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DOI no:
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Structure
15:915-927
(2007)
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PubMed id:
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Structure of BeF3- -modified response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition.
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P.Wassmann,
C.Chan,
R.Paul,
A.Beck,
H.Heerklotz,
U.Jenal,
T.Schirmer.
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ABSTRACT
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Cyclic di-guanosine monophosphate (c-di-GMP) is a ubiquitous bacterial second
messenger involved in the regulation of cell surface-associated traits and
persistence. We have determined the crystal structure of PleD from Caulobacter
crescentus, a response regulator with a diguanylate cyclase (DGC) domain, in its
activated form. The BeF(3)(-) modification of its receiver domain causes
rearrangement with respect to an adaptor domain, which, in turn, promotes dimer
formation, allowing for the efficient encounter of two symmetric catalytic
domains. The substrate analog GTPalphaS and two putative cations are bound to
the active sites in a manner similar to adenylate cyclases, suggesting an
analogous two-metal catalytic mechanism. An allosteric c-di-GMP-binding mode
that crosslinks DGC and an adaptor domain had been identified before. Here, a
second mode is observed that crosslinks the DGC domains within a PleD dimer.
Both modes cause noncompetitive product inhibition by domain immobilization.
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Selected figure(s)
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Figure 5.
Figure 5. Substrate Analog GTPαS and Mg^2+ Bound to the
Active Site of PleD
The omit map for the ligands is
contoured at 3σ. The DGC domain is shown in ribbon
representation; the GGEEF signature hairpin is shown in dark
blue, and all interacting residues and the P loop main chain
(residues 328–331) are shown in full. (c-di-GMP)[2] bound to
the I[p] site of the DGC domain can be seen in the rear.
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Figure 6.
Figure 6. Crosslinking of the DGC Domains by c-di-GMP
(A) Ribbon diagram of the DGC dimer along its symmetry axis;
both (c-di-GMP)[2] ligands and interacting residues are shown in
full. The (c-di-GMP)[2] ligands are bound to the I site (I[P]
site and the I[s,DGC] site of the adjacent subunit).
(B)
Close-up view of the intercalated (c-di-GMP)[2] ligand, which
crosslinks the two DGC domains (dark- and light-green surface
representation) by binding to the I[p] (Arg359, Asp362, Arg390)
and the I[s,DGC] (R313′) site of the adjacent domain.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2007,
15,
915-927)
copyright 2007.
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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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A.Duerig,
S.Abel,
M.Folcher,
M.Nicollier,
T.Schwede,
N.Amiot,
B.Giese,
and
U.Jenal
(2009).
Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression.
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Genes Dev, 23,
93.
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G.Minasov,
S.Padavattan,
L.Shuvalova,
J.S.Brunzelle,
D.J.Miller,
A.Baslé,
C.Massa,
F.R.Collart,
T.Schirmer,
and
W.F.Anderson
(2009).
Crystal Structures of YkuI and Its Complex with Second Messenger Cyclic Di-GMP Suggest Catalytic Mechanism of Phosphodiester Bond Cleavage by EAL Domains.
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J Biol Chem, 284,
13174-13184.
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PDB code:
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K.D.Smith,
S.V.Lipchock,
T.D.Ames,
J.Wang,
R.R.Breaker,
and
S.A.Strobel
(2009).
Structural basis of ligand binding by a c-di-GMP riboswitch.
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Nat Struct Mol Biol, 16,
1218-1223.
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PDB code:
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N.Tschowri,
S.Busse,
and
R.Hengge
(2009).
The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli.
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Genes Dev, 23,
522-534.
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R.Hengge
(2009).
Principles of c-di-GMP signalling in bacteria.
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Nat Rev Microbiol, 7,
263-273.
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T.Schirmer,
and
U.Jenal
(2009).
Structural and mechanistic determinants of c-di-GMP signalling.
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Nat Rev Microbiol, 7,
724-735.
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J.W.Hickman,
and
C.S.Harwood
(2008).
Identification of FleQ from Pseudomonas aeruginosa as a c-di-GMP-responsive transcription factor.
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Mol Microbiol, 69,
376-389.
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L.M.Holland,
S.T.O'Donnell,
D.A.Ryjenkov,
L.Gomelsky,
S.R.Slater,
P.D.Fey,
M.Gomelsky,
and
J.P.O'Gara
(2008).
A staphylococcal GGDEF domain protein regulates biofilm formation independently of cyclic dimeric GMP.
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J Bacteriol, 190,
5178-5189.
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N.De,
M.Pirruccello,
P.V.Krasteva,
N.Bae,
R.V.Raghavan,
and
H.Sondermann
(2008).
Phosphorylation-independent regulation of the diguanylate cyclase WspR.
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PLoS Biol, 6,
e67.
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PDB code:
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N.Sudarsan,
E.R.Lee,
Z.Weinberg,
R.H.Moy,
J.N.Kim,
K.H.Link,
and
R.R.Breaker
(2008).
Riboswitches in eubacteria sense the second messenger cyclic di-GMP.
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Science, 321,
411-413.
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R.Paul,
S.Abel,
P.Wassmann,
A.Beck,
H.Heerklotz,
and
U.Jenal
(2007).
Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization.
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J Biol Chem, 282,
29170-29177.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
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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459 a.a.
_CL
_MG
