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Molecule Parameter List for PP1A

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

PP1A 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	3	0	0	1

Accession and Pathway Details

Accession Name	Accession No.	Accession Type	Pathway Link
Mammalian_cell_ cycle	85	Network	Growth,  CELLDIV,  Rb_grp,   IE_GRP,  CycB_Grp,  Cdc20_Grp,   Cdh1_grp,  E2F,  CycA_Grp,   CycE_grp,  Early_Response_Genes,  Delayed_Response_Genes,   CycD_Grp
This is a fairly complete mass-action reimplementation of the Novak and Tyson mammalian cell cycle model. It is inexact on two counts. First, it replaces many rather abstracted equations with mass action and Michaelis-Menten forms of enzymes. Second, it does not handle the halving of cellular volume at the division point. Within these limitations, the model does most of what the original paper shows including oscillation of the relevant molecules.

PP1A acting as a Molecule in  Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
PP1A	Mammalian_cell_ cycle Accession No. : 85	Rb_grp Pathway No. : 1071	0	200	No

PP1A acting as an Enzyme in  Mammalian_cell_cycle Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
PP1A / k19	Mammalian_cell_ cycle Accession No. : 85	Rb_grp Pathway No. : 1071	100	2000	4	explicit E-S complex	Substrate Rb_P Product Rb
This is part of Eqn 20. k19 = 20. It is meant to represent a dephosph step of Rb_p. rate is k19*PP1A. rate in MM form is kcat * PP1A * Rb_P / (Km + Rb_P) Assume Km << Rb_P. To do so, Km = 0.01 Then kcat = k19. 7 Apr 2005. Actually should include substrate term. Take Km = 10 >> sub. Then kcat = Km * k19 = 200 18 April. Actually substrate levels are near 10. So need to scale up. Km = 100, kcat = Km * k19 = 2000

PP1A acting as a Substrate for an Enzyme in  Mammalian_cell_cycle Network

	Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
1	CycE  / k21_phiE	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99968	2500	4	explicit E-S complex	Substrate PP1A Product PP1
	Rate is just K21 * phiE * [CycE]. K21 = 1, phiE = 25. So rate= 25 * [CycE] MM rate = kcat * E.S/(Km + S) Let Km << S, then we get rate = kcat * E So if Km = 0.01, kcat = 25 7 Apr 2005. Actually should include substrate term. So, Km = 10, kcat = Km * K21 * phiE = 250 18 Apr 2005. Speeded up 10x.
2	CycA  / k21_phiE_A	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99968	2500	4	explicit E-S complex	Substrate PP1A Product PP1
	phiE is also used for the reaction catalyzed by A. So rates are identical to k21_phiE
3	CycB  / k21_phiB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10	200	4	explicit E-S complex	Substrate PP1A Product PP1
	phiB = 2. See calculation for k21_phiE

PP1A acting as a Product in a reaction in  Mammalian_cell_cycle 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
k21b	Mammalian_cell_ cycle Accession No. : 85	Rb_grp Pathway No. : 1071	10 (s^-1)	0 (s^-1)	-	-	Substrate PP1 Product PP1A
A dummy back reaction, implicit in the form of equation 19 18 Apr 2005. Speeded up 10x.