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Molecule Parameter List for CaM.PDE1

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
CaM.PDE1 participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1010001

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • AMPAR_traff_
    model1
  • 60Network
    Shared_Object_AMPAR_traff_model1 CaMKII CaM 
    PP1 PP2B PP1_PSD 
    PKA AC AMPAR 
    AMPAR_memb 
    This is the basic model of AMPAR trafficking bistability. It is based on Hayer and Bhalla, PLoS Comput. Biol. 2005. It includes the degradation and turnover of AMPARs. The CaMKII portion of the model is not bistable.

    CaM.PDE1 acting as a Molecule in  
    AMPAR_traff_model1 Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    CaM.PDE1
  • AMPAR_traff_
    model1

    Accession No. : 60
  • AC
    Pathway No. : 251
    00.09No
    Activity up 6x following Ca-CaM binding.

    CaM.PDE1 acting as an Enzyme in  
    AMPAR_traff_model1 Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    CaM.PDE1 /
    CaM.PDE1
  • AMPAR_traff_
    model1

    Accession No. : 60
  • AC
    Pathway No. : 251
    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.

    CaM.PDE1 acting as a Product in a reaction in  
    AMPAR_traff_model1 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
    CaM_bind_PDE1
  • AMPAR_traff_
    model1

    Accession No. : 60
  • AC
    Pathway No. : 251
    719.982
    (uM^-1 s^-1)
    5
    (s^-1)
    Kd(bf) = 0.0069(uM)-Substrate
    CaM-Ca4
    PDE1

    Product
    CaM.PDE1
    For olf epi PDE1, affinity is 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec. Then kf = 5 / (0.007 * 6e5) = 1.2e-3



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