DXR

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DXR reaction

The 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR, EC 1.1.1.267) is the second step in the MEP pathway that catalyses the production of 2-C-methyl-D-erythritol 4-phosphate (MEP) from 1-deoxy-D-xylulose 5-phosphate (DXP).

Modelling DXR

DXR is modelled reversible with the Michaelis-Menten rate law using Hanekom's generic random order bi-bi equation [1] [2]. There are a total of five kinetic parameters (2 forward Kms, 2 reverse Kms and 1 Kcat), and one thermodynamic parameter (Equilibrium constant , Keq).

V_\mathrm{DXR}= \cfrac{Kcat_\mathrm{forward} \bullet [DXR] \bullet \left(\cfrac{[DXP]}{Km_\mathrm{dxp}}\right) \bullet \left( \cfrac{[NADPH]}{Km_\mathrm{nadph}} \right) \bullet \left( 1 - \cfrac{\cfrac{[DXP]\cdot[NADPH]}{[MEP]\cdot[NADP]}}{Keq}\right)}{\left(1 +\cfrac{[DXP]}{Km_\mathrm{dxp}} + \cfrac{[NADP]}{Km_\mathrm{nadp}}\right) \bullet \left( 1 + \cfrac{[NADPH]}{Km_\mathrm{nadph}} + \cfrac{[MEP]}{Km_\mathrm{mep}}\right)}

DXR parameters

DXR Kcat.png
Parameter Direction Substrate Value Unit SEM Weight Description Reference
Kcat Forward DXP 70.3 1/min NaN 64 from Mycobacterium tuberculosis, expressed in E. coli, pH 7.9, 30C Dhiman2005, Br674260
Kcat Forward DXP 1740 1/min 1 32 from E. coli, pH 7.6, 37C, recombinant enzyme Fox2005, BR672040
Kcat Forward DXP 318 1/min NaN 32 Gene MtDXRfrom Mycobacterium tuberculosis, room temperature (20-22C), pH7.5 Henriksson2006, Br671075
Kcat Forward DXP 120 1/min 0.09 16 gene from Francisella tularensis, expressed in E. coli, pH8, 22C Jawaid2009, Br713353
Kcat Forward DXP 315 1/min 0.19 32 gene MtDXR from Mycobacterium tuberculosis, expressed in E. coli, pH 7.5, 25C. Experimental result, see Table 1. Liu2012, BR724346
Kcat Forward DXP 1980 1/min NaN 32 from E. coli, pH7.6, 37C Walker2005
Kcat Reverse DXR 78 1/min 0.1 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. And NADPH /NADH BRENDA_lit: 654748, Argyrou2004, Br654748
Kcat Forward DXR 126 1/min 0.1 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. And NADPH /NADH BRENDA_lit: 654748, Argyrou2004, Br654748
Kcat Forward DXR 300 1/min 0.1 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. And NADPH /NADH BRENDA_lit: 654748, Argyrou2004, Br654748
Kcat Forward DXR 96 1/min 0.1 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. And NADPH /NADH BRENDA_lit: 654748, Argyrou2004, Br654748
Kcat Forward DXR 1152 1/min 0.02 128 DXPS1; in vitro- S. coelicolor gene expressed in E. coli; pH 7.5, 47C. Cane2001
Kcat Forward DXR 1020 1/min NaN 16 dxr gene from Synechocystis sp. PCC6803 cloned into E. coli. pH 7.8, 37C, BRENDA_lit:671590 Fernandes2005, Br671590
Kcat Forward DXR 264 1/min NaN 8 The ispC gene from Arabidopsis thaliana, expressed in E. coli, pH 8.0, 37C Rohdich2006, Br673562
Kcat Reverse DXR 1.63 1/min NaN 8 The ispC gene from Arabidopsis thaliana, expressed in E. coli, pH 8.0, 37C Rohdich2006, Br673562
Kcat Forward DXR 17.4 1/min NaN 32 50C. from Thermotoga maritima. Kinetics were measured at different temperature: 50C and 85C, expressed in E. coli, pH 7.5, 50C. Takenoya2010, Br712892
Kcat Forward DXR 330 1/min NaN 32 85C. from Thermotoga maritima. Kinetics were measured at different temperature: 50C and 85C, expressed in E. coli, pH 7.5, 50C. Takenoya2010, Br712892
Kcat Forward DXR 840 1/min NaN 32 from Synechocystis sp. PCC6803, expressed in E. coli, pH7.5, 37C, with three metal ions, Mn2+, Mg2+, Co2+ Yin2003, Br654877
Kcat Forward DXR 300 1/min NaN 32 from Synechocystis sp. PCC6803, expressed in E. coli, pH7.5, 37C, with three metal ions, Mn2+, Mg2+, Co2+ Yin2003, Br654877
Kcat Forward DXR 258 1/min NaN 32 from Synechocystis sp. PCC6803, expressed in E. coli, pH7.5, 37C, with three metal ions, Mn2+, Mg2+, Co2+ Yin2003, Br654877
Kcat Reverse MEP 12.5 1/min NaN 64 from Mycobacterium tuberculosis, expressed in E. coli, pH 7.9, 30C Dhiman2005, Br674260
Kcat Reverse MEP 57 1/min 0.06 32 gene MtDXR from Mycobacterium tuberculosis, expressed in E. coli, pH 7.5, 25C. Experimental result, see Table 1. Liu2012, BR724346
Kcat Reverse NADP 25.9 1/min NaN 64 from Mycobacterium tuberculosis, expressed in E. coli, pH 7.9, 30C Dhiman2005, Br674260
Kcat Forward NADPH 47.3 1/min NaN 64 from Mycobacterium tuberculosis, expressed in E. coli, pH 7.9, 30C Dhiman2005, Br674260
Kcat Forward NADPH 78 1/min 0.04 16 gene from Francisella tularensis, expressed in E. coli, pH8, 22C Jawaid2009, Br713353
Kcat Forward NADPH 310000 1/min NaN 32 from E. coli, with CoCl2, wild-type enzyme, pH 7.0-8.5, temp >37C (40-60C) Kuzuyama2000, Br286428
Kcat Forward NADPH 130000 1/min NaN 32 from E. coli, with MgCl2, wild-type enzyme, pH 7.0-8.5, temp >37C (40-60C) Kuzuyama2000, Br286428
Kcat Forward NADPH 590000 1/min NaN 32 from E. coli, with MgCl2, wild-type enzyme, pH 7.0-8.5, temp >37C (40-60C) Kuzuyama2000, Br286428


DXR Kmdxp.png
Parameter Direction Substrate Value Unit Weight Description Reference
Km Forward DXP 42 µM 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. And NADPH /NADH BRENDA_lit: 654748, Argyrou2004, Br654748
Km Forward DXP 100 µM 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. And NADPH /NADH BRENDA_lit: 654748, Argyrou2004, Br654748
Km Forward DXP 4 µM 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. And NADPH /NADH BRENDA_lit: 654748, Argyrou2004, Br654748
Km Forward DXP 25.5 µM 32 from Toxoplasma gondii (eukaryote), expressed in E. coli, pH 7.6, 30C Cai2013, 724543
Km Forward DXP 190 µM 128 DXPS1; in vitro- S. coelicolor gene expressed in E. coli; pH 7.5, 47C. Cane2001
Km Forward DXP 47.1 µM 64 from Mycobacterium tuberculosis, expressed in E. coli, pH 7.9, 30C Dhiman2005, Br674260
Km Forward DXP 147.2 µM 8 from Coleus forskohlii (now known as Plectranthus barbatus), expressed in E. coli; pH 8.0, 37C, BRENDA_lit: 676660 Engpraset2005
Km Forward DXP 170 µM 16 dxr gene from Synechocystis sp. PCC6803 cloned into E. coli. pH 7.8, 37C, BRENDA_lit:671590 Fernandes2005, Br671590
Km Forward DXP 45 µM 32 from E. coli, pH 7.6, 37C, recombinant enzyme Fox2005, BR672040
Km Forward DXP 300 µM 16 gene from Zymomonas mobilis, expressed in E. coli, 40C, pH 8.0, Grolle2000, Br286424
Km Forward DXP 340 µM 32 Gene MtDXRfrom Mycobacterium tuberculosis, room temperature (20-22C), pH7.5 Henriksson2006, Br671075
Km Forward DXP 73 µM 32 gene from E. coli, pH 7.7, 37C, with the presence of 1mM MnCl2 and 3mM MgCl2 Hoeffler2002, Br655439
Km Forward DXP 97 µM 32 gene from E. coli, pH 7.7, 37C, with the presence of 1mM MnCl2 and 3mM MgCl2 Hoeffler2002, Br655439
Km Forward DXP 103.7 µM 16 gene from Francisella tularensis, expressed in E. coli, pH8, 22C Jawaid2009, Br713353
Km Forward DXP 250 µM 32 from E. coli, with MnCl2, wild-type enzyme, pH 7.0-8.5, temp >37C (40-60C) Kuzuyama2000, Br286428
Km Forward DXP 99 µM 32 from E. coli, with MgCl2, wild-type enzyme, pH 7.0-8.5, temp >37C (40-60C) Kuzuyama2000, Br286428
Km Forward DXP 60 µM 32 from E. coli, with CoCl2, wild-type enzyme, pH 7.0-8.5, temp >37C (40-60C) Kuzuyama2000, Br286428
Km Forward DXP 115 µM 32 gene MtDXR from Mycobacterium tuberculosis, expressed in E. coli, pH 7.5, 25C. Experimental result, see Table 1. Liu2012, BR724346
Km Forward DXP 132 µM 8 The ispC gene from Arabidopsis thaliana, expressed in E. coli, pH 8.0, 37C Rohdich2006, Br673562
Km Forward DXP 40 µM 32 50C. from Thermotoga maritima. Kinetics were measured at different temperature: 50C and 85C, expressed in E. coli, pH 7.5, 50C. Takenoya2010, Br712892
Km Forward DXP 110 µM 32 85C. from Thermotoga maritima. Kinetics were measured at different temperature: 50C and 85C, expressed in E. coli, pH 7.5, 50C. Takenoya2010, Br712892
Km Forward DXP 81 µM 32 from E. coli, pH7.6, 37C Walker2005
Km Forward DXP 310 µM 16 from E. coli, ph and temp not mentioned. Reference to method also not mentioned specifically. Wong2007, Br684434
Km Forward DXP 195 µM 32 from Synechocystis sp. PCC6803, expressed in E. coli, pH7.5, 37C, with three metal ions, Mn2+, Mg2+, Co2+ Yin2003, Br654877
Km Forward DXP 134 µM 32 from Synechocystis sp. PCC6803, expressed in E. coli, pH7.5, 37C, with three metal ions, Mn2+, Mg2+, Co2+ Yin2003, Br654877
Km Forward DXP 63 µM 32 from Synechocystis sp. PCC6803, expressed in E. coli, pH7.5, 37C, with three metal ions, Mn2+, Mg2+, Co2+ Yin2003, Br654877


DXR Kmnadph.png
Parameter Direction Substrate Value Unit Weight Description Reference
Km Forward NADPH 5 µM 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. BRENDA_lit: 654748, Argyrou2004, Br654748
Km Forward NADPH 3.3 µM 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. BRENDA_lit: 654748, Argyrou2004, Br654748
Km Forward NADPH 0.4 µM 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. BRENDA_lit: 654748, Argyrou2004, Br654748
Km Forward NADPH 190 µM 128 DXPS1; in vitro- S. coelicolor gene expressed in E. coli; pH 7.5, 47C. Cane2001
Km Forward NADPH 29.7 µM 64 from Mycobacterium tuberculosis, expressed in E. coli, pH 7.9, 30C Dhiman2005, Br674260
Km Forward NADPH 3.5 µM 16 dxr gene from Synechocystis sp. PCC6803 cloned into E. coli. pH 7.8, 37C, BRENDA_lit:671590 Fernandes2005, Br671590
Km Forward NADPH 0.5 µM 32 from E. coli, pH 7.6, 37C, recombinant enzyme Fox2005, BR672040
Km Forward NADPH 5 µM 16 gene from Zymomonas mobilis, expressed in E. coli, 40C, pH 8.0, Grolle2000, Br286424
Km Forward NADPH 7.2 µM 32 Gene MtDXRfrom Mycobacterium tuberculosis, room temperature (20-22C), pH7.5 Henriksson2006, Br671075
Km Forward NADPH 13.3 µM 16 gene from Francisella tularensis, expressed in E. coli, pH8, 22C Jawaid2009, Br713353
Km Forward NADPH 7.4 µM 32 from E. coli, with MnCl2, wild-type enzyme, pH 7.0-8.5, temp >37C (40-60C) Kuzuyama2000, Br286428
Km Forward NADPH 18 µM 32 from E. coli, with MgCl2, wild-type enzyme, pH 7.0-8.5, temp >37C (40-60C) Kuzuyama2000, Br286428
Km Forward NADPH 8.8 µM 32 from E. coli, with CoCl2, wild-type enzyme, pH 7.0-8.5, temp >37C (40-60C) Kuzuyama2000, Br286428
Km Forward NADPH 9.8 µM 32 gene MtDXR from Mycobacterium tuberculosis, expressed in E. coli, pH 7.5, 25C. Experimental result, see Table 1. Liu2012, BR724346
Km Forward NADPH 30 µM 8 The ispC gene from Arabidopsis thaliana, expressed in E. coli, pH 8.0, 37C Rohdich2006, Br673562
Km Forward NADPH 2.8 µM 32 50C.from Thermotoga maritima. Kinetics were measured at different temperature: 50C and 85C, expressed in E. coli, pH 7.5, 50C. Takenoya2010, Br712892
Km Forward NADPH 10.5 µM 32 85C. from Thermotoga maritima. Kinetics were measured at different temperature: 50C and 85C, expressed in E. coli, pH 7.5, 50C. Takenoya2010, Br712892
Km Forward NADPH 3.3 µM 32 from Synechocystis sp. PCC6803, expressed in E. coli, pH7.5, 37C, with three metal ions, Mn2+, Mg2+, Co2+ Yin2003, Br654877
Km Forward NADPH 5 µM 32 from Synechocystis sp. PCC6803, expressed in E. coli, pH7.5, 37C, with three metal ions, Mn2+, Mg2+, Co2+ Yin2003, Br654877


DXR Kmmep.png
Parameter Direction Substrate Value Unit Weight Description Reference
Km Reverse MEP 42 µM 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. And NADPH /NADH BRENDA_lit: 654748, Argyrou2004, Br654748
Km Reverse MEP 174 µM 64 from Mycobacterium tuberculosis, expressed in E. coli, pH 7.9, 30C Dhiman2005, Br674260
Km Reverse MEP 294 µM 32 gene from E. coli, pH 7.7, 37C, with the presence of 1mM MnCl2 and 3mM MgCl2 Hoeffler2002, Br655439
Km Reverse MEP 158 µM 32 gene from E. coli, pH 7.7, 37C, with the presence of 1mM MnCl2 and 3mM MgCl2 Hoeffler2002, Br655439
Km Reverse MEP 84 µM 32 gene MtDXR from Mycobacterium tuberculosis, expressed in E. coli, pH 7.5, 25C. Experimental result, see Table 1. Liu2012, BR724346
Km Forward MEP 972 µM 8 The ispC gene from Arabidopsis thaliana, expressed in E. coli, pH 8.0, 37C Rohdich2006, Br673562


DXR Kmnadp.png
Parameter Direction Substrate Value Unit Weight Description Reference
Km Reverse NADP 170 µM 64 from Mycobacterium tuberculosis, transformed into competent E. coli BL21 (DE3) cells. pH7.5, 25C, using three different cofactors Mg2+, Mn2+ and Co2+. And NADPH /NADH BRENDA_lit: 654748, Argyrou2004, Br654748
Km Reverse NADP 560.5 µM 64 from Mycobacterium tuberculosis, expressed in E. coli, pH 7.9, 30C Dhiman2005, Br674260
Km Reverse NADP 420 µM 32 gene MtDXR from Mycobacterium tuberculosis, expressed in E. coli, pH 7.5, 25C. Experimental result, see Table 1. Liu2012, BR724346
Km Forward NADP 471 µM 8 The ispC gene from Arabidopsis thaliana, expressed in E. coli, pH 8.0, 37C Rohdich2006, Br673562

References

  1. ↑ Hanekom, A. J. 2006. "Generic kinetic equations for modelling multisubstrate reactions in computational systems biology", MSc Thesis submitted at the University of Stellenbosch
  2. ↑ Sauro, H.M. "Enzyme kinetics for systems biology"
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