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Molecule Parameter List for 5primeGMP | 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 |
| 5primeGMP participated as | Molecule | Sum total of | Enzyme | Substrate of an enzyme | Product of an enzyme | Substrate in Reaction | Product in Reaction | | No. of occurrences | 1 | 0 | 0 | 0 | 3 | 0 | 0 |
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. |
5primeGMP acting as a Molecule in cGMP_regulation Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | 5primeGMP | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 0 | 0.0016667 | No | | 5primeGMP - The hydrolysed product from cGMP, by the catalytic activity of PDE's. In this case the cGMP specific PDE, PDE5. |
5primeGMP 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 | | 1 | PDE /
PDE_basal | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 0.979992 | 2.4 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
cGMP
Product
5primeGMP
| | 2 | 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
| | 3 | cGMP_PDE* /
PDE_active | cGMP_regulation
Accession No. : 34 | PDE
Pathway No. : 178 | 0.580001 | 3.87 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
cGMP
Product
5primeGMP
| | | In this cGMP_PDE* enzyme complex, there are more than one cGMP molecule bound, since initially, cGMP binding to the allosteric binding sites is essential for phosphorylation by PKG. Vmax initially from Turko et al., 1998, Biochem J, 329:505-510 and Kuroda et al., 2001, J Neurosci,21(15):5693-5702. PDE has a high catalytic rate for cGMP hydrolysis. Km values reported are ~1-2 uM in various studies, including studies with purified enzyme preparations.(Fink et al., JBC, 1999, 274(49):34613-34620 and cited refs in their paper). Value used here from Mehats et al., Trends in Endocrinology & Metabolism, 2002, 13(1):29-35. Values similar to those used by Kuroda et al.,J Neurosci, 2001, 21(15):5693-5702. Km for cGMP decreased from 0.98 to 0.58 uM and Vmax was reported to be slightly increased by phosphorylation. (Corbin et al., Eur J Biochem, 2000) |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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