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PDBsum entry 2byv

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protein links
Regulation PDB id
2byv
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Contents
Protein chain
922 a.a. *
Waters ×66
* Residue conservation analysis
PDB id:
2byv
Name: Regulation
Title: Structure of the camp responsive exchange factor epac2 in its auto-inhibited state
Structure: Rap guanine nucleotide exchange factor 4. Chain: e. Synonym: camp-regulated guanine nucleotide exchange factor ii, camp-gefii, exchange factor directly activated by camp 2, epac 2, camp-dependent rap1 guanine-nucleotide exchange factor. Engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.70Å     R-factor:   0.248     R-free:   0.297
Authors: H.Rehmann,A.Wittinghofer,J.L.Bos
Key ref:
H.Rehmann et al. (2006). Structure of the cyclic-AMP-responsive exchange factor Epac2 in its auto-inhibited state. Nature, 439, 625-628. PubMed id: 16452984 DOI: 10.1038/nature04468
Date:
08-Aug-05     Release date:   02-Feb-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9EQZ6  (RPGF4_MOUSE) -  Rap guanine nucleotide exchange factor 4
Seq:
Struc:
 
Seq:
Struc:
1011 a.a.
922 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     intracellular signal transduction   8 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
DOI no: 10.1038/nature04468 Nature 439:625-628 (2006)
PubMed id: 16452984  
 
 
Structure of the cyclic-AMP-responsive exchange factor Epac2 in its auto-inhibited state.
H.Rehmann, J.Das, P.Knipscheer, A.Wittinghofer, J.L.Bos.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
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.
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).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 439, 625-628) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20729090 A.Cukkemane, R.Seifert, and U.B.Kaupp (2011).
Cooperative and uncooperative cyclic-nucleotide-gated ion channels.
  Trends Biochem Sci, 36, 55-64.  
21338921 K.J.Herbst, C.Coltharp, L.M.Amzel, and J.Zhang (2011).
Direct activation of Epac by sulfonylurea is isoform selective.
  Chem Biol, 18, 243-251.  
22081014 P.D.Mace, Y.Wallez, M.K.Dobaczewska, J.J.Lee, H.Robinson, E.B.Pasquale, and S.J.Riedl (2011).
NSP-Cas protein structures reveal a promiscuous interaction module in cell signaling.
  Nat Struct Mol Biol, 18, 1381-1387.
PDB codes: 3t6a 3t6g
21444788 R.Selvaratnam, S.Chowdhury, B.VanSchouwen, and G.Melacini (2011).
Mapping allostery through the covariance analysis of NMR chemical shifts.
  Proc Natl Acad Sci U S A, 108, 6133-6138.  
20855527 M.Gloerich, B.Ponsioen, M.J.Vliem, Z.Zhang, J.Zhao, M.R.Kooistra, L.S.Price, L.Ritsma, F.J.Zwartkruis, H.Rehmann, K.Jalink, and J.L.Bos (2010).
Spatial regulation of cyclic AMP-Epac1 signaling in cell adhesion by ERM proteins.
  Mol Cell Biol, 30, 5421-5431.  
20055708 M.Gloerich, and J.L.Bos (2010).
Epac: defining a new mechanism for cAMP action.
  Annu Rev Pharmacol Toxicol, 50, 355-375.  
19912228 M.Grandoch, S.S.Roscioni, and M.Schmidt (2010).
The role of Epac proteins, novel cAMP mediators, in the regulation of immune, lung and neuronal function.
  Br J Pharmacol, 159, 265-284.  
19855995 M.Métrich, M.Berthouze, E.Morel, B.Crozatier, A.M.Gomez, and F.Lezoualc'h (2010).
Role of the cAMP-binding protein Epac in cardiovascular physiology and pathophysiology.
  Pflugers Arch, 459, 535-546.  
20551594 S.Seino, T.Shibasaki, and K.Minami (2010).
Pancreatic beta-cell signaling: toward better understanding of diabetes and its treatment.
  Proc Jpn Acad Ser B Phys Biol Sci, 86, 563-577.  
20512974 T.J.Sjoberg, A.P.Kornev, and S.S.Taylor (2010).
Dissecting the cAMP-inducible allosteric switch in protein kinase A RIalpha.
  Protein Sci, 19, 1213-1221.
PDB code: 3iia
19273589 B.Ponsioen, M.Gloerich, L.Ritsma, H.Rehmann, J.L.Bos, and K.Jalink (2009).
Direct spatial control of Epac1 by cyclic AMP.
  Mol Cell Biol, 29, 2521-2531.  
18937323 E.Aivatiadou, M.Ripolone, F.Brunetti, and G.Berruti (2009).
cAMP-Epac2-mediated activation of Rap1 in developing male germ cells: RA-RhoGAP as a possible direct down-stream effector.
  Mol Reprod Dev, 76, 407-416.  
19210747 G.Borland, B.O.Smith, and S.J.Yarwood (2009).
EPAC proteins transduce diverse cellular actions of cAMP.
  Br J Pharmacol, 158, 70-86.  
19525958 J.W.Taraska, M.C.Puljung, N.B.Olivier, G.E.Flynn, and W.N.Zagotta (2009).
Mapping the structure and conformational movements of proteins with transition metal ion FRET.
  Nat Methods, 6, 532-537.
PDB codes: 3etq 3ffq
19403523 R.Das, S.Chowdhury, M.T.Mazhab-Jafari, S.Sildas, R.Selvaratnam, and G.Melacini (2009).
Dynamically driven ligand selectivity in cyclic nucleotide binding domains.
  J Biol Chem, 284, 23682-23696.  
19141281 T.S.Freedman, H.Sondermann, O.Kuchment, G.D.Friedland, T.Kortemme, and J.Kuriyan (2009).
Differences in flexibility underlie functional differences in the Ras activators son of sevenless and Ras guanine nucleotide releasing factor 1.
  Structure, 17, 41-53.  
19553663 T.Tsalkova, D.K.Blumenthal, F.C.Mei, M.A.White, and X.Cheng (2009).
Mechanism of Epac activation: structural and functional analyses of Epac2 hinge mutants with constitutive and reduced activities.
  J Biol Chem, 284, 23644-23651.  
18404204 A.P.Kornev, S.S.Taylor, and L.F.Ten Eyck (2008).
A generalized allosteric mechanism for cis-regulated cyclic nucleotide binding domains.
  PLoS Comput Biol, 4, e1000056.  
18824540 C.Liu, M.Takahashi, Y.Li, S.Song, T.J.Dillon, U.Shinde, and P.J.Stork (2008).
Ras is required for the cyclic AMP-dependent activation of Rap1 via Epac2.
  Mol Cell Biol, 28, 7109-7125.  
18063584 D.Hochbaum, K.Hong, G.Barila, F.Ribeiro-Neto, and D.L.Altschuler (2008).
Epac, in synergy with cAMP-dependent protein kinase (PKA), is required for cAMP-mediated mitogenesis.
  J Biol Chem, 283, 4464-4468.  
17716863 G.G.Holz, O.G.Chepurny, and F.Schwede (2008).
Epac-selective cAMP analogs: new tools with which to evaluate the signal transduction properties of cAMP-regulated guanine nucleotide exchange factors.
  Cell Signal, 20, 10-20.  
18660803 H.Rehmann, E.Arias-Palomo, M.A.Hadders, F.Schwede, O.Llorca, and J.L.Bos (2008).
Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B.
  Nature, 455, 124-127.
PDB code: 3cf6
18250627 K.U.Wendt, M.S.Weiss, P.Cramer, and D.W.Heinz (2008).
Structures and diseases.
  Nat Struct Mol Biol, 15, 117-120.  
18411261 R.Das, M.T.Mazhab-Jafari, S.Chowdhury, S.SilDas, R.Selvaratnam, and G.Melacini (2008).
Entropy-driven cAMP-dependent allosteric control of inhibitory interactions in exchange proteins directly activated by cAMP.
  J Biol Chem, 283, 19691-19703.  
18167352 S.M.Harper, H.Wienk, R.W.Wechselberger, J.L.Bos, R.Boelens, and H.Rehmann (2008).
Structural dynamics in the activation of Epac.
  J Biol Chem, 283, 6501-6508.  
18176800 S.S.Roscioni, C.R.Elzinga, and M.Schmidt (2008).
Epac: effectors and biological functions.
  Naunyn Schmiedebergs Arch Pharmacol, 377, 345-357.  
18604457 X.Cheng, Z.Ji, T.Tsalkova, and F.Mei (2008).
Epac and PKA: a tale of two intracellular cAMP receptors.
  Acta Biochim Biophys Sin (Shanghai), 40, 651-662.  
17183361 H.Rehmann, A.Wittinghofer, and J.L.Bos (2007).
Capturing cyclic nucleotides in action: snapshots from crystallographic studies.
  Nat Rev Mol Cell Biol, 8, 63-73.  
17540168 J.L.Bos, H.Rehmann, and A.Wittinghofer (2007).
GEFs and GAPs: critical elements in the control of small G proteins.
  Cell, 129, 865-877.  
17283075 L.I.Jiang, J.Collins, R.Davis, K.M.Lin, D.DeCamp, T.Roach, R.Hsueh, R.A.Rebres, E.M.Ross, R.Taussig, I.Fraser, and P.C.Sternweis (2007).
Use of a cAMP BRET sensor to characterize a novel regulation of cAMP by the sphingosine 1-phosphate/G13 pathway.
  J Biol Chem, 282, 10576-10584.  
17785454 M.Brock, F.Fan, F.C.Mei, S.Li, C.Gessner, V.L.Woods, and X.Cheng (2007).
Conformational analysis of Epac activation using amide hydrogen/deuterium exchange mass spectrometry.
  J Biol Chem, 282, 32256-32263.  
16973695 G.G.Holz, G.Kang, M.Harbeck, M.W.Roe, and O.G.Chepurny (2006).
Cell physiology of cAMP sensor Epac.
  J Physiol, 577, 5.  
17000774 G.X.Shi, H.Rehmann, and D.A.Andres (2006).
A novel cyclic AMP-dependent Epac-Rit signaling pathway contributes to PACAP38-mediated neuronal differentiation.
  Mol Cell Biol, 26, 9136-9147.  
17084085 J.L.Bos (2006).
Epac proteins: multi-purpose cAMP targets.
  Trends Biochem Sci, 31, 680-686.  
16728394 K.K.Dao, K.Teigen, R.Kopperud, E.Hodneland, F.Schwede, A.E.Christensen, A.Martinez, and S.O.Døskeland (2006).
Epac1 and cAMP-dependent protein kinase holoenzyme have similar cAMP affinity, but their cAMP domains have distinct structural features and cyclic nucleotide recognition.
  J Biol Chem, 281, 21500-21511.  
17176054 S.Yu, F.Fan, S.C.Flores, F.Mei, and X.Cheng (2006).
Dissecting the mechanism of Epac activation via hydrogen-deuterium exchange FT-IR and structural modeling.
  Biochemistry, 45, 15318-15326.  
17075039 T.S.Freedman, H.Sondermann, G.D.Friedland, T.Kortemme, D.Bar-Sagi, S.Marqusee, and J.Kuriyan (2006).
A Ras-induced conformational switch in the Ras activator Son of sevenless.
  Proc Natl Acad Sci U S A, 103, 16692-16697.
PDB codes: 2ii0 2ije
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 codes are shown on the right.

 

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