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