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Molecule Parameter List for Cdc20

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

Cdc20 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	4	1	1	1	0

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.

Cdc20 acting as a Molecule in  Mammalian_cell_cycle Network

Name	Accession Name	Pathway Name	Initial Conc. (uM)	Volume (fL)	Buffered
Cdc20	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0	200	No

Cdc20 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
1	Cdc20 / k2_prime_prime	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	99.9992	100	4	explicit E-S complex	Substrate CycB Product degraded
	k2_prime_prime = 1. rate = k2_prime_prime * Cdc20 * CycB Using MM: rate = kcat * Cdc20 * CycB / (CycB + Km) Let Km >> CycB, ie, around 100. Then kcat = k2_prime_prime * Km = 100.
2	Cdc20 / Cdc20_deg_CycA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10	200	4	explicit E-S complex	Substrate CycA Product degraded
	Rate comes in as k30 = 20 Rate = [Cdc20]*[CycA] * k30. To put in MM form: Rate = [Cdc20]*[CycA] * kcat / (Km + [CycA]) where kcat = k30 * Km and Km >> [CycA]. Put Km = 1000, so kcat = 20000 25 March: use explicit enz form. Use rate = k3*k1/k2 = 20, which works if k2 >> k3. Then let k3 = 1, k2 = 10, k1 becomes 200 7 Apr 2005: Above won't work because of low Km consuming too much of the Cdc20 in the complex form. So use Km = 10, kcat = 200.
3	Cdc20 / Cdc20_deg_CycA_ Kip1	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	10	200	4	explicit E-S complex	Substrate CycA_Kip1 Product Kip1 degraded
	Rate comes in as k30 = 20 Same rate as for CycA alone. Rate = [Cdc20]*[CycA_Kip1] * k30. To put in MM form: Rate = [Cdc20]*[CycA_Kip1] * kcat / (Km + [CycA_Kip1]) where kcat = k30 * Km and Km >> [CycA_Kip1]. Put Km = 1000, so kcat = 20000 Similar to CycA alone, we instead get k2 = 10, k3 = 1, so k1 = 200. 19 Apr 2005: Go back to MM form because of low Km. Let Km = 10, then kcat = Km * k30 = 200.
4	Cdc20 / Cdh1_Cdc20	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.0100001	140	4	explicit E-S complex	Substrate Cdh1_i Product Cdh1
	k3 = 140 Km = j3 = 0.01

Cdc20 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
k14_enz  / k14	Mammalian_cell_ cycle Accession No. : 85	Cdc20_Grp Pathway No. : 1074	0.00500008	2.5	4	explicit E-S complex	Substrate Cdc20 Product Cdc20notA
Represented as k14.[Cdc20] / (J4 + [Cdc20]) But I suspect it should be J14. k14 = 2.5 J14 = 0.005 If we set enz = 1, Km = J14, kcat = k14, this equation applies.

Cdc20 acting as a Product of an Enzyme in  Mammalian_cell_cycle Network

Enzyme Molecule / Enzyme Activity	Accession Name	Pathway Name	Km (uM)	kcat (s^-1)	Ratio	Enzyme Type	Reagents
IEP  / k13	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.00499996	5	4	explicit E-S complex	Substrate Cdc20notA Product Cdc20
Represented as k13.[IEP].[Cdc20A]/(J13 + [Cdc20A]) which is a classical MM form. k13 = 5, J13 = 0.005

Cdc20 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
k12	Mammalian_cell_ cycle Accession No. : 85	Cdc20_Grp Pathway No. : 1074	1.5 (s^-1)	0 (s^-1)	-	-	Substrate Cdc20 Product degraded