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Molecule Parameter List for 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
GEF* participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1010110

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • MAPK-bistability
    -fig1c
  • 35Network
    Shared_Object_MAPK-bistability-fig1c Sos PKC 
    MAPK PLA2 Ras 
    PDGFR 
    Model for figure 1c in Bhalla US et al. Science (2002) 297(5583):1018-23.
    The demo for this figure is available here. This synaptic signaling model is without the MKP-1 feedback, so it is bistable and remains so over long periods.

    GEF* acting as a Molecule in  
    MAPK-bistability-fig1c Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    GEF*
  • MAPK-bistability
    -fig1c

    Accession No. : 35
  • Ras
    Pathway No. : 184
    01000No
    Phosphorylated and thereby activated form of GEF. See, e.g. Orita et al JBC 268:34 25542-25546 1993, Gulbins et al. It is not clear whether there is major specificity for tyr or ser/thr.

    GEF* acting as an Enzyme in  
    MAPK-bistability-fig1c Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    GEF* /
    GEF*-act-ras
  • MAPK-bistability
    -fig1c

    Accession No. : 35
  • Ras
    Pathway No. : 184
    0.5050510.024explicit E-S complexSubstrate
    GDP-Ras

    Product
    GTP-Ras
    Kinetics from Orita et al JBC 268(34):25542-25546. Note that the Vmax is slow, but it does match the slow GTP hydrolysis rates.

    GEF* acting as a Product of an Enzyme in  
    MAPK-bistability-fig1c Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    PKC-active  /
    PKC-act-GEF
  • MAPK-bistability
    -fig1c

    Accession No. : 35
  • Shared_Object_
    MAPK-bistability
    -fig1c

    Pathway No. : 179
  • 66.666744explicit E-S complexSubstrate
    inact-GEF

    Product
    GEF*
    Rate constants are generic PKC rates. See Chen et al 1993 Biochem 32:1032 This reaction activates GEF. Gives >= 2X stim of ras, and a 2X stim of MAPK over amount from direct phosph of c-raf. Note that it is a push-pull reaction, and also get effect through phosph and inact of GAPs.

    GEF* acting as a Substrate in a reaction in  
    MAPK-bistability-fig1c 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
    dephosph-GEF
  • MAPK-bistability
    -fig1c

    Accession No. : 35
  • Ras
    Pathway No. : 184
    0.1
    (s^-1)
    0
    (s^-1)
    --Substrate
    GEF*

    Product
    inact-GEF
    This rate is based on the known ratio of GDP-Ras to GTP-Ras. Basal: Ras.GTP = 7% Stimulated 15% Time course is within 10 min, probably much faster as not all early data points are there. See Gibbs et al JBC 265(33):20437-20422



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