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Table 2 Reaction-specific kinetic parameters used in kinetic modeling

From: Identification of novel metabolic interactions controlling carbon flux from xylose to ethanol in natural and recombinant yeasts

CtXRa NAD(H) (R 1) NADP(H) (R 2)
E POb POb
V f 1.0 1.3
V f/V r 13 25
K iA (mM) 0.18 ± 0.04 0.0019 ± 0.0001c
K mA (mM) 0.04 ± 0.01 0.005 ± 0.002
K mB (mM) 98 ± 22 108 ± 17
K iB (mM)d 392 3920
K iQ (mM) 0.344 ± 0.03 0.0059 ± 0.0004c
K mQ (mM) 0.019 ± 0.005 0.008 ± 0.001
K mP (mM) 529 ± 34 220 ± 18
K iP (mM) 758 ± 48 556 ± 48
K Haldane, eeq 134 142
K exp, eeq 142 156
GmXDHf(R 3)   PP (R 5), UG (R 9), LG (R 10)  
E POb V f POb
V f 1.0 K m (mM) 0.1
V r 12.6   
\({K_{\rm{m,NAD}^{+}}}\) (mM) 0.14 PGIh (R 6)  
K m,xylitol (mM) 14  V f POb
\({K_{\rm{i,NAD}^{+}}}\) (mM) 0.78  K m,F6P (mM) 0.15
K i,xylitol (mM)d 4.5  K m,G6P (mM) 0.30
K i,NADH (mM) 0.025  K eq 3.23
K m,NADH (mM) 0.073   
K m,xylulose (mM) 4.0 G6PDH (R 7)  
K i,xylulose (mM)g 1.0  V f POb
K Haldane, eeq 7 × 10−4  \({K_{\rm{m,NADP}^{+}}}\) (mM) 0.1
K exp, eeq (4-7) × 10−4  K hm,G6P (mM) 0.05
    K i,NADPH (mM) 0.20 (0.05)i
XK (R 4)    
 V f POb GND (R 8)  
 K m,xylulose (mM)h 0.31  V f POb
    K +m,NADP (mM) 0.02
    K hm,6PG (mM) 0.05
    K i,NADPH (mM) 0.02
  1. aA, B, P, Q relate to NAD(P)H, xylose, xylitol, and NAD(P)+, respectively
  2. bPO, values were found within a predefined range by parameter optimization (see main text and Additional file 1: Table S3)
  3. cValues obtained from ligand-binding analysis using fluorescence spectroscopy (this study)
  4. dValues calculated from Haldane relationship K eq = V 2f K iP K mQ/(V 2r K iB K mA) [38]
  5. eEquilibrium constants were calculated in accordance with the Haldane relationship [K Haldaneeq  = V f K mP K iQ/(V r K mB K iA)] [38]. Values can be compared to those experimentally obtained in this study (CtXR) or to reported K expeq [39, 40]. Calculated Gibbs free energies of reaction of 6 ± 1 kJ mol−1 for the isomerization of xylose into xylulose [ΔG r = −RTln(K HaldaneeqXR K HaldaneeqXDH ] or ΔG r = −RTln(K expeqXR K expeqXDH ) are in excellence accordance with a value of 4.3 kJ mol−1 calculated from standard transformed Gibbs free energies of formation [41]
  6. fReported kinetic parameters obtained from comprehensive full-kinetic study acquired at 25 °C in 50 mM potassium phosphate buffer pH 7.5 were applied [42]. A, B, P, and Q correspond to NAD+, xylitol, xylulose, and NADH, respectively. Note, to fulfill thermodynamic with respect to K expeq reported upper limits were used for V r (1800 ± 350 s−1), K B (12 ± 2 mM) and lower limits for K P (8 ± 4 mM)
  7. gValue was taken from [43]
  8. hValues of kinetic parameters for XK, G6PDH, 6PGDH, and PGI were from Refs. [33, 4446], respectively
  9. iValue referred to CBS4435 (BP000). Note based on a sensitivity analysis implemented in Copasi K i of both ScG6PDH and CtG6PDH did not significantly influence FCC and YCC