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(-) Description

Title :  THE STRUCTURE OF THE RACK1 INTERACTION SITES LOCATED WITHIN THE UNIQUE N-TERMINAL REGION OF THE CAMP-SPECIFIC PHOSPHODIESTERASE, PDE4D5.
 
Authors :  G. B. Bolger, K. J. Smith, A. Mccahill, E. I. Hyde, M. R. Steele, M. D. Houslay
Date :  20 Oct 00  (Deposition) - 18 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Hydrolase, Camp-Specific Phosphodiesterase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. J. Smith, G. S. Baillie, E. I. Hyde, X. Li, T. M. Houslay, A. Mccahill, A. J. Dunlop, G. B. Bolger, E. Klussmann, D. R. Adams, M. D. Houslay
1H Nmr Structural And Functional Characterisation Of A Camp-Specific Phosphodiesterase-4D5 (Pde4D5) N-Terminal Region Peptide That Disrupts Pde4D5 Interaction With The Signalling Scaffold Proteins, Beta-Arrestin And Rack1.
Cell. Signal V. 19 2612 2007
PubMed-ID: 17900862  |  Reference-DOI: 10.1016/J.CELLSIG.2007.08.015

(-) Compounds

Molecule 1 - CAMP SPECIFIC PHOSPHODIESTERASE PDE4D5
    ChainsA
    EC Number3.1.4.17
    FragmentRACK1 INTERACTION SITE WITHIN UNIQUE N-TERMINAL REGION (RESIDUES 12-49)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1E9K)

(-) Sites  (0, 0)

(no "Site" information available for 1E9K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E9K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E9K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E9K)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDEASE_IPS00126 3'5'-cyclic nucleotide phosphodiesterases signature.PDE4D_HUMAN502-513  1A:4-11

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.13aENST0000034063513aENSE00001559328chr5:59189625-59188995631PDE4D_HUMAN1-1521520--
1.21bENST0000034063521bENSE00001136096chr5:58511794-58511603192PDE4D_HUMAN152-216650--
1.22ENST0000034063522ENSE00001682119chr5:58489362-5848932637PDE4D_HUMAN216-228130--
1.23ENST0000034063523ENSE00001754547chr5:58481088-5848101574PDE4D_HUMAN229-253250--
1.24ENST0000034063524ENSE00001719283chr5:58476470-5847642150PDE4D_HUMAN253-270180--
1.31dENST0000034063531dENSE00001750566chr5:58334798-58334686113PDE4D_HUMAN270-307380--
1.33bENST0000034063533bENSE00000914184chr5:58289292-5828919994PDE4D_HUMAN308-339320--
1.34ENST0000034063534ENSE00001136103chr5:58287831-58287659173PDE4D_HUMAN339-396580--
1.35ENST0000034063535ENSE00001001090chr5:58286729-5828663199PDE4D_HUMAN397-429330--
1.36ENST0000034063536ENSE00001001087chr5:58285746-58285582165PDE4D_HUMAN430-484550--
1.37ENST0000034063537ENSE00001001091chr5:58284419-58284320100PDE4D_HUMAN485-518341A:1-15 (gaps)18
1.38ENST0000034063538ENSE00001175221chr5:58273172-58273018155PDE4D_HUMAN518-569521A:15-38 (gaps)44
1.39ENST0000034063539ENSE00001001088chr5:58272299-58272177123PDE4D_HUMAN570-610410--
1.40ENST0000034063540ENSE00001698537chr5:58271666-58271484183PDE4D_HUMAN611-671610--
1.41jENST0000034063541jENSE00001989721chr5:58270907-582648656043PDE4D_HUMAN672-8091380--

(-) Sequences/Alignments

NMR Structure
   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:38
 aligned with PDE4D_HUMAN | Q08499 from UniProtKB/Swiss-Prot  Length:809

    Alignment length:61
                                   510       520       530       540       550       560 
          PDE4D_HUMAN   501 IHDVDHPGVSNQFLINTNSELALMYNDSSVLENHHLAVGFKLLQEENCDIFQNLTKKQRQS 561
               SCOP domains d1e9ka_ A:                                                    SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhh---hhhhh......-------------..hhhh-------hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -PDEASE_I    ------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.37         ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.38  PDB: A:15-38 (gaps) [INCOMPLETE]  Transcript 1 (2)
                 1e9k A   1 VPEVDNPHCPNPWL---NEDLVKSLREN-------------LLQHEK-------SKTARKS  38
                                    10   |   |17       | -         - |    |  -    |   37 
                                        14  15        25            26   31      32      

   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  (1, 1)

NMR Structure
(-)
Class: Peptides (792)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1E9K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E9K)

(-) Gene Ontology  (52, 52)

NMR Structure(hide GO term definitions)
Chain A   (PDE4D_HUMAN | Q08499)
molecular function
    GO:0004115    3',5'-cyclic-AMP phosphodiesterase activity    Catalysis of the reaction: adenosine 3',5'-cyclic phosphate + H2O = adenosine 5'-phosphate.
    GO:0004114    3',5'-cyclic-nucleotide phosphodiesterase activity    Catalysis of the reaction: nucleoside 3',5'-cyclic phosphate + H2O = nucleoside 5'-phosphate.
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0031698    beta-2 adrenergic receptor binding    Interacting selectively and non-covalently with a beta-2 adrenergic receptor.
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0044325    ion channel binding    Interacting selectively and non-covalently with one or more specific sites on an ion channel, a protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective ion transport down its electrochemical gradient.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008081    phosphoric diester hydrolase activity    Catalysis of the hydrolysis of a phosphodiester to give a phosphomonoester and a free hydroxyl group.
    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).
    GO:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0071875    adrenergic receptor signaling pathway    A series of molecular signals generated as a consequence of an adrenergic receptor binding to one of its physiological ligands.
    GO:0086024    adrenergic receptor signaling pathway involved in positive regulation of heart rate    An adrenergic receptor signaling pathway that contributes to an increase in frequency or rate of heart contraction. Binding of adrenalin or noradrenalin to a beta-adrenergic receptor on the surface of the signal-receiving cell results in the activation of an intracellular Gs protein. Gs activates adenylate cyclase to increase intracellular cyclic-AMP (cAMP) levels. cAMP binds directly to F-channels to allow an inward flow of sodium (known as funny current, or If current). The funny current is responsible for membrane depolarization and an increase in heart rate.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0006198    cAMP catabolic process    The chemical reactions and pathways resulting in the breakdown of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    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:0071320    cellular response to cAMP    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate) stimulus.
    GO:0071872    cellular response to epinephrine stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epinephrine stimulus. Epinephrine is a catecholamine that has the formula C9H13NO3; it is secreted by the adrenal medulla to act as a hormone, and released by certain neurons to act as a neurotransmitter active in the central nervous system.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0061028    establishment of endothelial barrier    The establishment of a barrier between endothelial cell layers, such as those in the brain, lung or intestine, to exert specific and selective control over the passage of water and solutes, thus allowing formation and maintenance of compartments that differ in fluid and solute composition.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0045822    negative regulation of heart contraction    Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction.
    GO:0033137    negative regulation of peptidyl-serine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:1901898    negative regulation of relaxation of cardiac muscle    Any process that stops, prevents or reduces the frequency, rate or extent of relaxation of cardiac muscle.
    GO:0030593    neutrophil chemotaxis    The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
    GO:0032729    positive regulation of interferon-gamma production    Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0032743    positive regulation of interleukin-2 production    Any process that activates or increases the frequency, rate, or extent of interleukin-2 production.
    GO:0032754    positive regulation of interleukin-5 production    Any process that activates or increases the frequency, rate, or extent of interleukin-5 production.
    GO:0030814    regulation of cAMP metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    GO:0086004    regulation of cardiac muscle cell contraction    Any process that modulates the frequency, rate or extent of cardiac muscle cell contraction.
    GO:1901844    regulation of cell communication by electrical coupling involved in cardiac conduction    Any process that modulates the frequency, rate or extent of cell communication by electrical coupling involved in cardiac conduction.
    GO:0002027    regulation of heart rate    Any process that modulates the frequency or rate of heart contraction.
    GO:0010469    regulation of receptor activity    Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0010880    regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum    Any process that modulates the rate, frequency or extent of release of sequestered calcium ion into cytosol by the sarcoplasmic reticulum, the process in which the release of sequestered calcium ion by sarcoplasmic reticulum into cytosol occurs via calcium release channels.
    GO:0060314    regulation of ryanodine-sensitive calcium-release channel activity    Any process that modulates the activity of a ryanodine-sensitive calcium-release channel. The ryanodine-sensitive calcium-release channel catalyzes the transmembrane transfer of a calcium ion by a channel that opens when a ryanodine class ligand has been bound by the channel complex or one of its constituent parts.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0006939    smooth muscle contraction    A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0034704    calcium channel complex    An ion channel complex through which calcium ions pass.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0005891    voltage-gated calcium channel complex    A protein complex that forms a transmembrane channel through which calcium ions may pass in response to changes in membrane potential.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDE4D_HUMAN | Q084991mkd 1oyn 1ptw 1q9m 1tb7 1tbb 1xom 1xon 1xoq 1xor 1y2b 1y2c 1y2d 1y2e 1y2k 1zkn 2fm0 2fm5 2pw3 2qyn 3g4g 3g4i 3g4k 3g4l 3g58 3iad 3iak 3k4s 3sl3 3sl4 3sl5 3sl6 3sl8 3v9b 4ogb 4w1o 4wcu 5k1i 5k32 5tkb 5wqa

(-) Related Entries Specified in the PDB File

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