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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	4	5	4	0

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
fig3_CaMKII	2	Network	Shared_Object_fig3_CaMKII,  CaMKII,  CaM,   PP1,  PP2B,  PKA,   AC
This is the model file for figure 3 from Bhalla US and Iyengar R. Science (1999) 283(5400):381-7. It is a model of the Ca activation of CaMKII and other CaM-activated enzymes. It includes the regulatory phosphatases PP1 and PP2B (Calcineurin) acting on CaMKII and also includes CaM-activated adenylyl cyclase and PKA in the synapse. Demonstration script files for generating the figures in the paper, including figure 3, are available here.

cAMP acting as a Molecule in  fig3_CaMKII Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
cAMP	fig3_CaMKII Accession No. : 2	Shared_Object_ fig3_CaMKII Pathway No. : 12	0	1000	No

cAMP acting as a Substrate for an Enzyme in  fig3_CaMKII Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	cAMP-PDE  / PDE	fig3_CaMKII Accession No. : 2	AC Pathway No. : 18	19.8413	10	4	explicit E-S complex	Substrate cAMP Product AMP
2	cAMP-PDE*  / PDE*	fig3_CaMKII Accession No. : 2	AC Pathway No. : 18	19.8413	20	4	explicit E-S complex	Substrate cAMP Product AMP
3	PDE1  / PDE1	fig3_CaMKII Accession No. : 2	AC Pathway No. : 18	39.7	1.667	4.0012	explicit E-S complex	Substrate cAMP Product AMP
4	CaM.PDE1  / CaM.PDE1	fig3_CaMKII Accession No. : 2	AC Pathway No. : 18	39.6825	10	4	explicit E-S complex	Substrate cAMP Product AMP

cAMP acting as a Product of an Enzyme in  fig3_CaMKII Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	AC1-CaM  / kenz	fig3_CaMKII Accession No. : 2	AC Pathway No. : 18	20	18	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate ATP Product cAMP
2	AC2*  / kenz	fig3_CaMKII Accession No. : 2	AC Pathway No. : 18	20.1149	7	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate ATP Product cAMP
3	AC2-Gs  / kenz	fig3_CaMKII Accession No. : 2	AC Pathway No. : 18	20	18	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate ATP Product cAMP
4	AC1-Gs  / kenz	fig3_CaMKII Accession No. : 2	AC Pathway No. : 18	20	18	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate ATP Product cAMP
5	AC2*-Gs  / kenz	fig3_CaMKII Accession No. : 2	AC Pathway No. : 18	60	54	4	Classical Michaelis-Menten V = Etot.S.Kcat/Km+S	Substrate ATP Product cAMP

cAMP acting as a Substrate in a reaction in  fig3_CaMKII 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	fig3_CaMKII Accession No. : 2	PKA Pathway No. : 17	54 (uM^-1 s^-1)	33 (s^-1)	Kd(bf) = 0.6111(uM)	-	Substrate R2C2 cAMP Product R2C2-cAMP
	Kf = 54 /sec/uM, Kb = 33 /sec; PKA in normal human T lymphocytes. Hasler et al (1992) FASEB J 6:2735-2741 Kd =1e-07 M for type II, 5.6e-08 M for type I; Stephen B. Smith et al (1981) PNAS, USA 78: 1591-1595 Ka1 = 2.1e+07 /M which gives Kd = 47 nM, Kan = 5e+08 /M or Kd of 2nM from Fig.7
2	cAMP-bind-site-B 2	fig3_CaMKII Accession No. : 2	PKA Pathway No. : 17	54 (uM^-1 s^-1)	33 (s^-1)	Kd(bf) = 0.6111(uM)	-	Substrate R2C2-cAMP cAMP Product R2C2-cAMP2
	Kf = 54 /sec/uM, Kb = 33 /sec; Same Km (1e-07M) assumed as site B1. kf/kb = 0.7e-07M*1e06/(6e05^02) = 2e-13:2.77e-12
3	cAMP-bind-site-A 1	fig3_CaMKII Accession No. : 2	PKA Pathway No. : 17	75 (uM^-1 s^-1)	110 (s^-1)	Kd(bf) = 1.4667(uM)	-	Substrate R2C2-cAMP2 cAMP Product R2C2-cAMP3
	Kf = 75 /sec/uM, Kb = 110 /sec; This site has higher Kd for cAMP (kinetics within bovine myocardium) Dagfinn Ogreid and Stein Ove Doskeland (1981) FEBS Lett. 129(2):287-292
4	cAMP-bind-site-A 2	fig3_CaMKII Accession No. : 2	PKA Pathway No. : 17	75 (uM^-1 s^-1)	32.5 (s^-1)	Kd(bf) = 0.4333(uM)	-	Substrate R2C2-cAMP3 cAMP Product R2C2-cAMP4
	Now cAMP shows effects of cooperativity and PKA has a low Kd for cAMP.