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Enzyme List for pathway CELLDIV (Pathway Number 1070)

 Molecule Name/
Site Name 		Km (uM) kcat (1/s)Ratio
(k2/k3)		Enzyme TypeSubstrate Product
1 Enzyme Activity:
Ak6_etaA

Enzyme Molecule:
CycA		10.00025004explicit E-S complexCycA_Kip1
CycA
degraded
  See Ak6_etaE
2 Enzyme Activity:
Ak6_etaB

Enzyme Molecule:
CycB		9.999910004explicit E-S complexCycA_Kip1
CycA
degraded
  See Ak6_etaE
3 Enzyme Activity:
Ak6_etaE

Enzyme Molecule:
CycE		10.00025004explicit E-S complexCycA_Kip1
CycA
degraded
  Rate = V6 * [CycD_Kip1]. 6 Apr 2005. Rates were k1 = 500, k2 = 10, k3 = 1 in explicit E.S reaction form. Changed to MM as Km was too low. New values: Km = 10 kcat = Km * k6 * etaE = 500.
4 Enzyme Activity:
A_phosph_E2F

Enzyme Molecule:
CycA		9.9999104explicit E-S complexE2FA
E2FAP
  Rate equn has form [CycA].[E2F].k23 k23 = 1 MM equn has form [CycA].[E2F].kcat/(Km + E2F) So, we set kcat = Km * k23 where Km >> E2F 25 Mar. Better: Use explicit enz form. rate = k3.k1/k2 if k3 << k2. Let k3 = 1, k2 = 10, so we get k1 = k23 * 10 = 10. 6 Apr. Problem with explicit form is that the enz-substrate complex may affect the levels of the CycA, B etc. Back to MM.
5 Enzyme Activity:
A_phosph_
E2FA.Rb

Enzyme Molecule:
CycA		9.9999104explicit E-S complexE2FA.Rb
E2FAP.Rb
  Rate equn has form [CycA].[E2F].k23 k23 = 1 MM equn has form [CycA].[E2F].kcat/(Km + E2F) So, we set kcat = Km * k23 where Km >> E2F 25 March 2005 Use explicit form. rate = k23 = 1 = k3*k1/k2 where k3 << k2 So k3 = 1, k2 = 10, k1 = 10. 6 Apr 2005. Back to MM form because enz complex formation is depleting CycA, B etc.
6 Enzyme Activity:
B_phosph_E2FA

Enzyme Molecule:
CycB		9.9999104explicit E-S complexE2FA
E2FAP
  See A_phosph_E2F. Same rate of k23 = 1 applies.
7 Enzyme Activity:
B_phosph_
E2FA.Rb

Enzyme Molecule:
CycB		9.9999104explicit E-S complexE2FA.Rb
E2FAP.Rb
  See A_phosph_E2F. Same rate of k23 = 1 applies.
8 Enzyme Activity:
Cdc20_deg_CycA

Enzyme Molecule:
Cdc20		102004explicit E-S complexCycA
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.
9 Enzyme Activity:
Cdc20_deg_CycA_
Kip1

Enzyme Molecule:
Cdc20		102004explicit E-S complexCycA_Kip1
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.
10 Enzyme Activity:
Cdh1_Cdc20

Enzyme Molecule:
Cdc20		0.011404explicit E-S complexCdh1_i
Cdh1
  k3 = 140 Km = j3 = 0.01
11 Enzyme Activity:
Cdh1_CycA

Enzyme Molecule:
CycA		0.01124explicit E-S complexCdh1
Cdh1_i
  J4 = Km = 0.01 k4 = 40. GammaA = 0.3 kcat = k4 * GammaA = 12
12 Enzyme Activity:
Cdh1_CycB

Enzyme Molecule:
CycB		0.01404explicit E-S complexCdh1
Cdh1_i
  Eqn 12. J4 = Km = 0.01 k4 = 40 GammaB = 1 kcat = k4 * GammaB = 40
13 Enzyme Activity:
k11

Enzyme Molecule:
CycB		134explicit E-S complexAminoAcids
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.
14 Enzyme Activity:
k13

Enzyme Molecule:
IEP		0.00554explicit E-S complexCdc20notA
Cdc20
  Represented as k13.[IEP].[Cdc20A]/(J13 + [Cdc20A]) which is a classical MM form. k13 = 5, J13 = 0.005
15 Enzyme Activity:
k20_lambdaA

Enzyme Molecule:
CycA		10030004explicit E-S complexRb
Rb_P
  Km ~ 0, so rate ~ kcat. Here rate = k20 * lambdaA = 10 * 3 7 Apr 2005: Fix it: rate should have substrate term in it. Set Km = 10 >> substrate. Then, kcat = Km * k20 * lambdaA = 10 * 10 * 3 = 300
16 Enzyme Activity:
k20_lambdaA[1]

Enzyme Molecule:
CycA		10030004explicit E-S complexE2FAP.Rb
Rb_P
E2FAP
  Km ~ 0, so rate ~ kcat. Here rate = k20 * lambdaA = 10 * 3 7 Apr 2005: Fix it: rate should have substrate term in it. Set Km = 10 >> substrate. Then, kcat = Km * k20 * lambdaA = 10 * 10 * 3 = 300
17 Enzyme Activity:
k20_lambdaA[2]

Enzyme Molecule:
CycA		10030004explicit E-S complexE2FA.Rb
Rb_P
E2FA
  Km ~ 0, so rate ~ kcat. Here rate = k20 * lambdaA = 10 * 3 7 Apr 2005: Fix it: rate should have substrate term in it. Set Km = 10 >> substrate. Then, kcat = Km * k20 * lambdaA = 10 * 10 * 3 = 300
18 Enzyme Activity:
k20_lambdaB

Enzyme Molecule:
CycB		100.00250004explicit E-S complexRb
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
19 Enzyme Activity:
k20_lambdaB[1]

Enzyme Molecule:
CycB		100.00250004explicit E-S complexE2FAP.Rb
Rb_P
E2FAP
  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
20 Enzyme Activity:
k20_lambdaB[2]

Enzyme Molecule:
CycB		100.00250004explicit E-S complexE2FA.Rb
Rb_P
E2FA
  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
21 Enzyme Activity:
k20_lambdaD

Enzyme Molecule:
CycD		10033004explicit E-S complexRb
Rb_P
  With a low Km, rate ~ kcat. Here we have rate = k20 * lambda_d = 10 * 3.3 = 33. 7 Apr 2005. Actually should have the substrate term in here. Use the form Km >> substrate, so rate = kcat * sub * enz / Km so kcat = Km * k20 * lambda_d = 10 * 10 * 3.3 = 330
22 Enzyme Activity:
k20_lambdaD[1]

Enzyme Molecule:
CycD		10033004explicit E-S complexE2FAP.Rb
Rb_P
E2FAP
  With a low Km, rate ~ kcat. Here we have rate = k20 * lambda_d = 10 * 3.3 = 33. 7 Apr 2005. Actually should have the substrate term in here. Use the form Km >> substrate, so rate = kcat * sub * enz / Km so kcat = Km * k20 * lambda_d = 10 * 10 * 3.3 = 330 The idea here is that these reactions phosphorylate the Rb protein attached to E2FAP, so that Rb_P is released and E2FAP is left.
23 Enzyme Activity:
k20_lambdaD[2]

Enzyme Molecule:
CycD		10033004explicit E-S complexE2FA.Rb
Rb_P
E2FA
  With a low Km, rate ~ kcat. Here we have rate = k20 * lambda_d = 10 * 3.3 = 33. 7 Apr 2005. Actually should have the substrate term in here. Use the form Km >> substrate, so rate = kcat * sub * enz / Km so kcat = Km * k20 * lambda_d = 10 * 10 * 3.3 = 330 The idea here is that these reactions phosphorylate the Rb protein attached to E2FA, so that Rb_P is released and E2FA is left.
24 Enzyme Activity:
k20_lambdaE

Enzyme Molecule:
CycE		100.00250004explicit E-S complexRb
Rb_P
  For Km ~ 0, rate ~ kcat. rate = k20 * lambdaE = 10 * 5 7 Apr 2005. Actually need to put in substrate term too. Let Km = 10 >> sub. Then, rate ~ kcat * sub * prd /Km so kcat = Km * k20 * lambdaE = 10 * 10 * 5 = 500
25 Enzyme Activity:
k20_lambdaE[1]

Enzyme Molecule:
CycE		100.00250004explicit E-S complexE2FAP.Rb
Rb_P
E2FAP
  For Km ~ 0, rate ~ kcat. rate = k20 * lambdaE = 10 * 5 7 Apr 2005. Actually need to put in substrate term too. Let Km = 10 >> sub. Then, rate ~ kcat * sub * prd /Km so kcat = Km * k20 * lambdaE = 10 * 10 * 5 = 500
26 Enzyme Activity:
k20_lambdaE[2]

Enzyme Molecule:
CycE		100.00250004explicit E-S complexE2FA.Rb
Rb_P
E2FA
  For Km ~ 0, rate ~ kcat. rate = k20 * lambdaE = 10 * 5 7 Apr 2005. Actually need to put in substrate term too. Let Km = 10 >> sub. Then, rate ~ kcat * sub * prd /Km so kcat = Km * k20 * lambdaE = 10 * 10 * 5 = 500
27 Enzyme Activity:
k21_phiB

Enzyme Molecule:
CycB		102004explicit E-S complexPP1A
PP1
  phiB = 2. See calculation for k21_phiE
28 Enzyme Activity:
k21_phiE

Enzyme Molecule:
CycE		9.999725004explicit E-S complexPP1A
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.
29 Enzyme Activity:
k21_phiE_A

Enzyme Molecule:
CycA		9.999725004explicit E-S complexPP1A
PP1
  phiE is also used for the reaction catalyzed by A. So rates are identical to k21_phiE
30 Enzyme Activity:
k29

Enzyme Molecule:
E2FA		1000.02504explicit E-S complexMass_dup
CycA
  Represented as eps*k29*[E2FA]*[mass], where k29 is 0.05 Split into two steps, this one deals with the E2FA term. rate = Mass_dup * E2FA * kcat / (Km + Mass_dup) Note that Mass_dup will not change. Let Km >> Mass_dup and kcat = k29 * Km. then rate ~ Mass_dup * E2FA * k29 * Km / Km
31 Enzyme Activity:
k2_prime_prime

Enzyme Molecule:
Cdc20		99.99921004explicit E-S complexCycB
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.
32 Enzyme Activity:
k31

Enzyme Molecule:
CycB		0.010.74explicit E-S complexIE
IEP
  Represented as k31.[IE].[CycB]/(J31 + [IE]) k31 = 0.7 J31 = 0.01
33 Enzyme Activity:
k6_D_etaA

Enzyme Molecule:
CycA		10.00025004explicit E-S complexCycD_Kip1
CycD
degraded
  k3.k1/k2 = k6.etaA = 100*0.5 = 50 Also k3 << k2. Assume ratio is 10. Let k3 be reasonable, say 1. Then k2 = 10, k1 = 500. 6 April 2005: The above rates are bad because they give a very low Km and too much E.S. complex. So, back to MM: Km >> substrate, so Km = 10. Then kcat = Km * k6 * etaA = 10 * 100 * 0.5 = 500.
34 Enzyme Activity:
k6_D_etaB

Enzyme Molecule:
CycB		9.999910004explicit E-S complexCycD_Kip1
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
35 Enzyme Activity:
k6_D_etaE

Enzyme Molecule:
CycE		10.00025004explicit E-S complexCycD_Kip1
CycD
degraded
  Rate = V6 * [CycD_Kip1]. k3.k1/k2 = rate = k6 * etaE = 50. 6 Apr 2005. Old rates in explicit form were k1 = 500, k2 = 10, k3 = 1. Need to go back to MM form because the above explict rates give a very low Km, ie, lots of E.S complex. k6 = 100, etaE = 0.5, Let Km >> substrate, so Km = 10. Then kcat = Km * k6 * etaE = 500.
36 Enzyme Activity:
k6_E_etaA

Enzyme Molecule:
CycA		10.00025004explicit E-S complexCycE_Kip1
CycE
degraded
  See notes for k6_E_etaE. Explicit rates had been k1 = 500, k2 = 10, k3 = 1 but this gave a very low Km. So, back to MM: etaA = 0.5 so kcat = 500, Km = 10 as for k6_E_etaE
37 Enzyme Activity:
k6_E_etaB

Enzyme Molecule:
CycB		9.999910004explicit E-S complexCycE_Kip1
CycE
degraded
  See notes for k6_E_etaE. Here etaB = 1 so kcat = 1000, Km as before is 10
38 Enzyme Activity:
k6_E_etaE

Enzyme Molecule:
CycE		10.00025004explicit E-S complexCycE_Kip1
CycE
degraded
  k6 = 100, etaE = 0.5 Assume a large Km of 1000 so that the conc of the enzyme is negligible. Then rate is E.S.Vmax/Km. 6 April 2006 I had changed it over to an explict form earlier. Those values were k1 = 500, k2 = 10, k3 = 1. Cannot use as effective Km is very small so we would end up with lots of E.S complex. Change back to MM: Km = 10, kcat = Km * k6 * etaE = 500.
39 Enzyme Activity:
k6_kip1_A

Enzyme Molecule:
CycA		10.00025004explicit E-S complexKip1
degraded_kip
  k3.k1/k2 = k6.etaA = 100*0.5 = 50 Also k3 << k2. Assume ratio is 10. Let k3 be reasonable, say 1. Then k2 = 10, k1 = 500. 6 April 2005: The above rates are bad because they give a very low Km and too much E.S. complex. So, back to MM: Km >> substrate, so Km = 10. Then kcat = Km * k6 * etaA = 10 * 100 * 0.5 = 500.
40 Enzyme Activity:
k6_kip1_B

Enzyme Molecule:
CycB		9.999910004explicit E-S complexKip1
degraded_kip
  6 Apr 2005. Using MM form: k6 = 100 Let Km = 10 >> substrate. Then kcat = Km * k6 * eta_B = 1000
41 Enzyme Activity:
k6_kip1_E

Enzyme Molecule:
CycE		10.00025004explicit E-S complexKip1
degraded_kip
  Rate = V6 * [CycD_Kip1]. k3.k1/k2 = rate = k6 * etaE = 50. 6 Apr 2005. Old rates in explicit form were k1 = 500, k2 = 10, k3 = 1. Need to go back to MM form because the above explict rates give a very low Km, ie, lots of E.S complex. k6 = 100, etaE = 0.5, Let Km >> substrate, so Km = 10. Then kcat = Km * k6 * etaE = 500.
42 Enzyme Activity:
k7

Enzyme Molecule:
E2FA		11.24explicit E-S complexAminoAcids
CycE
  Represented simply as [E2FA]*k7, where k7 is 0.6 As AAs are at 1, we get rate = [AAs].[E2FA].kcat / (Km + [AAs]) So if we set Km = [AAs] = 1, then kcat = 1.2 gives our desired equation.
43 Enzyme Activity:
k8_CycA

Enzyme Molecule:
CycA		0.124explicit E-S complexCycE
degraded
44 Enzyme Activity:
k8_CycA_Kip1

Enzyme Molecule:
CycA		0.124explicit E-S complexCycE_Kip1
Kip1
degraded
45 Enzyme Activity:
k8_CycB

Enzyme Molecule:
CycB		0.10.14explicit E-S complexCycE
degraded
46 Enzyme Activity:
k8_CycB_Kip1

Enzyme Molecule:
CycB		0.10.14explicit E-S complexCycE_Kip1
Kip1
degraded
  k8 = 0.2, psiB = 0.05, so kcat = 0.1. J8 = 0.1
47 Enzyme Activity:
k8_CycE

Enzyme Molecule:
CycE		0.124explicit E-S complexCycE
degraded
  Autocatalysis step equation 5. Unfortunately cannot exactly represent the math of Equation 26. Note that we cannot merge this enzyme with k6_etaE because this is in the explicit form to get a little closer to the mathematical form.
48 Enzyme Activity:
k8_CycE_Kip1

Enzyme Molecule:
CycE		0.124explicit E-S complexCycE_Kip1
Kip1
degraded
  Autocatalysis step equation 5. Unfortunately cannot exactly represent the math of Equation 26. Note that we cannot merge this enzyme with k6_etaE because this is in the explicit form to get a little closer to the mathematical form.
49 Enzyme Activity:
k9

Enzyme Molecule:
DRG		154explicit E-S complexAminoAcids
CycD
  Represented simply as [DRG]*k9, where k9 is 2.5. As AAs are at 1, we get rate = [AAs].[DRG].kcat / (Km + [AAs]) So if we set Km = [AAs] = 1, then kcat = 5 gives our desired equation.
50 Enzyme Activity:
k_prime_17

Enzyme Molecule:
ERG		10.74explicit E-S complexAminoAcids
DRG
  k17_prime = 0.35. rate = epsilon * k17_prime * [ERG] Assume AA = 1, Km = 1. Then rate = kcat * AA * ERG / (Km + AA) gives kcat = 0.7
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