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Molecule Parameter List for cGMP.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 | | cGMP_regulation | 34 | Network |
Shared_Object_cGMP_regulation, GC, PDE | Though Corbin JD. et al. Eur J Biochem. (2000) 267(9):2760-7 has been mentioned in the citation, this model has been made with inputs from different literature sources, each of which has been mentioned in the notes sections. This model features hydrolysis of cGMP by bovine PDE, phosphorylation of PDE by bovine lung PKG, and activation of bovine lung PKG by cGMP binding. These mechanisms are known to be involved in cGMP level regulation. Rates have been used from different sources and the model has been tested based on Corbin JD. et al., since their work involved measuring the PDE phosphorylation and PDE activity.
On replicating Figures 2, 3 and 4 from their paper, there is approx 30% difference in results but the qualitative shape of the curves is very similar. This might be due to the fact that the Vmax values were used from different literature sources. This might lead to the discrepancy in the numbers in this model. The values shown in this model are near estimated physiological levels.In order to replicate the Figures more closely, we have run additional simulations with concentration terms changed so as to replicate the experimental conditions exactly. |
cGMP.PDE acting as a Molecule in cGMP_regulation Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | cGMP.PDE | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 0 | 0.0016667 | No | | cGMP bound PDE. Binding of cGMP to the allosteric cGMP-binding sites has been reported to be required for phosphorylation by cGMP-dep protein Kinase, and the elements contributing to the dimerization of this protein are located in or near the allosteric cGMP-binding sites, though the function of dimerization is unknown. (Fink et al., JBC, 1999, 274(49):34613-34620) |
cGMP.PDE acting as an Enzyme in cGMP_regulation Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | cGMP.PDE /
cGMP.PDE_basal
| cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 0.979992 | 2.4 | 4 | explicit E-S complex | Substrate
cGMP
Product
5primeGMP
|
cGMP.PDE acting as a Substrate for an Enzyme in cGMP_regulation Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | cGMP2.PKG /
PKG_act | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 10 | 0.6022 | 4 | explicit E-S complex | Substrate
cGMP.PDE
Product
cGMP_PDE*
| | Phosphorylation of PDE actually increases the enzyme activity. And occupation of the allosteric binding sites by cGMP is necessary for phosphorylation by PKG. Phosphorylation following the occupation of the allosteric sites by cGMP. (Gibson, Eur J Pharmacol,2001,411:1-10, Corbin et al., 2000, Eur J Biochem, 267:2760-2767). Phosphorylation resulted in increases in phosphate content up to 0.6 mol per PDE5 subunit. (Corbin et al., 2000), and since PKG is known to catalyze autophosphorylation, it was found to incorporate 2 mol per PDE5 subunit in 60 mins. |
cGMP.PDE acting as a Product of an Enzyme in cGMP_regulation Network
Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | Myo_phosphatase /
PP1 | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 10 | 1.98 | 4 | explicit E-S complex | Substrate
cGMP_PDE*
Product
cGMP.PDE
|
cGMP.PDE acting as a Product in a reaction in cGMP_regulation 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 | | PDEbind_cGMP | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 10
(uM^-1 s^-1) | 13
(s^-1) | Kd(bf) = 1.3(uM) | - | Substrate
PDE
cGMP
Product
cGMP.PDE
| | Kd ~1.3 uM. (Turko et al., JBC, 1996, 271(36):22240-22244, and Corbin et al., Eur J Biochem, 2000,267:2760-2767) |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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