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Molecule Parameter List for PKA-active

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

*PKA-active* 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	3	0	0	1	2

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning	77	Network	Shared_Object_Ajay_Bhalla_2004_PKM_MKP3_Tuning, PKC, PLA2, PLCbeta, Ras, Gq, MAPK, EGFR, Sos, PLC_g, CaMKII, CaM, PP1, PP2B, PKA, AC, MKP3, PKM
This model is based on Ajay SM, Bhalla US. Eur J Neurosci. 2004 Nov;20(10):2671-80. This is the feedforward model with MPK3 from figure 8a.

PKA-active acting as a Molecule in Ajay_Bhalla_2004_PKM_MKP3_Tuning Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
PKA-active	Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Accession No. : 77	Shared_Object_ Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Pathway No. : 329	0	1.5	No

PKA-active acting as an Enzyme in Ajay_Bhalla_2004_PKM_MKP3_Tuning Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	PKA-active / PKA-phosph-GEF	Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Accession No. : 77	Shared_Object_ Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Pathway No. : 329	7.49996	9	4	explicit E-S complex	Substrate inact-GEF Product inact-GEF*
	This pathway inhibits Ras when cAMP is elevated. See: Hordijk et al JBC 269:5 3534-3538 1994 Burgering et al EMBO J 12:11 4211-4220 1993 The rates are the same as used in PKA-phosph-I1
2	PKA-active / PKA-phosph-I1	Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Accession No. : 77	Shared_Object_ Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Pathway No. : 329	7.49996	9	4	explicit E-S complex	Substrate I1 Product I1*
	#s from Bramson et al CRC crit rev Biochem 15:2 93-124. They have a huge list of peptide substrates and I have chosen high-ish rates. These consts give too much PKA activity, so lower Vmax 1/3. Now, k1 = 3e-5, k2 = 36, k3 = 9 (still pretty fast). Also lower Km 1/3 so k1 = 1e-5 Cohen et al FEBS Lett 76:182-86 1977 say rate =30% PKA act on phosphokinase beta.
3	PKA-active / phosph-PDE	Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Accession No. : 77	Shared_Object_ Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Pathway No. : 329	7.49996	9	4	explicit E-S complex	Substrate cAMP-PDE Product cAMP-PDE*
	Same rates as PKA-phosph-I1

PKA-active acting as a Substrate in a reaction in Ajay_Bhalla_2004_PKM_MKP3_Tuning 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
inhib-PKA	Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Accession No. : 77	PKA Pathway No. : 343	60.0003 (uM^-1 s^-1)	1 (s^-1)	Kd(bf) = 0.0167(uM)	-	Substrate PKA-active PKA-inhibitor Product inhibited-PKA
This has to be set to zero for matching the expts in vitro. In vivo we need to consider the inhibition though. kf = 1e-5 kb = 1

PKA-active acting as a Product in a reaction in Ajay_Bhalla_2004_PKM_MKP3_Tuning Network

	Name	Accession Name	Pathway Name	Kf	Kb	Kd	tau	Reagents
1	Release-C1	Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Accession No. : 77	PKA Pathway No. : 343	60 (s^-1)	18 (uM^-1 s^-1)	Kd(cb) = 0.3(uM)	-	Substrate R2C2-cAMP4 Product PKA-active R2C-cAMP4
	This has to be fast, as the activation of PKA by cAMP is also fast. kf was 10
2	Release-C2	Ajay_Bhalla_ 2004_PKM_MKP3_ Tuning Accession No. : 77	PKA Pathway No. : 343	60 (s^-1)	18 (uM^-1 s^-1)	Kd(cb) = 0.3(uM)	-	Substrate R2C-cAMP4 Product PKA-active R2-cAMP4

Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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