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Molecule Parameter List for PKA-active

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
PKA-active participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1030012

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Ajay_Bhalla_
    2004_PKM_Tuning
  • 76Network
    PKC Shared_Object_Ajay_Bhalla_2004_PKM_tuning PLA2 
    PLCbeta Gq MAPK 
    Ras EGFR Sos 
    PLC_g CaMKII CaM 
    PP1 PP2B PKA 
    AC PKM 
    This model is taken from the Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the reference feedforward model from Figure 8a.

    PKA-active acting as a Molecule in  
    Ajay_Bhalla_2004_PKM_Tuning Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    PKA-active
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_tuning

    Pathway No. : 312
  • 01.5No

    PKA-active acting as an Enzyme in  
    Ajay_Bhalla_2004_PKM_Tuning Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1PKA-active /
    PKA-phosph-GEF
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_tuning

    Pathway No. : 312
  • 7.4999694explicit E-S complexSubstrate
    inact-GEF

    Product
    inact-GEF*
        This pathway inhibits Ras when cAMP is elevated. See: Hordijk et al JBC 269:5 3534-3538 1994 Burgering et al EMBO J 12:11 4211-4220 1993 The rates are the same as used in PKA-phosph-I1
    2PKA-active /
    PKA-phosph-I1
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_tuning

    Pathway No. : 312
  • 7.4999694explicit E-S complexSubstrate
    I1

    Product
    I1*
        #s from Bramson et al CRC crit rev Biochem 15:2 93-124. They have a huge list of peptide substrates and I have chosen high-ish rates. These consts give too much PKA activity, so lower Vmax 1/3. Now, k1 = 3e-5, k2 = 36, k3 = 9 (still pretty fast). Also lower Km 1/3 so k1 = 1e-5 Cohen et al FEBS Lett 76:182-86 1977 say rate =30% PKA act on phosphokinase beta.
    3PKA-active /
    phosph-PDE
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_tuning

    Pathway No. : 312
  • 7.4999694explicit E-S complexSubstrate
    cAMP-PDE

    Product
    cAMP-PDE*
        Same rates as PKA-phosph-I1

    PKA-active acting as a Substrate in a reaction in  
    Ajay_Bhalla_2004_PKM_Tuning 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
    inhib-PKA
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PKA
    Pathway No. : 326
    60.0003
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.0167(uM)-Substrate
    PKA-active
    PKA-inhibitor

    Product
    inhibited-PKA
    This has to be set to zero for matching the expts in vitro. In vivo we need to consider the inhibition though. kf = 1e-5 kb = 1

    PKA-active acting as a Product in a reaction in  
    Ajay_Bhalla_2004_PKM_Tuning 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
    1Release-C1
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PKA
    Pathway No. : 326
    60
    (s^-1)
    18
    (uM^-1 s^-1)
    Kd(cb) = 0.3(uM)-Substrate
    R2C2-cAMP4

    Product
    PKA-active
    R2C-cAMP4
      This has to be fast, as the activation of PKA by cAMP is also fast. kf was 10
    2Release-C2
  • Ajay_Bhalla_
    2004_PKM_Tuning

    Accession No. : 76
  • PKA
    Pathway No. : 326
    60
    (s^-1)
    18
    (uM^-1 s^-1)
    Kd(cb) = 0.3(uM)-Substrate
    R2C-cAMP4

    Product
    PKA-active
    R2-cAMP4



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