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Molecule Parameter List for 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
PDE1 participated asMoleculeSum total ofEnzymeSubstrate of an enzymeProduct of an enzymeSubstrate in ReactionProduct in Reaction
No. of occurrences1010010

Accession and Pathway Details
Accession NameAccession No.Accession TypePathway Link
  • Synaptic_
    Network
  • 16Network
    Shared_Object_Synaptic_Network PKC PLA2 
    PLCbeta Gq MAPK 
    Ras EGFR Sos 
    PLC_g CaMKII CaM 
    PP1 PP2B PKA 
    AC CaRegulation 
    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 Biophys J. 2002 Aug;83(2):740-52
    Bhalla US J Comput Neurosci. 2002 Jul-Aug;13(1):49-62

    PDE1 acting as a Molecule in  
    Synaptic_Network Network
    NameAccession NamePathway NameInitial Conc.
    (uM)
    Volume
    (fL)
    Buffered
    PDE1
  • Synaptic_
    Network

    Accession No. : 16
  • AC
    Pathway No. : 85
    21000No
    CaM-Dependent PDE. 66KDa Borisy et al J Neurosci 12(3):915-923 About 0.6% of membrane protein. so estimate 2 uM as conc in brain. Also see Conti et al Adv Sec Mess Phosphoprotein Res 1992 25:87-99

    PDE1 acting as an Enzyme in  
    Synaptic_Network Network
    Enzyme Molecule /
    Enzyme Activity
    Accession NamePathway NameKm (uM)kcat (s^-1)RatioEnzyme TypeReagents
    PDE1 /
    PDE1
  • Synaptic_
    Network

    Accession No. : 16
  • AC
    Pathway No. : 85
    39.71.6674.0012explicit E-S complexSubstrate
    cAMP

    Product
    AMP
    From Borisy et al J Neurosci 12(3):915-923 the basal rate goes up 6x with Ca stimulation. Km = 40. The stimulated Vmax in this paper is very low. But Conti et al 1994 Biochem 34:7979-7987 report a 2000x purified form which has a stimulated Vmax of 10 umol/min/mg or about 10/sec (given that the mol wt is around 65KDa.). Here we use a Vmax = 1/6 of the CaM stim form.

    PDE1 acting as a Substrate in a reaction in  
    Synaptic_Network 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
  • Synaptic_
    Network

    Accession No. : 16
  • AC
    Pathway No. : 85
    720
    (uM^-1 s^-1)
    5
    (s^-1)
    Kd(bf) = 0.0069(uM)-Substrate
    CaM-Ca4
    PDE1

    Product
    CaM.PDE1
    Borisy et al J Neurosci 12(3):915-923 For olf epithelium PDE1, affinity is 7 nM CaM and about 2 uM Ca which is consistent with it binding Ca4.CaM at 7 nM. Assume same for brain. Reaction should be pretty fast. Assume kb = 5/sec.



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