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Molecule Parameter List for cAMP

The statistics table lists the distribution of a molecule acting either as a substrate, product, enzyme or as a molecule within the network.
The text color of a molecule is highlighted by color.
Statistics
cAMP participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1004250

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • AMPAR_traff_
    model0
  • 59Network
    Shared_Object_AMPAR_traff_model0 CaMKII CaM 
    PP1 PP2B PP1_PSD 
    PKA AC AMPAR 
    AMPAR_memb 
    This is model 0 from Hayer and Bhalla, PLoS Comput Biol 2005. It has a bistable model of AMPAR traffick, plus a non-bistable model of CaMKII. This differs from the reference model (model 1) in that model0 lacks degradation and turno ver reactions for AMPAR.

    cAMP acting as a Molecule in  
    AMPAR_traff_model0 Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    cAMP
  • AMPAR_traff_
    model0

    Accession No. : 59
  • AC
    Pathway No. : 241
    00.09No
    The conc of this has been a problem. Schaecter and Benowitz use 50 uM, but Shinomura et al have < 5. So I have altered the cAMP-dependent rates in the PKA model to reflect this.

    cAMP acting as a Substrate for an Enzyme in  
    AMPAR_traff_model0 Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1cAMP-PDE  /
    PDE
  • AMPAR_traff_
    model0

    Accession No. : 59
  • AC
    Pathway No. : 241
    19.8411104explicit E-S complexSubstrate
    cAMP

    Product
    AMP
        Best rates are from Conti et al Biochem 34 7979-7987 1995. Though these are for the Sertoli cell form, it looks like they carry nicely into alternatively spliced brain form. See Sette et al JBC 269:28 18271-18274 Km ~2 uM, Vmax est ~ 10 umol/min/mg for pure form. Brain protein is 93 kD but this was 67. So k3 ~10, k2 ~40, k1 ~4.2e-6
    2cAMP-PDE*  /
    PDE*
  • AMPAR_traff_
    model0

    Accession No. : 59
  • AC
    Pathway No. : 241
    19.8413204explicit E-S complexSubstrate
    cAMP

    Product
    AMP
        This form has about twice the activity of the unphosphorylated form. See Sette et al JBC 269:28 18271-18274 1994. We'll ignore cGMP effects for now.
    3PDE1  /
    PDE1
  • AMPAR_traff_
    model0

    Accession No. : 59
  • AC
    Pathway No. : 241
    39.69991.6674.0012explicit E-S complexSubstrate
    cAMP

    Product
    AMP
        Rate is 1/6 of the CaM stim form. We'll just reduce all lf k1, k2, k3 so that the Vmax goes down 1/6.
    4CaM.PDE1  /
    CaM.PDE1
  • AMPAR_traff_
    model0

    Accession No. : 59
  • AC
    Pathway No. : 241
    39.6831104explicit E-S complexSubstrate
    cAMP

    Product
    AMP
        Max activity ~10umol/min/mg in presence of lots of CaM. Affinity is low, 40 uM. k3 = 10, k2 = 40, k1 = (50/40) / 6e5.

    cAMP acting as a Product of an Enzyme in  
    AMPAR_traff_model0 Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1AC1-CaM  /
    kenz
  • AMPAR_traff_
    model0

    Accession No. : 59
  • AC
    Pathway No. : 241
    299.9984.54Classical Michaelis-Menten
    V = Etot.S.Kcat/Km+S
    Substrate
    ATP

    Product
    cAMP
        17 Feb 2005 Halved Vmax as the amount of enzyme has been doubled to get an integer value in the spine. 18 Feb 2005. Updated Km from BRENDA: EC No 4.6.1.1 Rat Km: 0.95 mM Turnover 12/sec. Human Km: 0.3 mM 12 umol/min/mg for mammalia, turnover is 12/sec See PMID 8663304 by Dessauer and Gilman JBC 271 1996 Unfortunately turnover range is from 34 down to 0.1 in different studies, according to BRENDA.
    2AC2*  /
    kenz
  • AMPAR_traff_
    model0

    Accession No. : 59
  • AC
    Pathway No. : 241
    300.00224Classical Michaelis-Menten
    V = Etot.S.Kcat/Km+S
    Substrate
    ATP

    Product
    cAMP
        Reduced Km to match expt data for basal activation of AC2 by PKC. Now k1 = 2.9e-6, k2 = 72, k3 = 18 18 Feb: Raised Km to 300 based on BRENDA data. Unlikely to make much difference, given the vast amount of ATP.

    cAMP acting as a Substrate in a reaction in  
    AMPAR_traff_model0 Network
    Kd is calculated only for second order reactions, like nA+nB <->nC or nA<->nC+nD, where n is number and A,B,C,D are molecules, where as for first order reactions Keq is calculated. Kd for higher order reaction are not consider.
     NameAccession NamePathway NameKfKbKdtauReagents
    1
  • cAMP-bind-site-B
    1
  • AMPAR_traff_
    model0

    Accession No. : 59
  • PKA
    Pathway No. : 240
    54
    (uM^-1 s^-1)
    33
    (s^-1)
    Kd(bf) = 0.6111(uM)-Substrate
    R2C2
    cAMP

    Product
    R2C2-cAMP
      Hasler et al FASEB J 6:2734-2741 1992 say Kd =1e-7M for type II, 5.6e-8 M for type I. Take mean which comes to 2e-13 #/cell Smith et al PNAS USA 78:3 1591-1595 1981 have better data. First kf/kb=2.1e7/M = 3.5e-5 (#/cell). Ogreid and Doskeland Febs Lett 129:2 287-292 1981 have figs suggesting time course of complete assoc is < 1 min.
    2
  • cAMP-bind-site-B
    2
  • AMPAR_traff_
    model0

    Accession No. : 59
  • PKA
    Pathway No. : 240
    54
    (uM^-1 s^-1)
    33
    (s^-1)
    Kd(bf) = 0.6111(uM)-Substrate
    R2C2-cAMP
    cAMP

    Product
    R2C2-cAMP2
      For now let us set this to the same Km (1e-7M) as site B. This gives kf/kb = .7e-7M * 1e6 / (6e5^2) : 1/(6e5^2) = 2e-13:2.77e-12 Smith et al have better values. They say that this is cooperative, so the consts are now kf/kb =8.3e-4
    3
  • cAMP-bind-site-A
    1
  • AMPAR_traff_
    model0

    Accession No. : 59
  • PKA
    Pathway No. : 240
    75.0006
    (uM^-1 s^-1)
    110
    (s^-1)
    Kd(bf) = 1.4667(uM)-Substrate
    R2C2-cAMP2
    cAMP

    Product
    R2C2-cAMP3
    4
  • cAMP-bind-site-A
    2
  • AMPAR_traff_
    model0

    Accession No. : 59
  • PKA
    Pathway No. : 240
    75.0006
    (uM^-1 s^-1)
    32.5
    (s^-1)
    Kd(bf) = 0.4333(uM)-Substrate
    R2C2-cAMP3
    cAMP

    Product
    R2C2-cAMP4
    5cAMP_diffusion
  • AMPAR_traff_
    model0

    Accession No. : 59
  • AC
    Pathway No. : 241
    300
    (s^-1)
    5.4
    (s^-1)
    Not applicable**-Substrate
    cAMP

    Product
    cAMP_in_dend
      Represents diffusion, from a volume of 9e-20 to 5e-18. Assuming neck dimensions of 0.1 x 0.1 microns, this works out to a diffusion const of about 270 um^2/sec, which is pretty conservative. It is what cAMP does in frog cilia.
    ** This is a trasport reation between compartments of different volumes. Therefore Kd is not applicable. Please Note Kf, Kb units are in number of molecules instead of concentration



    Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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