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Molecule Parameter List for CycB

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

*CycB* 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	1	15	3	1	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.

CycB acting as a Molecule in Mammalian_cell_cycle Network

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

CycB acting as a Summed Molecule in Mammalian_cell_cycle Network

Accession Name	Pathway Name	Target	Input
Mammalian_cell_ cycle Accession No. : 85	CycB_Grp Pathway No. : 1073	CycB_dup	CycB

CycB 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	CycB / k20_lambdaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100.002	5000	4	explicit E-S complex	Substrate Rb Product Rb_P
	With Km ~ 0, rate ~ kcat. Here rate = k20 lambdaB = 10 * 5 7 Apr 2005. Changed to include substrate term. Use Km = 10 >> sub, so kcat = Km * k20 * lambdaB = 10 * 10 * 5 = 500*
2	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
3	CycB / k31	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.00999989	0.7	4	explicit E-S complex	Substrate IE Product IEP
	Represented as k31.[IE].[CycB]/(J31 + [IE]) k31 = 0.7 J31 = 0.01
4	CycB / k11	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	1	3	4	explicit E-S complex	Substrate AminoAcids Product Cdc20notA
	Represented simply as [CycB]k11, where k11 is 1.5. As AAs are at 1, we get rate = [AAs].[CycB].kcat / (Km + [AAs]) So if we set Km = [AAs] = 1, then kcat = 3 gives our desired equation.*
5	CycB / Cdh1_CycB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.0099998	40	4	explicit E-S complex	Substrate Cdh1 Product Cdh1_i
	Eqn 12. J4 = Km = 0.01 k4 = 40 GammaB = 1 kcat = k4 GammaB = 40*
6	CycB / B_phosph_E2FA	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	10	4	explicit E-S complex	Substrate E2FA Product E2FAP
	See A_phosph_E2F. Same rate of k23 = 1 applies.
7	CycB / B_phosph_ E2FA.Rb	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	10	4	explicit E-S complex	Substrate E2FA.Rb Product E2FAP.Rb
	See A_phosph_E2F. Same rate of k23 = 1 applies.
8	CycB / Ak6_etaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate CycA_Kip1 Product CycA degraded
	See Ak6_etaE
9	CycB / k8_CycB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.0999992	0.1	4	explicit E-S complex	Substrate CycE Product degraded
10	CycB / k6_E_etaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate CycE_Kip1 Product CycE degraded
	See notes for k6_E_etaE. Here etaB = 1 so kcat = 1000, Km as before is 10
11	CycB / k6_D_etaB	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate CycD_Kip1 Product CycD degraded
	6 Apr 2005. Earlier used explicit E.S complex form with k1 = 1000, k2 = 10, k3 = 1. This gave low Km and lots of E.S. complex. So shift to MM form: k6 = 100, etaB = 1. Let Km = 10 >> substrate. Then kcat = Km * k6 * etaB = 1000
12	CycB / k8_CycB_Kip1	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	0.0999992	0.1	4	explicit E-S complex	Substrate CycE_Kip1 Product Kip1 degraded
	k8 = 0.2, psiB = 0.05, so kcat = 0.1. J8 = 0.1
13	CycB / k6_kip1_B	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	9.99992	1000	4	explicit E-S complex	Substrate Kip1 Product degraded_kip
	6 Apr 2005. Using MM form: k6 = 100 Let Km = 10 >> substrate. Then kcat = Km k6 * eta_B = 1000*
14	CycB / k20_lambdaB[1]	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100.002	5000	4	explicit E-S complex	Substrate E2FAP.Rb Product E2FAP Rb_P
	With Km ~ 0, rate ~ kcat. Here rate = k20 lambdaB = 10 * 5 7 Apr 2005. Changed to include substrate term. Use Km = 10 >> sub, so kcat = Km * k20 * lambdaB = 10 * 10 * 5 = 500*
15	CycB / k20_lambdaB[2]	Mammalian_cell_ cycle Accession No. : 85	CELLDIV Pathway No. : 1070	100.002	5000	4	explicit E-S complex	Substrate E2FA.Rb Product E2FA Rb_P
	With Km ~ 0, rate ~ kcat. Here rate = k20 lambdaB = 10 * 5 7 Apr 2005. Changed to include substrate term. Use Km = 10 >> sub, so kcat = Km * k20 * lambdaB = 10 * 10 * 5 = 500*

CycB 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	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	Cdh1_i / Cdh1_i_k2_prime	Mammalian_cell_ cycle Accession No. : 85	Cdh1_grp Pathway No. : 1075	100.002	5	4	explicit E-S complex	Substrate CycB Product degraded
	k2_prime = 0.05. so actually this reaction is pretty negligible. rate = k2_prime * Cdh1_i * CycB From MM kinetics, rate = kcat * Cdh1_i * CycB / (CycB + Km). Let Km >>CycB, so Km = 10. Then kcat = k2_prime * Km = 0.5
3	Cdh1 / Cdh1_k2	Mammalian_cell_ cycle Accession No. : 85	Cdh1_grp Pathway No. : 1075	100	2000	4	explicit E-S complex	Substrate CycB Product degraded
	k2 = 20 Let Km = 100, so it is >> substrate. Then kcat = Km k2 = 2000*

CycB 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
CycB_synth / k1	Mammalian_cell_ cycle Accession No. : 85	CycB_Grp Pathway No. : 1073	0.01	0.6	4	explicit E-S complex	Substrate CycB_dimer Product CycB
k1 = 0.6. J1 = 0.1 rate = k1([CycB]/J1)^2 / (1 + ([cycB]/J1)^2 ) 2nd order term comes from dimerization, assume rate = k1 * dimer. Doing our usual assumption of AA = Km = 1, we get kcat = 2 * k1 = 1.2 7 April. Revisit this. Multiply expression above and below by J1^2. Then we have standard MM form, with k1 = kcat, and J1^2 = Km. 19 Apr 2005. Altered layout so that dimer form is in substrate, which it should have been all along.

CycB 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
k1_prime	Mammalian_cell_ cycle Accession No. : 85	CycB_Grp Pathway No. : 1073	0.1 (s^-1)	0 (s^-1)	-	-	Substrate AminoAcids Product CycB
k1_prime = 0.1

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