Difference between revisions of "DXR"

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| 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 ||  
 
| 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 ||  
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[[File:DXR_Kmnadph.png | left |600px ]]
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{|class="wikitable"
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! Parameter
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! Direction
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! Substrate
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! Value
 +
! Unit
 +
! Weight
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! Description
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! Reference
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|-
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| 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
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| 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
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| 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
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|-
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| Km || Forward || NADPH || 190 || µM || 128 || DXPS1; in vitro- S. coelicolor gene expressed in E. coli; pH 7.5, 47C.  || Cane2001
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| Km || Forward || NADPH || 29.7 || µM || 64 || from Mycobacterium tuberculosis, expressed in E. coli, pH 7.9, 30C || Dhiman2005, Br674260
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| 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
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| Km || Forward || NADPH || 0.5 || µM || 32 || from E. coli, pH 7.6, 37C, recombinant enzyme || Fox2005, BR672040
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| Km || Forward || NADPH || 5 || µM || 16 || gene from Zymomonas mobilis, expressed in E. coli, 40C, pH 8.0,  || Grolle2000, Br286424
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| Km || Forward || NADPH || 7.2 || µM || 32 || Gene MtDXRfrom Mycobacterium tuberculosis, room temperature (20-22C), pH7.5 || Henriksson2006, Br671075
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| Km || Forward || NADPH || 13.3 || µM || 16 || gene from Francisella tularensis, expressed in E. coli,  pH8, 22C || Jawaid2009, Br713353
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| 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
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| 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
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| 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
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|-
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| 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
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|-
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| Km || Forward || NADPH || 30 || µM || 8 || The ispC gene from Arabidopsis thaliana, expressed in E. coli, pH 8.0, 37C || Rohdich2006, Br673562
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|-
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| 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
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| 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
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|-
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| 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
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|-
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| 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
 
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Revision as of 16:38, 23 March 2017

You can go back to main page of the kinetic model here.


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 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

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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