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Molecule Parameter List for cAMP | 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 | 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 |
cAMP acting as a Molecule in Synaptic_Network Network
cAMP acting as a Substrate for 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. |
cAMP 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 | AC1-CaM /
kenz | Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 20 | 18 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
ATP
Product
cAMP
| | | Vmax is assumed to be the same as that for the Gs-stimulated form. The rates are from: Smigel 1986 JBC 261(4):1976-1982 who has 8.27 umol/min/mg with forskolin stimulated AC. Tang et al JBC 266(13):8595-8603 have an almost identical Vmax of 8 umol/min/mg. This comes to a Vmax of 18/sec. The Km is pretty immaterial since the vast excess of ATP means that the enzyme will normally be saturated. This is a pretty fast enzyme. Note that the saturation of the enzyme means that the regulatory reactions have to involve the complex rather than the free enzyme. | | 2 | AC2* /
kenz | Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 20.1149 | 7 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
ATP
Product
cAMP
| | | The Vmax is scaled down to 7/sec from the Gs-stimulated form. This is constrained because we have a measure of basal activity due to basal phosphorylation by PKC. Two papers measure activation of AC2 by phosphorylation without Gs: Jacobowitz et al JBC 268(6):3829-3832 (Stim 3x) and Yoshimura and Cooper 1993 JBC 26(7):4604-4607 (Stim 9x). The conditions are somewhat different in the two cases. The reference maximally stimulated Vmax is 18/sec from Smigel 1986 JBC 261(4):1976-1982 who has 8.27 umol/min/mg with forskolin stimulated AC. Tang et al JBC 266(13):8595-8603 have an almost identical Vmax of 8 umol/min/mg. This comes to a Vmax of 18/sec. The Km is pretty immaterial since the vast excess of ATP means that the enzyme will normally be saturated. This is a pretty fast enzyme. Note that the saturation of the enzyme means that the regulatory reactions have to involve the complex rather than the free enzyme. | | 3 | AC2-Gs /
kenz | Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 20 | 18 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
ATP
Product
cAMP
| | | Vmax is assumed to be the same as for AC1. This is consistent since there is a good match between the mixture of ACs tested by Smigel 1986 JBC 261(4):1976-1982 who has 8.27 umol/min/mg with forskolin stimulated AC. Tang et al JBC 266(13):8595-8603 have an almost identical Vmax of 8 umol/min/mg for AC1. This comes to a Vmax of 18/sec. The Km is pretty immaterial since the vast excess of ATP means that the enzyme will normally be saturated. This is a pretty fast enzyme. Note that the saturation of the enzyme means that the regulatory reactions have to involve the complex rather than the free enzyme. | | 4 | AC1-Gs /
kenz | Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 20 | 18 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
ATP
Product
cAMP
| | | Vmax is from Smigel 1986 JBC 261(4):1976-1982 who has 8.27 umol/min/mg with forskolin stimulated AC. Tang et al JBC 266(13):8595-8603 have an almost identical Vmax of 8 umol/min/mg. This comes to a Vmax of 18/sec. The Km is pretty immaterial since the vast excess of ATP means that the enzyme will normally be saturated. This is a pretty fast enzyme. Note that the saturation of the enzyme means that the regulatory reactions have to involve the complex rather than the free enzyme. | | 5 | AC2*-Gs /
kenz | Synaptic_
Network
Accession No. : 16 | AC
Pathway No. : 85 | 60 | 54 | 4 | Classical Michaelis-Menten
V = Etot.S.Kcat/Km+S | Substrate
ATP
Product
cAMP
| | | The Km is higher here but it is still well below the level of ATP so the enzyme remains saturated. The Vmax is 3x higher than the reference forskolin stimulated form. This scale factor is a compromise between the 2x rise reported by Jacobowitz et al JBC 268(6): 3829-3832 and the 9x rise reported by Yoshimura and Cooper 1993 JBC 268(7):4604-4607. The reference Vmax is from Smigel 1986 JBC 261(4):1976-1982 who has 8.27 umol/min/mg with forskolin stimulated AC. Tang et al JBC 266(13):8595-8603 have an almost identical Vmax of 8 umol/min/mg. This comes to a Vmax of 18/sec. The Km is pretty immaterial since the vast excess of ATP means that the enzyme will normally be saturated. This is a pretty fast enzyme. Note that the saturation of the enzyme means that the regulatory reactions have to involve the complex rather than the free enzyme. |
cAMP acting as a Substrate in a reaction in Synaptic_Network 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 | | 1 | cAMP-bind-site-B
1 | Synaptic_
Network
Accession No. : 16 | PKA
Pathway No. : 84 | 54
(uM^-1 s^-1) | 33
(s^-1) | Kd(bf) = 0.6111(uM) | - | Substrate
R2C2
cAMP
Product
R2C2-cAMP
| | | Hasler et al FASEB J 6:2734-2741 1992 say Kd =1e-7M for type II, 5.6e-8 M for type I. Smith et al PNAS USA 78:3 1591-1595 1981 say that Ka1 is 2.1e7/M which gives a Kd of 47 nM, Kan = 5e8/M or Kd of 2nM. I prefer numbers from Ogreid and Doskeland Febs Lett 129:2 287-292 1981. Their conditions are more physiological. They have figs suggesting time course of complete assoc is < 1 min. | | 2 | cAMP-bind-site-B
2 | Synaptic_
Network
Accession No. : 16 | PKA
Pathway No. : 84 | 54
(uM^-1 s^-1) | 33
(s^-1) | Kd(bf) = 0.6111(uM) | - | Substrate
R2C2-cAMP
cAMP
Product
R2C2-cAMP2
| | | For now let us set this to the same Km (1e-7M) as site B1. This gives kf/kb = .7e-7M * 1e6 / (6e5^2) : 1/(6e5^2) = 2e-13:2.77e-12 | | 3 | cAMP-bind-site-A
1 | Synaptic_
Network
Accession No. : 16 | PKA
Pathway No. : 84 | 75
(uM^-1 s^-1) | 110
(s^-1) | Kd(bf) = 1.4667(uM) | - | Substrate
R2C2-cAMP2
cAMP
Product
R2C2-cAMP3
| | | This site has a higher Kd for cAMP. See Ogreid and Doskeland 1982 FEBS Lett 150:1 161-166 | | 4 | cAMP-bind-site-A
2 | Synaptic_
Network
Accession No. : 16 | PKA
Pathway No. : 84 | 75
(uM^-1 s^-1) | 32.5
(s^-1) | Kd(bf) = 0.4333(uM) | - | Substrate
R2C2-cAMP3
cAMP
Product
R2C2-cAMP4
| | | Cooperativity kicks in, now we have a low Kd for cAMP. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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