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Molecule Parameter List for AMP | 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 |
| AMP 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 | 4 | 0 | 0 |
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 |
AMP acting as a Molecule in Synaptic_Network Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | AMP | Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 10 | 0.0016667 | Yes | | AMP is a tightly regulated metabolite, so here we simply buffer it to its resting value. The value doesn't really matter to any of the calculations since it acts like a one-way sink. |
AMP acting as a Product of an Enzyme in Synaptic_Network Network
| | Enzyme Molecule /
Enzyme Activity | Accession Name | Pathway Name | Km (uM) | kcat (s^-1) | Ratio | Enzyme Type | Reagents | | 1 | cAMP-PDE /
PDE | Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 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 Borisy et al J Neurosci 12(3):915-923 also have estimates with a Km of 40 uM specifically for brain PDE. The Vmax is very low and it looks like the purification is not good. Combining this with data from the Conti paper and the Sette paper, it looks like a fair compromise is Km ~20 uM, Vmax est ~ 10 umol/min/mg or about 10/sec. | | 2 | cAMP-PDE* /
PDE* | Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 19.8413 | 20 | 4 | explicit E-S complex | Substrate
cAMP
Product
AMP
| | | This form has about twice the activity of the unphosphorylated form. See Sette et al JBC 269:28 18271-18274 1994. We'll ignore cGMP effects for now. The Vmax is therefore scaled to twice the value used in the unstimulated PDE enzyme. | | 3 | 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. | | 4 | CaM.PDE1 /
CaM.PDE1 | Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 39.6825 | 10 | 4 | explicit E-S complex | Substrate
cAMP
Product
AMP
| | | From Conti et al 1995 Biochem 34:7979-7987 the stimulated Vmax is ~10umol/min/mg in presence of lots of CaM. This works out to about 10/sec. Affinity is low, 40 uM. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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