| | Molecule Name/
Site Name | Km (uM) | kcat (1/s) | Ratio
(k2/k3) | Enzyme Type | Substrate | Product |
| 1 |
Enzyme Activity:
craf**-deph
Enzyme Molecule:
PPhosphatase2A | 15.6566 | 6 | 4.16667 | explicit E-S complex | craf-1**
| craf-1*
|
| | Ueki et al JBC 269(22) pp 15756-15761 1994 show hyperphosphorylation of craf, so this is there to dephosphorylate it. Identity of phosphatase is not known to me, but it may be PP2A like the rest, so I have made it so. |
| 2 |
Enzyme Activity:
craf-deph
Enzyme Molecule:
PPhosphatase2A | 15.6566 | 6 | 4.16667 | explicit E-S complex | craf-1*
| craf-1
|
| | See parent PPhosphatase2A for parms |
| 3 |
Enzyme Activity:
MAPK*-feedback
Enzyme Molecule:
MAPK* | 25.641 | 10 | 4 | explicit E-S complex | craf-1*
| craf-1**
|
| | Ueki et al JBC 269(22):15756-15761 show the presence of this step, but not the rate consts, which are derived from Sanghera et al JBC 265(1):52-57, 1990, see the deriv in the MAPK* notes. |
| 4 |
Enzyme Activity:
MAPKK-deph
Enzyme Molecule:
PPhosphatase2A | 15.6566 | 6 | 4.16667 | explicit E-S complex | MAPKK*
| MAPKK-ser
|
| | See: Kyriakis et al Nature 358 pp 417-421 1992 Ahn et al Curr Op Cell Biol 4:992-999 1992 for this pathway. See parent PPhosphatase2A for parms. |
| 5 |
Enzyme Activity:
MAPKK-deph-ser
Enzyme Molecule:
PPhosphatase2A | 15.6566 | 6 | 4.16667 | explicit E-S complex | MAPKK-ser
| MAPKK
|
| 6 |
Enzyme Activity:
MKP1-thr-deph
Enzyme Molecule:
MKP-1 | 0.0666667 | 1 | 4 | explicit E-S complex | MAPK*
| MAPK-tyr
|
| | See MKP1-tyr-deph |
| 7 |
Enzyme Activity:
MKP1-tyr-deph
Enzyme Molecule:
MKP-1 | 0.0666667 | 1 | 4 | explicit E-S complex | MAPK-tyr
| MAPK
|
| | The original kinetics have been modified to obey the k2 = 4 * k3 rule, while keeping kcat and Km fixed. As noted in the NOTES, the only constraining data point is the time course of MAPK dephosphorylation, which this model satisfies. It would be nice to have more accurate estimates of rate consts and MKP-1 levels from the literature. Effective Km : 67 nM kcat = 1.43 umol/min/mg |
| 8 |
Enzyme Activity:
phosph_Sos
Enzyme Molecule:
MAPK* | 2.5641 | 10 | 4 | explicit E-S complex | Sos
| Sos*
|
| | See Porfiri and McCormick JBC 271:10 pp5871 1996 for the existence of this step. We'll take the rates from the ones used for the phosph of Raf by MAPK. Sep 17 1997: The transient activation curve matches better with k1 up by 10 x. |
| 9 |
Enzyme Activity:
PKA-phosph-GEF
Enzyme Molecule:
PKA-active | 7.5 | 9 | 4 | explicit E-S complex | inact-GEF
| inact-GEF*
|
| | This pathway inhibits Ras when cAMP is elevated. See: Hordijk et al JBC 269:5 3534-3538 1994 Burgering et al EMBO J 12:11 4211-4220 1993 The rates are the same as used in PKA-phosph-I1 |
| 10 |
Enzyme Activity:
PKC-act-GEF
Enzyme Molecule:
PKC-active | 3.33333 | 4 | 4 | explicit E-S complex | inact-GEF
| GEF*
|
| | Rate consts from PKC-act-raf. This reaction activates GEF. It can lead to at least 2X stim of ras, and a 2X stim of MAPK over and above that obtained via direct phosph of c-raf. Note that it is a push-pull reaction, and there is also a contribution through the phosphorylation and inactivation of GAPs. The original PKC-act-raf rate consts are too fast. We lower K1 by 10 X |
| 11 |
Enzyme Activity:
PKC-act-raf
Enzyme Molecule:
PKC-active | 66.6667 | 4 | 4 | explicit E-S complex | craf-1
| craf-1*
|
| | Rate consts from Chen et al Biochem 32, 1032 (1993) k3 = k2 = 4 k1 = 9e-5 recalculated gives 1.666e-5, which is not very different. Looks like k3 is rate-limiting in this case: there is a huge amount of craf locked up in the enz complex. Let us assume a 10x higher Km, ie, lower affinity. k1 drops by 10x. Also changed k2 to 4x k3. Lowerd k1 to 1e-6 to balance 10X DAG sensitivity of PKC |
| 12 |
Enzyme Activity:
PKC-inact-GAP
Enzyme Molecule:
PKC-active | 3.33333 | 4 | 4 | explicit E-S complex | GAP
| GAP*
|
| | Rate consts copied from PCK-act-raf This reaction inactivates GAP. The idea is from the Boguski and McCormick review. |
| 13 |
Enzyme Activity:
Sos.Ras_GEF
Enzyme Molecule:
Shc*.Sos.Grb2 | 0.505051 | 0.02 | 4 | explicit E-S complex | GDP-Ras
| GTP-Ras
|
