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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 |
Accession and Pathway Details | |
| Accession Name | Accession No. | Accession Type | Pathway Link | Synaptic_
Network | 16 | Network |
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
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | PDE1 | Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 2 | 1000 | No | | 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 Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | PDE1 /
PDE1
| Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 39.7 | 1.667 | 4.0012 | explicit E-S complex | Substrate
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. |
| Name | Accession Name | Pathway Name | Kf | Kb | Kd | tau | Reagents | | 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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