CMK

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.

$CDPME + ATP \rightleftharpoons CDPME2P + ADP$

Equation Rate

CMK is modelled reversible using random bi-bi generic Michaelis-Menten equation

$V_\mathrm{CMK} = \cfrac{\left ( Kcat_\mathrm{forward} \cdot [CMK]\right ) \cdot \left (\cfrac{[CDP-ME]}{Km_\mathrm{CDP-ME}} \right ) \cdot \left(\cfrac{[ATP]}{Km_\mathrm{ATP}} \right) \cdot \left (1 - \cfrac{\cfrac{[CDP-ME2P]\cdot[ADP]}{[CDPME]\cdot[ATP]}}{K_\mathrm{eq}} \right)}{\left(1 + \cfrac{[CDP-ME]}{Km_\mathrm{CDP-ME}} + \cfrac{[ADP]}{Km_\mathrm{ADP}}\right)\cdot \left (1+ \cfrac{[ATP]}{Km_\mathrm{ATP}} +\cfrac{[CDP-ME2P]}{Km_\mathrm{CDP-ME2P}} \right)}$

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
121	NaN	8	Additive	Putative ispE gene from A. aeolicus transformed into E. coli, pH 8.5, 60C	Sgraja, et. al. 2008
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
222	0	8	Additive	Putative ispE gene from A. aeolicus transformed into E. coli, pH 8.5, 60C	Sgraja, et. al. 2008
20	0	32	Additive	Gene from E. coli, pH not specified, 22C,pH8.0, experiments were done in triplicate.	Tang2011, Br721831

6. Equilibrium constant (Keq)

Equilibrium constants are calculated from the Van't Hofft Isotherm equation: