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Molecule Parameter List for PPX

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

PPX 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	0	0	1	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.

PPX acting as a Molecule in  Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
PPX	Mammalian_cell_ cycle Accession No. : 85	IE_GRP Pathway No. : 1072	1	200	No
From the notes on the equations: We assuem that the activity of this phosphatase (in the nucleus, where it opposes the action of CycB/Cdk1) is proportional to translational efficiency epsilon. Hence, when epsilon drops to 05, both kinase and phosphatase acting on IE are halved.

PPX 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
PPX / k32	Mammalian_cell_ cycle Accession No. : 85	IE_GRP Pathway No. : 1072	0.01	1.8	4	explicit E-S complex	Substrate IEP Product IE
Represented as k32.[PPx].[IEP] / (J32 + [IEP]) k32 = 1.8 J32 = 0.01

PPX acting as a Substrate 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
k34	Mammalian_cell_ cycle Accession No. : 85	IE_GRP Pathway No. : 1072	0.05 (s^-1)	0 (s^-1)	-	-	Substrate PPX Product degraded

PPX 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
k33	Mammalian_cell_ cycle Accession No. : 85	IE_GRP Pathway No. : 1072	0.05 (s^-1)	0 (s^-1)	-	-	Substrate AminoAcids Product PPX