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PDBsum entry 2byv
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References listed in PDB file
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Key reference
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Title
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Structure of the cyclic-Amp-Responsive exchange factor epac2 in its auto-Inhibited state.
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Authors
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H.Rehmann,
J.Das,
P.Knipscheer,
A.Wittinghofer,
J.L.Bos.
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Ref.
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Nature, 2006,
439,
625-628.
[DOI no: ]
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PubMed id
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Abstract
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Epac proteins (exchange proteins directly activated by cAMP) are
guanine-nucleotide-exchange factors (GEFs) for the small GTP-binding proteins
Rap1 and Rap2 that are directly regulated by the second messenger cyclic AMP and
function in the control of diverse cellular processes, including cell adhesion
and insulin secretion. Here we report the three-dimensional structure of
full-length Epac2, a 110-kDa protein that contains an amino-terminal regulatory
region with two cyclic-nucleotide-binding domains and a carboxy-terminal
catalytic region. The structure was solved in the absence of cAMP and shows the
auto-inhibited state of Epac. The regulatory region is positioned with respect
to the catalytic region by a rigid, tripartite beta-sheet-like structure we
refer to as the 'switchboard' and an ionic interaction we call the 'ionic
latch'. As a consequence of this arrangement, the access of Rap to the catalytic
site is sterically blocked. Mutational analysis suggests a model for
cAMP-induced Epac activation with rigid body movement of the regulatory region,
the features of which are universally conserved in cAMP-regulated proteins.
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Figure 1.
Figure 1: Structure of Epac2. a, Domain organization of Epac.
The same colour code is used throughout the figures. CDC25-HD,
CDC25-homology domain; cNBD, cyclic-nucleotide-binding domain;
DEP, Dishevelled, Egl-10, Pleckstrin domain; RA, Ras-association
domain; REM, Ras-exchange motif. b, Ribbon diagram of Epac2 in
stereo view. Missing connectivity is indicated by coloured
dotted lines. The green ball indicates the cAMP-binding site in
cNBD-B. HP, helical hairpin of the CDC25-HD (dark blue); SB,
switchboard; IL, ionic latch (doted black lines); CH, connecting
helix (helix H4 in ref 13). c, Surface representation of Epac.
d, Superposition of Epac and the Ras-Sos complex. The RA, DEP
and REM domains are omitted. Only Ras (magenta) from the Ras-Sos
complex is shown.
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Figure 2.
Figure 2: Anchoring points between the regulatory and catalytic
regions. a, The switchboard is formed by strands provided by
cNBD-B (dark green), the REM domain (orange) and the loop of the
helical hairpin (HP) of CDC25-HD (blue). Peptides are reduced to
polyglycine. Hydrogen bonding by main-chain atoms is indicated
by dotted lines. b, The REM domain (orange) interacts tightly
with the C-terminal helix of the helical hairpin (blue). Thick C
 traces
highlight the parts of the switchboard shown in a. c, The ionic
latch between cNBD-B (green) and CDC25-HD (blue). CH, connecting
helix (see Fig. 1b).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2006,
439,
625-628)
copyright 2006.
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Secondary reference #1
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Title
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Structure and regulation of the camp-Binding domains of epac2.
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Authors
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H.Rehmann,
B.Prakash,
E.Wolf,
A.Rueppel,
J.De rooij,
J.L.Bos,
A.Wittinghofer.
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Ref.
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Nat Struct Biol, 2003,
10,
26-32.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Structure of Epac. a, Domain organization of Epac1
and 2. Indicated color code is used throughout the figure. b,
Stereo view of a 2F[o] - F[c] composite omitted electron density
map (contoured at 1.5  ).
The hydrophobic environment of Leu408 and Phe435 is shown.
Different parts of the peptide chain are highlighted by
individual colors. c, Ribbon diagram of the regulatory domain of
Epac2 with N and C termini as indicated. The C-terminal extra
helix of the DEP domain is dark green. d, Amino acid sequence,
with secondary structure annotation. The phosphate-binding
cassette (PBC) is indicated in red letters. Dashed lines
indicate portions of the polypeptide chain not visible in the
electron density. e, The two possible arrangements (1 and 2) for
the first cNMP-binding domain relative to the second (see text).
Arrangement 1 corresponds to (c). Dotted lines, linker 1 and 2,
indicate the minimal path of the polypeptide chain required to
bridge the gap in both arrangements.
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Figure 2.
Figure 2. Ribbon diagram of the DEP domains of Epac and
Dishevelled. The DEP domains of Epac (yellow and green) and
Dishevelled (gray) are superimposed on each other. Secondary
structure elements are labeled as in Fig. 1c. N and C termini,
as well as the position of the residues forming the dipole, are
indicated as follows: '1' corresponds to Asp225^Epac and
Glu448^Dvl1; '2' to Glu222^Epac and Asp445^Dvl1; and '3' to
Lys212^Epac and Lys434^Dvl1.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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