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Molecule Parameter List for cGMP2.PKG | 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. |
cGMP2.PKG acting as a Molecule in cGMP_regulation Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | cGMP2.PKG | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 0 | 0.0016667 | No | | Phosphorylated cGMP-dependent protein kinase. cGMP binding to the inactive cGK activates it, making it participate in further downstream regulatory processes, mostly through phosphorylation regulation of its substrates. Here it phosphorylates PDE, which hydrolyses cGMP to 5primeGMP, thus maintaining the intracellular nucleotide levels. The activity of PDE is supposed to be enhanced following phosphorylation by PKG. |
cGMP2.PKG 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 | | 1 | 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. | | 2 | cGMP2.PKG /
sGCppase_act
| cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 0.5 | 12.31 | 4 | explicit E-S complex | Substrate
sGC-ppase
Product
sGC-ppase*
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cGMP2.PKG 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 | | fast_site_bind | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 10
(uM^-1 s^-1) | 37
(s^-1) | Kd(bf) = 3.7(uM) | - | Substrate
cGMP
cGMP.PKG
Product
cGMP2.PKG
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| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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