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Molecule Parameter List for cAMP-PDE | 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 | | PKA_2003 | 47 | Network |
Shared_Object_PKA_2003, PKA, AC,
Gs | | This model consists of receptor-ligand interaction, G-protein activation, Adenylyl cyclase mediated formation of cAMP and activation of PKA in the neuron. Demonstration programs using this model described in Bhalla US. (2004) Biophys J. 87(2):733-44 to generate a dose-response curve using stochastic calculations are available here. |
cAMP-PDE acting as a Molecule in PKA_2003 Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | cAMP-PDE | PKA_2003
Accession No. : 47 | AC
Pathway No. : 197 | 0.5 | 1000 | No | | The levels of the PDE are not known at this time. However, enough kinetic info and info about steady-state levels of cAMP etc are around to make it possible to estimate this at about 0.5 uM. |
cAMP-PDE acting as an Enzyme in PKA_2003 Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | cAMP-PDE /
PDE
| PKA_2003
Accession No. : 47 | AC
Pathway No. : 197 | 19.8413 | 10 | 4 | explicit E-S complex | Substrate
cAMP
Product
AMP
| | Best rates are from Conti et al Biochem 34 7979-7987 1995. Though these are for the Sertoli cell form, it looks like they carry nicely into alternatively spliced brain form. See Sette et al JBC 269:28 18271-18274 Km ~2 uM, Vmax est ~ 10 umol/min/mg for pure form. Brain protein is 93 kD but this was 67. So k3 ~10, k2 ~40, k1 ~4.2e-6 |
cAMP-PDE acting as a Substrate for an Enzyme in PKA_2003 Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | PKA-active /
phosph-PDE | PKA_2003
Accession No. : 47 | Shared_Object_
PKA_2003
Pathway No. : 195 | 7.5 | 9 | 4 | explicit E-S complex | Substrate
cAMP-PDE
Product
cAMP-PDE*
| | See Bramson et al CRC crit rev Biochem 15:2 93-124. The rates there are for peptide substrates and too fast. Scaled down by a factor of 3 as per Cohen et al FEBS Lett 76:182-86 (1977). |
cAMP-PDE acting as a Product in a reaction in PKA_2003 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 | | dephosph-PDE | PKA_2003
Accession No. : 47 | AC
Pathway No. : 197 | 0.1
(s^-1) | 0
(s^-1) | - | - | Substrate
cAMP-PDE*
Product
cAMP-PDE
| | The rates for this are poorly constrained. In adipocytes (probably a different PDE) the dephosphorylation is complete within 15 min, but there are no intermediate time points so it could be much faster. Identity of phosphatase etc is still unknown. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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