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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

cAMP 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	2	1	4	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
PKA_2003	47	Network	Shared_Object_PKA_2003,  PKA,  AC,   Gs
This model consists of receptor-ligand interaction, G-protein activation, Adenylyl cyclase mediated formation of cAMP and activation of PKA in the neuron. Demonstration programs using this model described in Bhalla US. (2004) Biophys J. 87(2):733-44 to generate a dose-response curve using stochastic calculations are available here.

cAMP acting as a Molecule in  PKA_2003 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
cAMP	PKA_2003 Accession No. : 47	Shared_Object_ PKA_2003 Pathway No. : 195	0	1000	No
Key second messenger.

cAMP acting as a Substrate for an Enzyme in  PKA_2003 Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	cAMP-PDE  / PDE	PKA_2003 Accession No. : 47	AC Pathway No. : 197	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 Km ~2 uM, Vmax est ~ 10 umol/min/mg for pure form. Brain protein is 93 kD but this was 67. So k3 ~10, k2 ~40, k1 ~4.2e-6
2	cAMP-PDE*  / PDE*	PKA_2003 Accession No. : 47	AC Pathway No. : 197	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.

cAMP acting as a Product of an Enzyme in  PKA_2003 Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
Gs.AC  / cyclase	PKA_2003 Accession No. : 47	AC Pathway No. : 197	20	18	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate ATP Product cAMP
See Feinstein et al PNAS 88:10173-10177, Jacobowitz et al JBC 286(6):3829-3832 Smigel, JBC 261(4):1976-1982 (1986)

cAMP acting as a Substrate in a reaction in  PKA_2003 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	PKA_2003 Accession No. : 47	PKA Pathway No. : 196	54 (uM^-1 s^-1)	33 (s^-1)	Kd(bf) = 0.6111(uM)	-	Substrate R2C2 cAMP Product cAMP.R2C2
	Hasler et al (1992 jun) FASEB J. 6(9):2735-41 say Kd =1e-7M for type II, 5.6e-8 M for type I. Take mean which comes to 2e-13 #/cell Smith et al (1981 Mar) Proc Natl Acad Sci U S A 78(3) 1591-1595 have better data. First kf/kb=2.1e7/M = 3.5e-5 (#/cell).Ogreid and Doskeland (1981 Jul 6) FEBS Lett 129(2) 287-292 have figs suggesting time course of complete assoc is < 1 min.
2	cAMP-bind-site-B 2	PKA_2003 Accession No. : 47	PKA Pathway No. : 196	54 (uM^-1 s^-1)	33 (s^-1)	Kd(bf) = 0.6111(uM)	-	Substrate cAMP cAMP.R2C2 Product cAMP2.R2C2
	For now let us set this to the same Km (1e-7M) as site B. This gives kf/kb = .7e-7M * 1e6 / (6e5^2) : 1/(6e5^2) = 2e-13:2.77e-12 Smith et al (1981 Mar) Proc Natl Acad Sci U S A 78(3) 1591-1595 have better values. They say that this is cooperative, so the consts are now kf/kb =8.3e-4
3	cAMP-bind-site-A 1	PKA_2003 Accession No. : 47	PKA Pathway No. : 196	75 (uM^-1 s^-1)	110 (s^-1)	Kd(bf) = 1.4667(uM)	-	Substrate cAMP cAMP2.R2C2 Product cAMP3.R2C2
4	cAMP-bind-site-A 2	PKA_2003 Accession No. : 47	PKA Pathway No. : 196	75 (uM^-1 s^-1)	32.5 (s^-1)	Kd(bf) = 0.4333(uM)	-	Substrate cAMP cAMP3.R2C2 Product cAMP4.R2C2