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Molecule Parameter List for cAMP-PDE

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-PDE 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	1	1	0	0	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
CaMKII_model3	63	Network	Shared_Object_CaMKII_model3,  CaMKII,  CaM,   PP1,  PP2B,  PP1_PSD,   AC,  PKA
This is the complete model of CaMKII bistability, model 3. It exhibits bistability in CaMKII activation due to autophosphorylation at the PSD and local saturation of PP1. This version of model 3 includes PKA regulatory input. This has little effect on the deterministic calculations, but the PKA pathway introduces a lot of noise which causes a difference in stochastic runs.

cAMP-PDE acting as a Molecule in  CaMKII_model3 Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
cAMP-PDE	CaMKII_model3 Accession No. : 63	AC Pathway No. : 269	0.5556	0.09	No
The levels of the PDE are not known at this time. However, enough kinetic info and info about steady-state levels of cAMP etc are around to make it possible to estimate this. 18 Feb 2005: After some playing with initial conc, it is now back at 0.5 uM.

cAMP-PDE acting as an Enzyme in  CaMKII_model3 Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
cAMP-PDE / PDE	CaMKII_model3 Accession No. : 63	AC Pathway No. : 269	19.8411	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

cAMP-PDE acting as a Substrate for an Enzyme in  CaMKII_model3 Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PKA-active  / phosph-PDE	CaMKII_model3 Accession No. : 63	Shared_Object_ CaMKII_model3 Pathway No. : 263	7.50008	9	4	explicit E-S complex	Substrate cAMP-PDE Product cAMP-PDE*
Same rates as PKA-phosph-I1

cAMP-PDE acting as a Product in a reaction in  CaMKII_model3 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
dephosph-PDE	CaMKII_model3 Accession No. : 63	AC Pathway No. : 269	0.01 (s^-1)	0 (s^-1)	-	-	Substrate cAMP-PDE* Product cAMP-PDE
The rates for this are poorly constrained. In adipocytes (probably a different PDE) the dephosphorylation is complete within 15 min, but there are no intermediate time points so it could be much faster. Identity of phosphatase etc is still unknown.