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Molecule Parameter List for inact-GEF

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
inact-GEF participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1002022

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning
  • 77Network
    Shared_Object_Ajay_Bhalla_2004_PKM_MKP3_Tuning PKC PLA2 
    PLCbeta Ras Gq 
    MAPK EGFR Sos 
    PLC_g CaMKII CaM 
    PP1 PP2B PKA 
    AC MKP3 PKM 
    This model is based on Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the feedforward model with MPK3 from figure 8a.

    inact-GEF acting as a Molecule in  
    Ajay_Bhalla_2004_PKM_MKP3_Tuning Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    inact-GEF
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Ras
    Pathway No. : 333
    0.11.5No
    Assume that SoS is present only at 50 nM. Revised to 100 nM to get equil to experimentally known levels.

    inact-GEF acting as a Substrate for an Enzyme in  
    Ajay_Bhalla_2004_PKM_MKP3_Tuning Network
     Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    1PKA-active  /
    PKA-phosph-GEF
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Pathway No. : 329
  • 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
    2PKC-active  /
    PKC-act-GEF
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Shared_Object_
    Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Pathway No. : 329
  • 3.3333244explicit E-S complexSubstrate
    inact-GEF

    Product
    GEF*
        Rate consts from PKC-act-raf. This reaction activates GEF. It can lead to at least 2X stim of ras, and a 2X stim of MAPK over and above that obtained via direct phosph of c-raf. Note that it is a push-pull reaction, and there is also a contribution through the phosphorylation and inactivation of GAPs. The original PKC-act-raf rate consts are too fast. We lower K1 by 10 X

    inact-GEF acting as a Substrate in a reaction in  
    Ajay_Bhalla_2004_PKM_MKP3_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
    1bg-act-GEF
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Ras
    Pathway No. : 333
    6
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.1667(uM)-Substrate
    BetaGamma
    inact-GEF

    Product
    GEF-Gprot-bg
      SoS/GEF is present at 50 nM ie 3e4/cell. BetaGamma maxes out at 9e4. Assume we have 1/3 of the GEF active when the BetaGamma is 1.5e4. so 1e4 * kb = 2e4 * 1.5e4 * kf, so kf/kb = 3e-5. The rate of this equil should be reasonably fast, say 1/sec
    2CaM-bind-GEF
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Ras
    Pathway No. : 333
    199.998
    (uM^-1 s^-1)
    1
    (s^-1)
    Kd(bf) = 0.005(uM)-Substrate
    CaM-Ca4
    inact-GEF

    Product
    CaM-GEF
      We have no numbers for this. It is probably between the two extremes represented by the CaMKII phosph states, and I have used guesses based on this. kf=1e-4 kb=1 The reaction is based on Farnsworth et al Nature 376 524-527 1995 2 Aug 2004 Raised Kf from 60 to 200 to achieve higher MAPK activation following Ca stimulus for PKM models. 3 Aug 2004. Lowered Kf to 100.

    inact-GEF acting as a Product in a reaction in  
    Ajay_Bhalla_2004_PKM_MKP3_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
    1dephosph-GEF
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Ras
    Pathway No. : 333
    1
    (s^-1)
    0
    (s^-1)
    --Substrate
    GEF*

    Product
    inact-GEF
    2
  • dephosph-inact-G
    EF*
  • Ajay_Bhalla_
    2004_PKM_MKP3_
    Tuning

    Accession No. : 77
  • Ras
    Pathway No. : 333
    1
    (s^-1)
    0
    (s^-1)
    --Substrate
    inact-GEF*

    Product
    inact-GEF



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