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PDBsum entry 1o7f

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protein links
Regulation PDB id
1o7f
Jmol
Contents
Protein chain
421 a.a. *
Waters ×69
* Residue conservation analysis
PDB id:
1o7f
Name: Regulation
Title: Crystal structure of the regulatory domain of epac2
Structure: Camp-dependent rap1 guanine-nucleotide exchange factor. Chain: a. Fragment: cnmp-binding domain, dishevelled-egl-pleckstrin (dep), cnmb-binding domain, residues 1-463. Engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.5Å     R-factor:   0.244     R-free:   0.278
Authors: H.Rehmann,B.Prakash,E.Wolf,A.Rueppel,J.De Rooij,J.L.Bos, A.Wittinghofer
Key ref:
H.Rehmann et al. (2003). Structure and regulation of the cAMP-binding domains of Epac2. Nat Struct Biol, 10, 26-32. PubMed id: 12469113 DOI: 10.1038/nsb878
Date:
04-Nov-02     Release date:   11-Nov-02    
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.
421 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cAMP-dependent protein kinase complex   1 term 
  Biological process     intracellular signal transduction   2 terms 
  Biochemical function     cAMP-dependent protein kinase regulator activity     1 term  

 

 
DOI no: 10.1038/nsb878 Nat Struct Biol 10:26-32 (2003)
PubMed id: 12469113  
 
 
Structure and regulation of the cAMP-binding domains of Epac2.
H.Rehmann, B.Prakash, E.Wolf, A.Rueppel, J.de Rooij, J.L.Bos, A.Wittinghofer.
 
  ABSTRACT  
 
Cyclic adenosine monophosphate (cAMP) is a universal second messenger that, in eukaryotes, was believed to act only on cAMP-dependent protein kinase A (PKA) and cyclic nucleotide-regulated ion channels. Recently, guanine nucleotide exchange factors specific for the small GTP-binding proteins Rap1 and Rap2 (Epacs) were described, which are also activated directly by cAMP. Here, we have determined the three-dimensional structure of the regulatory domain of Epac2, which consists of two cyclic nucleotide monophosphate (cNMP)-binding domains and one DEP (Dishevelled, Egl, Pleckstrin) domain. This is the first structure of a cNMP-binding domain in the absence of ligand, and comparison with previous structures, sequence alignment and biochemical experiments allow us to delineate a mechanism for cyclic nucleotide-mediated conformational change and activation that is most likely conserved for all cNMP-regulated proteins. We identify a hinge region that couples cAMP binding to a conformational change of the C-terminal regions. Mutations in the hinge of Epac can uncouple cAMP binding from its exchange activity.
 
  Selected figure(s)  
 
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.
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.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2003, 10, 26-32) copyright 2003.  
  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.  
21430265 S.Schünke, M.Stoldt, J.Lecher, U.B.Kaupp, and D.Willbold (2011).
Structural insights into conformational changes of a cyclic nucleotide-binding domain in solution from Mesorhizobium loti K1 channel.
  Proc Natl Acad Sci U S A, 108, 6121-6126.
PDB code: 2kxl
21070946 J.Rinaldi, J.Wu, J.Yang, C.Y.Ralston, B.Sankaran, S.Moreno, and S.S.Taylor (2010).
Structure of yeast regulatory subunit: a glimpse into the evolution of PKA signaling.
  Structure, 18, 1471-1482.
PDB code: 3of1
20055708 M.Gloerich, and J.L.Bos (2010).
Epac: defining a new mechanism for cAMP action.
  Annu Rev Pharmacol Toxicol, 50, 355-375.  
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.  
19170062 M.Niimura, T.Miki, T.Shibasaki, W.Fujimoto, T.Iwanaga, and S.Seino (2009).
Critical role of the N-terminal cyclic AMP-binding domain of Epac2 in its subcellular localization and function.
  J Cell Physiol, 219, 652-658.  
19359484 N.Popovych, S.R.Tzeng, M.Tonelli, R.H.Ebright, and C.G.Kalodimos (2009).
Structural basis for cAMP-mediated allosteric control of the catabolite activator protein.
  Proc Natl Acad Sci U S A, 106, 6927-6932.
PDB code: 2wc2
19465888 S.Schünke, M.Stoldt, K.Novak, U.B.Kaupp, and D.Willbold (2009).
Solution structure of the Mesorhizobium loti K1 channel cyclic nucleotide-binding domain in complex with cAMP.
  EMBO Rep, 10, 729-735.
PDB code: 2k0g
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.  
  18663135 H.Liu, J.A.Enyeart, and J.J.Enyeart (2008).
ACTH inhibits bTREK-1 K+ channels through multiple cAMP-dependent signaling pathways.
  J Gen Physiol, 132, 279-294.  
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.  
18619611 S.L.Altieri, G.M.Clayton, W.R.Silverman, A.O.Olivares, E.M.De la Cruz, L.R.Thomas, and J.H.Morais-Cabral (2008).
Structural and energetic analysis of activation by a cyclic nucleotide binding domain.
  J Mol Biol, 381, 655-669.
PDB codes: 3cl1 3clp 3co2
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.  
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.  
17562314 G.E.Flynn, K.D.Black, L.D.Islas, B.Sankaran, and W.N.Zagotta (2007).
Structure and rearrangements in the carboxy-terminal region of SpIH channels.
  Structure, 15, 671-682.
PDB codes: 2ptm 2q0a
17573905 I.Usynin, C.Klotz, and U.Frevert (2007).
Malaria circumsporozoite protein inhibits the respiratory burst in Kupffer cells.
  Cell Microbiol, 9, 2610-2628.  
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.  
17074757 R.Das, and G.Melacini (2007).
A model for agonism and antagonism in an ancient and ubiquitous cAMP-binding domain.
  J Biol Chem, 282, 581-593.  
17182741 R.Das, V.Esposito, M.Abu-Abed, G.S.Anand, S.S.Taylor, and G.Melacini (2007).
cAMP activation of PKA defines an ancient signaling mechanism.
  Proc Natl Acad Sci U S A, 104, 93-98.  
16990133 D.R.Ballon, P.L.Flanary, D.P.Gladue, J.B.Konopka, H.G.Dohlman, and J.Thorner (2006).
DEP-domain-mediated regulation of GPCR signaling responses.
  Cell, 126, 1079-1093.  
16613879 G.Kang, O.G.Chepurny, B.Malester, M.J.Rindler, H.Rehmann, J.L.Bos, F.Schwede, W.A.Coetzee, and G.G.Holz (2006).
cAMP sensor Epac as a determinant of ATP-sensitive potassium channel activity in human pancreatic beta cells and rat INS-1 cells.
  J Physiol, 573, 595-609.  
16452984 H.Rehmann, J.Das, P.Knipscheer, A.Wittinghofer, and J.L.Bos (2006).
Structure of the cyclic-AMP-responsive exchange factor Epac2 in its auto-inhibited state.
  Nature, 439, 625-628.
PDB code: 2byv
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.  
16786292 L.Yang, W.Huang, H.Wang, R.Cai, Y.Xu, and H.Huang (2006).
Characterizations of a hypomorphic argonaute1 mutant reveal novel AGO1 functions in Arabidopsis lateral organ development.
  Plant Mol Biol, 61, 63-78.  
16500960 M.Berrera, S.Pantano, and P.Carloni (2006).
cAMP Modulation of the cytoplasmic domain in the HCN2 channel investigated by molecular simulations.
  Biophys J, 90, 3428-3433.  
16407249 M.T.Branham, L.S.Mayorga, and C.N.Tomes (2006).
Calcium-induced acrosomal exocytosis requires cAMP acting through a protein kinase A-independent, Epac-mediated pathway.
  J Biol Chem, 281, 8656-8666.  
17073662 R.L.Brown, T.Strassmaier, J.D.Brady, and J.W.Karpen (2006).
The pharmacology of cyclic nucleotide-gated channels: emerging from the darkness.
  Curr Pharm Des, 12, 3597-3613.  
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.  
15573383 C.Civera, B.Simon, G.Stier, M.Sattler, and M.J.Macias (2005).
Structure and dynamics of the human pleckstrin DEP domain: distinct molecular features of a novel DEP domain subfamily.
  Proteins, 58, 354-366.
PDB code: 1w4m
16207083 C.Hahnefeld, D.Moll, M.Goette, and F.W.Herberg (2005).
Rearrangements in a hydrophobic core region mediate cAMP action in the regulatory subunit of PKA.
  Biol Chem, 386, 623-631.  
15692043 C.Kim, N.H.Xuong, and S.S.Taylor (2005).
Crystal structure of a complex between the catalytic and regulatory (RIalpha) subunits of PKA.
  Science, 307, 690-696.
PDB codes: 1u7e 3fhi
15644130 D.Bridges, M.E.Fraser, and G.B.Moorhead (2005).
Cyclic nucleotide binding proteins in the Arabidopsis thaliana and Oryza sativa genomes.
  BMC Bioinformatics, 6, 6.  
15618393 H.M.Berman, L.F.Ten Eyck, D.S.Goodsell, N.M.Haste, A.Kornev, and S.S.Taylor (2005).
The cAMP binding domain: an ancient signaling module.
  Proc Natl Acad Sci U S A, 102, 45-50.  
15813735 M.Eiting, G.Hagelüken, W.D.Schubert, and D.W.Heinz (2005).
The mutation G145S in PrfA, a key virulence regulator of Listeria monocytogenes, increases DNA-binding affinity by stabilizing the HTH motif.
  Mol Microbiol, 56, 433-446.
PDB codes: 2beo 2bgc
15591041 M.Gupta, and S.J.Yarwood (2005).
MAP1A light chain 2 interacts with exchange protein activated by cyclic AMP 1 (EPAC1) to enhance Rap1 GTPase activity and cell adhesion.
  J Biol Chem, 280, 8109-8116.  
15210692 A.Y.Wu, X.B.Tang, S.E.Martinez, K.Ikeda, and J.A.Beavo (2004).
Molecular determinants for cyclic nucleotide binding to the regulatory domains of phosphodiesterase 2A.
  J Biol Chem, 279, 37928-37938.  
15550931 B.Ponsioen, J.Zhao, J.Riedl, F.Zwartkruis, G.van der Krogt, M.Zaccolo, W.H.Moolenaar, J.L.Bos, and K.Jalink (2004).
Detecting cAMP-induced Epac activation by fluorescence resonance energy transfer: Epac as a novel cAMP indicator.
  EMBO Rep, 5, 1176-1180.  
14594805 E.C.Young, and N.Krougliak (2004).
Distinct structural determinants of efficacy and sensitivity in the ligand-binding domain of cyclic nucleotide-gated channels.
  J Biol Chem, 279, 3553-3562.  
15550244 G.M.Clayton, W.R.Silverman, L.Heginbotham, and J.H.Morais-Cabral (2004).
Structural basis of ligand activation in a cyclic nucleotide regulated potassium channel.
  Cell, 119, 615-627.
PDB codes: 1u12 1vp6
15221855 G.M.Springett, H.Kawasaki, and D.R.Spriggs (2004).
Non-kinase second-messenger signaling: new pathways with new promise.
  Bioessays, 26, 730-738.  
15274925 J.Wu, S.Brown, N.H.Xuong, and S.S.Taylor (2004).
RIalpha subunit of PKA: a cAMP-free structure reveals a hydrophobic capping mechanism for docking cAMP into site B.
  Structure, 12, 1057-1065.
PDB code: 1rl3
14625280 K.M.Zawadzki, and S.S.Taylor (2004).
cAMP-dependent protein kinase regulatory subunit type IIbeta: active site mutations define an isoform-specific network for allosteric signaling by cAMP.
  J Biol Chem, 279, 7029-7036.  
15545605 L.M.DiPilato, X.Cheng, and J.Zhang (2004).
Fluorescent indicators of cAMP and Epac activation reveal differential dynamics of cAMP signaling within discrete subcellular compartments.
  Proc Natl Acad Sci U S A, 101, 16513-16518.  
14660679 T.Shibasaki, Y.Sunaga, K.Fujimoto, Y.Kashima, and S.Seino (2004).
Interaction of ATP sensor, cAMP sensor, Ca2+ sensor, and voltage-dependent Ca2+ channel in insulin granule exocytosis.
  J Biol Chem, 279, 7956-7961.  
15231839 V.O.Nikolaev, M.Bünemann, L.Hein, A.Hannawacker, and M.J.Lohse (2004).
Novel single chain cAMP sensors for receptor-induced signal propagation.
  J Biol Chem, 279, 37215-37218.  
12819211 A.E.Christensen, F.Selheim, J.de Rooij, S.Dremier, F.Schwede, K.K.Dao, A.Martinez, C.Maenhaut, J.L.Bos, H.G.Genieser, and S.O.Døskeland (2003).
cAMP analog mapping of Epac1 and cAMP kinase. Discriminating analogs demonstrate that Epac and cAMP kinase act synergistically to promote PC-12 cell neurite extension.
  J Biol Chem, 278, 35394-35402.  
12707263 H.Rehmann, A.Rueppel, J.L.Bos, and A.Wittinghofer (2003).
Communication between the regulatory and the catalytic region of the cAMP-responsive guanine nucleotide exchange factor Epac.
  J Biol Chem, 278, 23508-23514.  
12888551 H.Rehmann, F.Schwede, S.O.Døskeland, A.Wittinghofer, and J.L.Bos (2003).
Ligand-mediated activation of the cAMP-responsive guanine nucleotide exchange factor Epac.
  J Biol Chem, 278, 38548-38556.  
12819788 M.Maillet, S.J.Robert, M.Cacquevel, M.Gastineau, D.Vivien, J.Bertoglio, J.L.Zugaza, R.Fischmeister, and F.Lezoualc'h (2003).
Crosstalk between Rap1 and Rac regulates secretion of sAPPalpha.
  Nat Cell Biol, 5, 633-639.  
  12881228 Z.Lu, T.R.Kolodecik, S.Karne, M.Nyce, and F.Gorelick (2003).
Effect of ligands that increase cAMP on caerulein-induced zymogen activation in pancreatic acini.
  Am J Physiol Gastrointest Liver Physiol, 285, G822-G828.  
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.