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Molecule Parameter List for IP3-56K_IP4-1K | 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 | Osc_Ca_
IP3metabolism | 32 | Network |
MIPP, CaMKII, CaM,
PKC, IP3-3K, Gq,
PLCbeta, 134_dephos, 145_dephos,
IP4-system, IHP-system, 1345_dephos,
CaRegulation, Othmer-Tang-model | | This network models an oscillatory calcium response to GPCR mediated PLCbeta activation, alongwith detailed InsP3 metabolism in the neuron. It is similar to the Osc_Ca_IP3metab model (accession 24) except that some enzymes in the InsP3 metabolism network have been modified to have reversible kinetics rather than Michaelis-Menten kinetics. The modified enzymes belong to the groups: IP4-system, IP3-3K, 145_dephos and 134_dephos. Mishra J, Bhalla US. Biophys J. 2002 Sep;83(3):1298-316. |
IP3-56K_IP4-1K acting as a Molecule in Osc_Ca_IP3metabolism Network
| Name | Accession Name | Pathway Name | Initial Conc.
(uM) | Volume
(fL) | Buffered | | IP3-56K_IP4-1K | Osc_Ca_
IP3metabolism
Accession No. : 32 | IP4-system
Pathway No. : 167 | 1.632 | 1000 | No | | Combined Ins(134)P3 5,6-kinase and Ins(3456)P4 1-kinase: from Yang and Shears, Biochem J 2000, 351: 551-555. Conc from Wilson and Majerus, JBC 271(20); 1996: 11904-10 5,6K Reaction products Ins(1346)P4 and Ins(1345)P4 are generated in a ratio of 2.3-5 : 1 Enzyme inhibition by products, as depicted in previous versions of the model, removed because it is now shown that enzyme is multi-tasking and reversible with respect to these products: Ho et al, Curr Biol 2002, 12: 1-20. This non M-M ability has been incorporated. But cycling to Ins(346)P3 by this enzyme not included because rest of Ins(346)P3 network biology is unknown in mammals. |
IP3-56K_IP4-1K acting as a Substrate in a reaction in Osc_Ca_IP3metabolism 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 | | 1 | IP3-Kcmplx-on | Osc_Ca_
IP3metabolism
Accession No. : 32 | IP4-system
Pathway No. : 167 | 4.2666
(uM^-1 s^-1) | 1.024
(s^-1) | Kd(bf) = 0.24(uM) | - | Substrate
IP3(134)
IP3-56K_IP4-1K
Product
IP3-56Kcmplx
| | | Kf and Kb are equivalent to k1 and k2 for InsP3 56-K, calculated from enzyme Km and Vmax: Yang and Shears, BiochemJ 2000, 351: 551-555 | | 2 | ip4-1k-on | Osc_Ca_
IP3metabolism
Accession No. : 32 | IP4-system
Pathway No. : 167 | 31.2001
(uM^-1 s^-1) | 2.496
(s^-1) | Kd(bf) = 0.08(uM) | - | Substrate
IP3-56K_IP4-1K
IP4(3456)
Product
ip4_1k_cmplx
| | | Rates derives from enzyme Km and Vmax values: Yang and Shears, Biochem J 2000, 351: 551-555. |
IP3-56K_IP4-1K acting as a Product in a reaction in Osc_Ca_IP3metabolism 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 | | 1 | 6kinase | Osc_Ca_
IP3metabolism
Accession No. : 32 | IP4-system
Pathway No. : 167 | 0.256
(s^-1) | 0
(uM^-1 s^-1) | - | - | Substrate
IP3-56Kcmplx
Product
IP3-56K_IP4-1K
IP4(1346)
| | | Kf = Vmax for IP3 56-K from Yang and Shears, Biochem J 2000; 351:551-555 Enzyme reversibility reported in Ho et al, Curr Biol 2002, 12: 1-20. But backflow calculations do not show that Kb needs to be incorporated | | 2 | 5kinase | Osc_Ca_
IP3metabolism
Accession No. : 32 | IP4-system
Pathway No. : 167 | 0.0701
(s^-1) | 0.006
(uM^-1 s^-1) | Kd(cb) = 0.086(uM) | - | Substrate
IP3-56Kcmplx
Product
IP3-56K_IP4-1K
IP4(1345)
| | | Kf = 0.274 times Vmax of IP3 56-K as product ratio of Ins(1345)P4 : Ins(1346)P4 is 1 : 2.3-5 from Wilson and Majerus, JBC 271; 1996 Kb ascertained from dG calculations for equilibrium conditions., for a dG = -10 kJ/mol Also enzyme reversibility reported in Ho et al, Curr Biol 2002, 12: 1-20 | | 3 | ip4-1k-off | Osc_Ca_
IP3metabolism
Accession No. : 32 | IP4-system
Pathway No. : 167 | 0.624
(s^-1) | 0.056
(uM^-1 s^-1) | Kd(cb) = 0.0897(uM) | - | Substrate
ip4_1k_cmplx
Product
IP3-56K_IP4-1K
IP5(13456)
| | | Kf = enzyme Vmax : Yang and Shears, Biochem J 2000, 351, 551-5. Kb ascertained from dG calculations for equilibrium product substrate conditions. Ho et al, Curr Biol 2002, 12: 1-20 report a Vmax for reverse reaction of 0.0656 /sec. But this cannot be exactly incorporated unless Km for InsP5 is also known. Simulations show that incorporation of this reverse reaction can maintain basal InsP4 levels but cannot achieve the stimulated InsP4 levels shown in Ho et al. Hence the separate InsP5 1pase is retained. |
| Database compilation and code copyright (C) 2022, Upinder S. Bhalla and NCBS/TIFR
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