Difference between revisions of "CMK"
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=== 1. Km for CDP-ME=== | === 1. Km for CDP-ME=== | ||
+ | |||
+ | {|class="wikitable" | ||
+ | ! Parameter value || Error|| Weight || Error type || Details || Reference | ||
+ | |- | ||
+ | | 250 || 12.94 || 0.55 || Multiplicative|| EC 2.7.1.* Km values from E. coli || BRENDA | ||
+ | |- | ||
+ | | 153 || 14.55 || 0.22 || Multiplicative|| EC 2.7.1.* Km values from all organisms || BRENDA | ||
+ | |- | ||
+ | | 250 || 13.92 || 0.13 || Multiplicative|| EC 2.7.*.* Km values from E. coli ||BRENDA | ||
+ | |- | ||
+ | | 200 || 15.10 || 0.06 || Multiplicative|| EC 2.7.*.* Km values from all organisms || BRENDA | ||
+ | |- | ||
+ | | 140 || 24.91 || 0.03 || Multiplicative|| EC 2.*.*.* Km values from E. coli || BRENDA | ||
+ | |- | ||
+ | | 166 || 19.64 || 0.01 || Multiplicative|| EC 2.*.*.* Km values from all organisms|| BRENDA | ||
+ | |- | ||
+ | | 206.70 || 12.50 || 16 || Additive || Wild type M. tuberculosis IspE, transformed into E. coli, pH 7.0, 37C . Values calculated from averaged data from 3 independent experiments. Kinetics for truncated IspE enzymes were also measured for M. tuberculosis, B. pseudomallei in this study but not included in this entry || Eoh, et. al. 2009 <ref>Eoh2009</ref> | ||
+ | |- | ||
+ | | 121 || NaN || 8 || Additive || Putative ispE gene from A. aeolicus transformed into E. coli, pH 8.5, 60C || Sgraja, et. al. 2008 <ref>Sgraja2008, Br686699</ref> | ||
+ | |- | ||
+ | | 200 || NaN || 32 || Additive || Gene from E. coli, pH not specified, 22C,pH8.0, experiments were done in triplicate. || Tang2011, Br721831 | ||
+ | |} | ||
+ | |||
+ | [[File:CMK_CDPME.png | center | 500px | *Km values distribution for CDPME*. The blue lines represent the values reported in literature and the height of these lines corresponds to the degree of weightings assigned to them. The asterisks denote the generic Km values obtained from BRENDA. The height of these asterisks does not reflect the true weightings of these generic values as they were assigned a very low weight. The asterisks' y-axis location is set in such way for clarity.]] | ||
+ | |||
=== 2. Km for ATP=== | === 2. Km for ATP=== | ||
+ | |||
+ | {| class="wikitable" | ||
+ | ! Parameter value || Error|| Weight || Error type || Details || Reference | ||
+ | |- | ||
+ | | 250 || 12.94 || 0.55 || Multiplicative|| EC 2.7.1.* Km values from E. coli || BRENDA | ||
+ | |- | ||
+ | | 153 || 14.55 || 0.22 || Multiplicative|| EC 2.7.1.* Km values from all organisms || BRENDA | ||
+ | |- | ||
+ | | 250 || 13.92 || 0.13 || Multiplicative|| EC 2.7.*.* Km values from E. coli ||BRENDA | ||
+ | |- | ||
+ | | 200 || 15.10 || 0.06 || Multiplicative|| EC 2.7.*.* Km values from all organisms || BRENDA | ||
+ | |- | ||
+ | | 140 || 24.91 || 0.03 || Multiplicative|| EC 2.*.*.* Km values from E. coli || BRENDA | ||
+ | |- | ||
+ | | 166 || 19.64 || 0.01 || Multiplicative|| EC 2.*.*.* Km values from all organisms|| BRENDA | ||
+ | |- | ||
+ | | 20.70 || 1.20 || 16 || Additive|| wild type M. tuberculosis IspE, transformed into E. coli, pH 7.0, 37C . Values calculated from averaged data from 3 independent experiments. Kinetics for truncated IspE enzymes were also measured for M. tuberculosis, B. pseudomallei in this study but not included in this entry || Eoh, et. al. 2009 <ref>Eoh2009</ref> | ||
+ | |- | ||
+ | | 222 || 0 || 8 || Additive|| Putative ispE gene from A. aeolicus transformed into E. coli, pH 8.5, 60C || Sgraja, et. al. 2008 <ref>Sgraja2008, Br686699</ref> | ||
+ | |- | ||
+ | | 20 || 0 || 32 || Additive|| Gene from E. coli, pH not specified, 22C,pH8.0, experiments were done in triplicate. || Tang2011, Br721831 | ||
+ | |} | ||
+ | |||
+ | [[File:CMK_ATP.png | center | 500px | *Km values distribution for CDPME*. The blue lines represent the values reported in literature and the height of these lines corresponds to the degree of weightings assigned to them. The asterisks denote the generic Km values obtained from BRENDA. The height of these asterisks does not reflect the true weightings of these generic values as they were assigned a very low weight. The asterisks' y-axis location is set in such way for clarity.]] | ||
+ | |||
=== 3. Km for CDP-ME2P=== | === 3. Km for CDP-ME2P=== | ||
=== 4. Km for ADP=== | === 4. Km for ADP=== | ||
=== 5. Forward Kcat=== | === 5. Forward Kcat=== | ||
=== 6. Equilibrium constant (Keq)=== | === 6. Equilibrium constant (Keq)=== | ||
+ | |||
+ | Equilibrium constants are calculated from the Van't Hofft Isotherm equation: | ||
== References == | == References == | ||
<references /> | <references /> |
Latest revision as of 23:14, 7 March 2017
Contents
The reaction
4-(cytidine 5′-diphospho)-2-C-methyl-D-erythritol kinase (CMK) catalyses the production of CDP-ME2P from CDP-ME. This ATP-dependent reaction is the fourth step in the non-mevalonate or methylerythritol-phosphate (MEP) pathway.
Equation Rate
CMK is modelled reversible using random bi-bi generic Michaelis-Menten equation [1]
where :
Parameter | Description | Units |
---|---|---|
VCMK | Reaction rate for CMK | μM/min |
Kcatforward | Forward turnover number | min-1 |
KmCDPME | Michaelis-Menten constant for CDPME | μM |
KmATP | Michaelis-Menten constant for ATP | μM |
KmCDPME2P | Michaelis-Menten constant for CDPME2P | μM |
KmADP | Michaelis-Menten constant for ADP | μM |
Keq | Equilibrium constant | unitless |
[CDPME] | CDPME concentration | μM |
[ATP] | ATP concentration | μM |
[CDPME2P] | CDPME2P concentration | μM |
[ADP] | ADP concentration | μM |
Parameters
To model CMK using the equation above, a total of 6 parameters are required. For each of this parameter, a lognormal distribution is generated using our PROMENADE pipeline. To include all uncertainties surrounding these parameters, generic parameter values are obtained from BRENDA and is also processed through PROMENADE.
1. Km for CDP-ME
Parameter value | Error | Weight | Error type | Details | Reference |
---|---|---|---|---|---|
250 | 12.94 | 0.55 | Multiplicative | EC 2.7.1.* Km values from E. coli | BRENDA |
153 | 14.55 | 0.22 | Multiplicative | EC 2.7.1.* Km values from all organisms | BRENDA |
250 | 13.92 | 0.13 | Multiplicative | EC 2.7.*.* Km values from E. coli | BRENDA |
200 | 15.10 | 0.06 | Multiplicative | EC 2.7.*.* Km values from all organisms | BRENDA |
140 | 24.91 | 0.03 | Multiplicative | EC 2.*.*.* Km values from E. coli | BRENDA |
166 | 19.64 | 0.01 | Multiplicative | EC 2.*.*.* Km values from all organisms | BRENDA |
206.70 | 12.50 | 16 | Additive | Wild type M. tuberculosis IspE, transformed into E. coli, pH 7.0, 37C . Values calculated from averaged data from 3 independent experiments. Kinetics for truncated IspE enzymes were also measured for M. tuberculosis, B. pseudomallei in this study but not included in this entry | Eoh, et. al. 2009 [2] |
121 | NaN | 8 | Additive | Putative ispE gene from A. aeolicus transformed into E. coli, pH 8.5, 60C | Sgraja, et. al. 2008 [3] |
200 | NaN | 32 | Additive | Gene from E. coli, pH not specified, 22C,pH8.0, experiments were done in triplicate. | Tang2011, Br721831 |
2. Km for ATP
Parameter value | Error | Weight | Error type | Details | Reference |
---|---|---|---|---|---|
250 | 12.94 | 0.55 | Multiplicative | EC 2.7.1.* Km values from E. coli | BRENDA |
153 | 14.55 | 0.22 | Multiplicative | EC 2.7.1.* Km values from all organisms | BRENDA |
250 | 13.92 | 0.13 | Multiplicative | EC 2.7.*.* Km values from E. coli | BRENDA |
200 | 15.10 | 0.06 | Multiplicative | EC 2.7.*.* Km values from all organisms | BRENDA |
140 | 24.91 | 0.03 | Multiplicative | EC 2.*.*.* Km values from E. coli | BRENDA |
166 | 19.64 | 0.01 | Multiplicative | EC 2.*.*.* Km values from all organisms | BRENDA |
20.70 | 1.20 | 16 | Additive | wild type M. tuberculosis IspE, transformed into E. coli, pH 7.0, 37C . Values calculated from averaged data from 3 independent experiments. Kinetics for truncated IspE enzymes were also measured for M. tuberculosis, B. pseudomallei in this study but not included in this entry | Eoh, et. al. 2009 [4] |
222 | 0 | 8 | Additive | Putative ispE gene from A. aeolicus transformed into E. coli, pH 8.5, 60C | Sgraja, et. al. 2008 [5] |
20 | 0 | 32 | Additive | Gene from E. coli, pH not specified, 22C,pH8.0, experiments were done in triplicate. | Tang2011, Br721831 |
3. Km for CDP-ME2P
4. Km for ADP
5. Forward Kcat
6. Equilibrium constant (Keq)
Equilibrium constants are calculated from the Van't Hofft Isotherm equation: