DXS

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The DXS reaction (EC 2.2.1.7)

$Pyruvate + G3P \rightleftharpoons DXP + CO2$

Deoxyxylulose-5-phosphate synthase (DXS) catalyses the production of 1-deoxy-D-xylulose 5-phosphate (DXP) from pyruvate and glyceraldehyde 3-phosphate (G3P). This reaction is the first step in the MEP pathway.

Modelling DXS

In the kinetic model, the DXS reaction is modelled with reversible Michaelis-Menten using the Hanekom bi-bi random order generic equation. In total, this reaction requires five kinetic parameters (Kms for all substrates and products, and a forward Kcat) and one thermodynamic parameter (Equilibrium constant, Keq).

$V_\mathrm{DXS}= \cfrac{Kcat_\mathrm{forward} \bullet [DXS] \bullet \left( \cfrac{[Pyr]}{Km_\mathrm{DXS}} \right) \bullet \left( \cfrac{[G3P]}{Km_\mathrm{g3p}} \right) \bullet \left( 1 - \cfrac{\left( \cfrac{[DXP]\bullet[CO2]}{[Pyr]\bullet[G3P]} \right)}{K_\mathrm{eq}} \right)} {\left( 1 + \cfrac {[Pyr]}{Km_\mathrm{pyr}} + \cfrac{[CO2]}{Km_\mathrm{co2}}\right) \bullet \left( 1 + \cfrac{[G3P]}{Km_\mathrm{g3p}} + \cfrac{[DXP]}{KM_\mathrm{dxp}} \right)}$

DXS parameters

Parameter	Direction	Substrate	Value	Unit	Weight	Description	Reference
Kcat	Forward	DXS	229.7	1/min	16	from E. coli wild type DXS, with non-optimal buffer: 40mM Tris, pH 8, 37C ; Km_GAP:52.5 +/- 8.3 microM; Km_pyruvate: 86.3 +/- 16.2 microM, kcat: 145.50 +/- 12.7 1/min	Brammer2011, Br719975
Kcat	Forward	DXS	153.6	1/min	16	from E. coli wild type DXS, with non-optimal buffer: 40mM Tris, pH 8, 37C ; Km_GAP:52.5 +/- 8.3 microM; Km_pyruvate: 86.3 +/- 16.2 microM, kcat: 145.50 +/- 12.7 1/min	Brammer2011, Br719975
Kcat	Forward	DXS	145.5	1/min	16	from E. coli wild type DXS, with non-optimal buffer: 40mM Tris, pH 8, 37C ; Km_GAP:52.5 +/- 8.3 microM; Km_pyruvate: 86.3 +/- 16.2 microM, kcat: 145.50 +/- 12.7 1/min	Brammer2011, Br719975
Kcat	Forward	DXS	209	1/min	16	from E. coli wild type DXS, with non-optimal buffer: 100mM Tris, pH 8, 37C ; Km_GAP:279.0+/- 7.2microM; Km_pyruvate: 74.70+/- 7.3 microM, kcat: 209.0 +/- 6.3 1/min	Brammer2011, Br719975
Kcat	Forward	DXS	173	1/min	16	from E. coli wild type DXS, with non-optimal buffer: 100mM Tris, pH 8, 37C ; Km_GAP:279.0+/- 7.2microM; Km_pyruvate: 74.70+/- 7.3 microM, kcat: 209.0 +/- 6.3 1/min	Brammer2011, Br719975
Kcat	Forward	DXS	246	1/min	16	from E. coli wild type DXS, with non-optimal buffer: 100mM Tris, pH 8, 37C ; Km_GAP:279.0+/- 7.2microM; Km_pyruvate: 74.70+/- 7.3 microM, kcat: 209.0 +/- 6.3 1/min	Brammer2011, Br719975
Kcat	Forward	GAP	48	1/min	256	Taken from Cane 2001's ref20. E.coli DXS in 40mM Tris, pH7.5, 37¡C. Km pyruvate 2.9 ± 0.5 mM.	Boronat1999
Kcat	Forward	GAP	66	1/min	128	DXPS2; in vitro- S. coelicolor gene expressed in E. coli; pH 7.5, 47C.	Cane2001
Kcat	Forward	GAP	114	1/min	8	from R. capsulatus, pH 7.4, 37C	Eubanks2003, Br657953
Kcat	Forward	GAP	660	1/min	64	from Plasmodium, expressed in E. coli. Look at Table 3. pH7-7.5;37C, Km_GAp:19 +/- 4 microM; Km_Pyruvate: 870 +/- 110 microM.	Handa2013, Br719510
Kcat	Forward	GAP	1608	1/min	8	dxs11 from Agrobacterium tumefaciens, pH8.0, 37¡C, expressed in E. coli	Lee2007, Br674982
Kcat	Forward	GAP	120	1/min	64	from Botrycoccus braunnii. Three recombinant enzymes used: DXS-I, DXS-II, DXS-III which are different by the digestion pattern using Xhol and BamHI. expressed in E. coli; pH 7.8 , 32 C; Km 1800 +/- 200 microM	Matsushima2012, Br720765
Kcat	Forward	GAP	120	1/min	64	from Botrycoccus braunnii. Three recombinant enzymes used: DXS-I, DXS-II, DXS-III which are different by the digestion pattern using Xhol and BamHI. expressed in E. coli; pH 7.8 , 32 C; Km 1800 +/- 200 microM	Matsushima2012, Br720765
Kcat	Forward	GAP	360	1/min	64	from Botrycoccus braunnii. Three recombinant enzymes used: DXS-I, DXS-II, DXS-III which are different by the digestion pattern using Xhol and BamHI. expressed in E. coli; pH 7.8 , 32 C; Km 1800 +/- 200 microM	Matsushima2012, Br720765
Kcat	Forward	Pyruvate	570	1/min	64	from Plasmodium, expressed in E. coli. Look at Table 3. pH7-7.5;37C, Km_GAp:19 +/- 4 microM; Km_Pyruvate: 870 +/- 110 microM.	Handa2013, Br719510
Kcat	Forward	Pyruvate	144	1/min	64	from Botrycoccus braunnii. Three recombinant enzymes used: DXS-I, DXS-II, DXS-III which are different by the digestion pattern using Xhol and BamHI. expressed in E. coli; pH 7.8 , 32 C; Km 1800 +/- 200 microM	Matsushima2012, Br720765
Kcat	Forward	Pyruvate	114	1/min	64	from Botrycoccus braunnii. Three recombinant enzymes used: DXS-I, DXS-II, DXS-III which are different by the digestion pattern using Xhol and BamHI. expressed in E. coli; pH 7.8 , 32 C; Km 1800 +/- 200 microM	Matsushima2012, Br720765
Kcat	Forward	Pyruvate	312	1/min	64	from Botrycoccus braunnii. Three recombinant enzymes used: DXS-I, DXS-II, DXS-III which are different by the digestion pattern using Xhol and BamHI. expressed in E. coli; pH 7.8 , 32 C; Km 1800 +/- 200 microM	Matsushima2012, Br720765