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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REGULATORY DOMAIN OF EPAC2
 
Authors :  H. Rehmann, B. Prakash, E. Wolf, A. Rueppel, J. De Rooij, J. L. Bos, A. Wittinghofer
Date :  04 Nov 02  (Deposition) - 11 Nov 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Epac2, Camp-Gef2, Camp, Campb Binding Doamin, Gef, Exchange Factor, Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Rehmann, B. Prakash, E. Wolf, A. Rueppel, J. De Rooij, J. L. Bos, A. Wittinghofer
Structure And Regulation Of The Camp-Binding Domains Of Epac2
Nat. Struct. Biol. V. 10 26 2002
PubMed-ID: 12469113  |  Reference-DOI: 10.1038/NSB878

(-) Compounds

Molecule 1 - CAMP-DEPENDENT RAP1 GUANINE-NUCLEOTIDE EXCHANGE FACTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T2
    Expression System Taxid: 562
    Fragment: CNMP-BINDING DOMAIN, DISHEVELLED-EGL-PLECKSTRIN (DEP), CNMB-BINDING DOMAIN, RESIDUES 1-463
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1O7F)

(-) Sites  (0, 0)

(no "Site" information available for 1O7F)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O7F)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:160 -Pro A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O7F)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.RPGF4_MOUSE43-146
356-457		  2A:43-146
A:338-439
2DEPPS50186 DEP domain profile.RPGF4_MOUSE216-291  1A:198-273

(-) Exons   (0, 0)

(no "Exon" information available for 1O7F)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:421
 aligned with RPGF4_MOUSE | Q9EQZ6 from UniProtKB/Swiss-Prot  Length:1011

    Alignment length:451
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462 
          RPGF4_MOUSE    13 AEWIACLDKRPLERSSEDVDIIFTRLKGVKAFEKFHPNLLRQICLCGYYENLEKGITLFRQGDIGTNWYAVLAGSLDVKVSETSSHQDAVTICTLGIGTAFGESILDNTPRHATIVTRESSELLRIEQEDFKALWEKYRQYMAGLLAPPYGVMETGSNNDRIPDKENTPLIEPHVPLRPAHTITKVPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDKYLFYRFLDDEREDAPLPTEEEKKECDEELQDTMLLLSQMGPDAHMRMILRKPPGQRTVDDLEIIYDELLHIKALSHLSTTVKRELAGVLIFESHAKGGTVLFNQGEEGTSWYIILKGSVNVVIYGKGVVCTLHEGDDFGKLALVNDAPRAASIVLREDNCHFLRVDKEDFNRILRDVEAN 463
               SCOP domains d1o7fa2 A:13-167 Regulatory domain of Epac2, domains 1 and 3                                                                                               ------------------------------d1o7fa1 A:180-321 Regulatory domain of epac2, domain 2                                                                                        d1o7fa3 A:322-445 Regulatory domain of Epac2, domains 1 and 3                                                                SCOP domains
               CATH domains 1o7fA01 A:13-167 Jelly Rolls                                                                                                                               -------------------------------1o7fA02 A:181-336 'winged helix' repressor DNA binding domain                                                                                               1o7fA03 A:337-445 Jelly Rolls                                                                                 CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DEP-1o7fA01 A:201-271                                                  -------------------------------------------------------------------------------------cNMP_binding-1o7fA02 A:357-443                                                         -- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------cNMP_binding-1o7fA03 A:357-443                                                         -- Pfam domains (2)
         Sec.struct. author hhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhheeeee....eee.......eeeeeee..eeeee....hhhhheeeeee....eehhhhhhh.....eeee...eeeeeeehhhhhhhhhhhhhhh.............------------------------------...hhhhhhhhhhhhhhhhhhhhhheeee....eeeeeeehhhhhhhhhhh.....hhhhhhhhhhhhhhh..eee............eeee.hhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhheeeee.....eee.......eeeeeee.eeeeee...eeeeeee...ee.hhhhh.......eeee....eeeeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------CNMP_BINDING_3  PDB: A:43-146 UniProt: 43-146                                                           ---------------------------------------------------------------------DEP  PDB: A:198-273 UniProt: 216-291                                        ----------------------------------------------------------------CNMP_BINDING_3  PDB: A:338-439 UniProt: 356-457                                                       ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o7f A  13 AEWIACLDKRPLERSSEDVDIIFTRLKGVKAFEKFHPNLLRQICLCGYYENLEKGITLFRQGDIGTNWYAVLAGSLDVKVSETSSHQDAVTICTLGIGTAFGESILDNTPRHATIVTRESSELLRIEQEDFKALWEKYRQYMAGLLAPPYGVMET------------------------------VPSEKILRAGKILRIAILSRAPHMIRDRKYHLKTYRQCCVGTELVDWMIQQTSCVHSRTQAVGMWQVLLEDGVLNHVDQERHFQDKYLFYRFLDDEREDAPLPTEEEKKECDEELQDTMLLLSQMGPDAHMRMILRKPPGQRTVDDLEIIYDELLHIKALSHLSTTVKRELAGVLIFESHAKGGTVLFNQGEEGTSWYIILKGSVNVVIYGKGVVCTLHEGDDFGKLALVNDAPRAASIVLREDNCHFLRVDKEDFNRILRDVEAN 445
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162    |    -         -         -     | 184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444 
                                                                                                                                                                                    167                            180
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: DEP] (7)
(-)
Clan: no clan defined [family: cNMP_binding] (41)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RPGF4_MOUSE | Q9EQZ6)
molecular function
    GO:0017016    Ras GTPase binding    Interacting selectively and non-covalently with any member of the Ras superfamily of monomeric GTPases.
    GO:0005088    Ras guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0005085    guanyl-nucleotide exchange factor activity    Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0019933    cAMP-mediated signaling    Any intracellular signal transduction in which the signal is passed on within the cell via cyclic AMP (cAMP). Includes production of cAMP, and downstream effectors that further transmit the signal within the cell.
    GO:0017156    calcium ion regulated exocytosis    The release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle by fusion of the vesicle with the plasma membrane of a cell, induced by a rise in cytosolic calcium-ion levels.
    GO:0006887    exocytosis    A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell.
    GO:0030073    insulin secretion    The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0043547    positive regulation of GTPase activity    Any process that activates or increases the activity of a GTPase.
    GO:0017157    regulation of exocytosis    Any process that modulates the frequency, rate or extent of exocytosis.
    GO:0007264    small GTPase mediated signal transduction    Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RPGF4_MOUSE | Q9EQZ6: 2byv 3cf6 4f7z 4mgi 4mgk 4mgy 4mgz 4mh0

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