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PDBsum entry 3cf6
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protein ligands Protein-protein interface(s) links
Signaling protein/gtp-binding protein PDB id
3cf6

 

 

 

 

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Contents
Protein chains
627 a.a. *
150 a.a. *
Ligands
SP1 ×2
SO4
Waters ×274
* Residue conservation analysis
PDB id:
3cf6
Name: Signaling protein/gtp-binding protein
Title: Structure of epac2 in complex with cyclic-amp and rap
Structure: Rap guanine nucleotide exchange factor (gef) 4. Chain: e. Fragment: unp residues 306-993. Engineered: yes. Ras-related protein rap-1b. Chain: r. Fragment: unp residues 1-167. Synonym: gtp-binding protein smg p21b, rap1b. Engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Gene: rapgef4. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: gst fusion. Homo sapiens. Human.
Resolution:
2.20Å     R-factor:   0.244     R-free:   0.265
Authors: H.Rehmann,E.Arias-Palomo,M.A.Hadders,F.Schwede,O.Llorca,J.L.Bos
Key ref:
H.Rehmann et al. (2008). Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B. Nature, 455, 124-127. PubMed id: 18660803 DOI: 10.1038/nature07187
Date:
02-Mar-08     Release date:   29-Jul-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc:  
Struc: 627 a.a.
Protein chain
Pfam   ArchSchema ?
P61224  (RAP1B_HUMAN) -  Ras-related protein Rap-1b from Homo sapiens
Seq:
Struc: 		184 a.a.
150 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain R: E.C.3.6.5.2  - small monomeric GTPase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: GTP + H2O = GDP + phosphate + H+
GTP
 + H2O
 =
GDP
Bound ligand (Het Group name = SP1)
matches with 72.41% similarity 		+ phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1038/nature07187 Nature 455:124-127 (2008)
PubMed id: 18660803  
 
 
Structure of Epac2 in complex with a cyclic AMP analogue and RAP1B.
H.Rehmann, E.Arias-Palomo, M.A.Hadders, F.Schwede, O.Llorca, J.L.Bos.
 
  ABSTRACT  
 
Epac proteins are activated by binding of the second messenger cAMP and then act as guanine nucleotide exchange factors for Rap proteins. The Epac proteins are involved in the regulation of cell adhesion and insulin secretion. Here we have determined the structure of Epac2 in complex with a cAMP analogue (Sp-cAMPS) and RAP1B by X-ray crystallography and single particle electron microscopy. The structure represents the cAMP activated state of the Epac2 protein with the RAP1B protein trapped in the course of the exchange reaction. Comparison with the inactive conformation reveals that cAMP binding causes conformational changes that allow the cyclic nucleotide binding domain to swing from a position blocking the Rap binding site towards a docking site at the Ras exchange motif domain.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Active Epac 2. a, Domain organization of Epac2. Residues that were subjected to mutational analysis are indicated. The same colour code is used throughout the figures. Hinge (residues 432–445, dark green); helical hairpin (residues 906 to 946, dark blue). CDC25-HD, CDC25 homology domain; CNB, cyclic nucleotide binding domain; DEP, Dishevelled, Egl-10, Pleckstrin domain; RA, Ras-association domain; REM, Ras-exchange motif. b, Left, inactive Epac2 (first CNB and DEP domain omitted); right, active Epac2 305 Sp-cAMPS RAP1B. RAP1B is shown orange; Sp-cAMPS and SO[4]^2- are shown in ball and stick representation. Arrow, movement of the second CNB domain; straight lines, missing connectivity; dotted lines, ionic latch (IL); asterisks, interface between the REM and the CNB domain; HP, helical hairpin; PBC, phosphate binding cassette. c, RAP1B placed into the inactive structure. d, The crystal structure of Epac2 305 Sp-cAMPS RAP1B was fitted into the EM density reconstruction (grey grid) of full length Epac2 cAMP RAP1B. Yellow surface, difference density. 		Figure 2.
Figure 2: Sp-cAMPS induced conformational changes. a, Superposition of the active and inactive second CNB domain. The arrows indicate the movement of the hinge and the lid region. Light green, active conformation; dark green, inactive conformation; grey, no difference in conformation. b, Interactions of Sp-cAMPS with the CNB domain and the REM domain. Hydrogen bonds are shown by dotted lines; w, water. c, Interaction of Lys 405 with the hinge-lid region.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 455, 124-127) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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
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.  
20624123 M.Noda, C.Takahashi, T.Matsuzaki, and H.Kitayama (2010).
What we learn from transformation suppressor genes: lessons from RECK.
  Future Oncol, 6, 1105-1116.  
19615876 B.Boettner, and L.Van Aelst (2009).
Control of cell adhesion dynamics by Rap1 signaling.
  Curr Opin Cell Biol, 21, 684-693.  
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.  
19645719 E.Yaman, R.Gasper, C.Koerner, A.Wittinghofer, and U.H.Tazebay (2009).
RasGEF1A and RasGEF1B are guanine nucleotide exchange factors that discriminate between Rap GTP-binding proteins and mediate Rap2-specific nucleotide exchange.
  FEBS J, 276, 4607-4616.  
19091745 J.H.Raaijmakers, and J.L.Bos (2009).
Specificity in ras and rap signaling.
  J Biol Chem, 284, 10995-10999.  
19546222 M.T.Branham, M.A.Bustos, G.A.De Blas, H.Rehmann, V.E.Zarelli, C.L.Treviño, A.Darszon, L.S.Mayorga, and C.N.Tomes (2009).
Epac activates the small G proteins Rap1 and Rab3A to achieve exocytosis.
  J Biol Chem, 284, 24825-24839.  
19617623 P.Wang, Q.Wang, J.Sun, J.Wu, H.Li, N.Zhang, Y.Huang, B.Su, R.K.Li, L.Liu, Y.Zhang, H.P.Elsholtz, J.Hu, H.Y.Gaisano, and T.Jin (2009).
POU homeodomain protein Oct-1 functions as a sensor for cyclic AMP.
  J Biol Chem, 284, 26456-26465.  
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.  
19564687 S.H.Scheres, and J.M.Carazo (2009).
Introducing robustness to maximum-likelihood refinement of electron-microsopy data.
  Acta Crystallogr D Biol Crystallogr, 65, 672-678.  
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.  
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.  
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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