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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
3d_fold_model8Network
Shared_Object_3d_fold_model PKC MAPK 
PLA2 Ras 
This model is an annotated version of the synaptic signaling network.
The primary reference is Bhalla US and Iyengar R. Science (1999) 283(5400):381-7 but several of the model pathways have been updated Bhalla US, Ram PT, Iyengar R. Science. 2002 Aug 9;297(5583):1018-23.

GEF* acting as a Molecule in  
3d_fold_model Network
NameAccession NamePathway NameInitial Conc.
(uM)
Volume
(fL)
Buffered
GEF*3d_fold_model
Accession No. : 8
Ras
Pathway No. : 58
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  
3d_fold_model Network
Enzyme Molecule /
Enzyme Activity
Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
GEF* /
GEF*-act-ras
3d_fold_model
Accession No. : 8
Ras
Pathway No. : 58
0.5050510.024explicit E-S complexSubstrate
GDP-Ras

Product
GTP-Ras
Kinetics same as GEF-bg-act-ras

GEF* acting as a Product of an Enzyme in  
3d_fold_model Network
Enzyme Molecule /
Enzyme Activity
Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
PKC-active  /
PKC-act-GEF
3d_fold_model
Accession No. : 8
  • Shared_Object_
    3d_fold_model

    Pathway No. : 54
  • 3.3333344explicit 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

    GEF* acting as a Substrate in a reaction in  
    3d_fold_model 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-GEF3d_fold_model
    Accession No. : 8
    Ras
    Pathway No. : 58
    1
    (s^-1)
    0
    (s^-1)
    --Substrate
    GEF*

    Product
    inact-GEF



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