-862.
|
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|
PDB code:
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|
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|
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R.J.Lewis,
S.Krzywda,
J.A.Brannigan,
J.P.Turkenburg,
K.Muchová,
E.J.Dodson,
I.Barák,
and
A.J.Wilkinson
(2000).
The trans-activation domain of the sporulation response regulator Spo0A revealed by X-ray crystallography.
|
| |
Mol Microbiol, 38,
198-212.
|
 |
|
PDB code:
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|
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R.P.Garg,
J.Huang,
W.Yindeeyoungyeon,
T.P.Denny,
and
M.A.Schell
(2000).
Multicomponent transcriptional regulation at the complex promoter of the exopolysaccharide I biosynthetic operon of Ralstonia solanacearum.
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C.Birck,
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and
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(1999).
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Structure, 7,
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PDB code:
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D.Yan,
H.S.Cho,
C.A.Hastings,
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(1999).
The structure of the signal receiver domain of the Arabidopsis thaliana ethylene receptor ETR1.
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| |
Structure, 7,
1547-1556.
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PDB code:
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J.A.Freeman,
and
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(1999).
A genetic analysis of the function of LuxO, a two-component response regulator involved in quorum sensing in Vibrio harveyi.
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| |
Acta Crystallogr D Biol Crystallogr, 55,
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PDB code:
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M.N.Levit,
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(1999).
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D.Kahn,
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Structural transitions in the FixJ receiver domain.
|
| |
Structure, 7,
1517-1526.
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PDB codes:
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P.Heikinheimo,
A.Goldman,
C.Jeffries,
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Phosphorylation-induced dimerization of the FixJ receiver domain.
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C-terminal DNA binding stimulates N-terminal phosphorylation of the outer membrane protein regulator OmpR from Escherichia coli.
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(1998).
Signal transduction in bacteria: molecular mechanisms of stimulus-response coupling.
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The most recent references are shown first.
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only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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