Extended Data Table 3|.
NAD+ kinetic parameters for hUGDHa
| hUGDH |
Km (NAD+, mM) |
K0.5b (NAD+, mM) |
Hill (h) |
Kcatc (S-1) |
UDX (Ki, μM) |
αnadd | # of Data Pointse |
|---|---|---|---|---|---|---|---|
| FL | ------------- | 0.8 ± 0.20 | 0.8 ± 0.1 | 0.9 ± 0.08 | ------------- | ------------- | 18 |
| ΔID | ------------- | 0.3 ±0.06 | 0.6 ± 0.1 | 0.7 ±0.03 | ------------- | ------------- | 12 |
| FL-dimer | 2.0 ± 0.26 | ------------- | ------------- | 0.1 ± 0.01 | 2.1 ±0.4 | 0.9 ±0.2 | 37 |
| ΔID-dimer | 3.2 ±0.10 | ------------- | ------------- | 0.2 ±0.01 | 3.6 ±0.8 | 0.6 ±0.2 | 47 |
| R1 | ------------- | 0.4 ± 0.03 | 0.9 ±0.1 | 0.7 ±0.01 | ------------- | ------------- | 17 |
| R2 | ------------- | 0.8 ±0.14 | 0.7 ± 0.1 | 0.7 ±0.01 | ------------- | ------------- | 15 |
| −Lys | ------------- | 2.9 ±0.61 | 0.8 ± 0.1 | 0.6 ±0.04 | ------------- | ------------- | 10 |
| −Pro | ------------- | 0.5 ±0.06 | 0.6 ± 0.1 | 1.2 ±0.03 | ------------- | ------------- | 12 |
| 0.13×FL | ------------- | 0.4 ±0.03 | 0.7 ± 0.1 | 1.0 ±0.03 | ------------- | ------------- | 13 |
| 0.26×FL | ------------- | 0.2 ± 0.03 | 0.8 ± 0.2 | 0.8 ±0.05 | ------------- | ------------- | 11 |
| 0.5×FL | ------------- | 0.3 ±0.03 | 0.9 ±0.1 | 0.9 ±0.02 | ------------- | ------------- | 12 |
| 2×FL | ------------- | 1.4 ±0.31 | 0.8 ±0.1 | 0.9 ±0.01 | ------------- | ------------- | 18 |
| 0.13×Ser | ------------- | 0.9 ±0.24 | 0.7 ±0.1 | 1.2 ±0.10 | ------------- | ------------- | 12 |
| 0.26×Ser | ------------- | 1.0 ± 0.27 | 0.7 ± 0.1 | 1.1 ± 0.09 | ------------- | ------------- | 15 |
| 0.5×Ser | ------------- | 1.2 ±0.34 | 0.7 ± 0.1 | 1.1 ± 0.09 | ------------- | ------------- | 13 |
| Ser | 1.3 ± 0.19 | 0.7 ± 0.1 | 1.0 ± 0.04 | ------------- | ------------- | 13 | |
Kinetic parameters and associated standard errors (±) for all constructs were derived from global analyses of data in Extended Data Fig. 2
Hexameric hUGDH displays negative cooperativity with NAD+ binding, which indicates a mix of high affinity and low affinity sites23–28. In previous work, we showed that the native hUGDHFL K0.5 of 0.8 mM NAD+ corresponds to a mix of high and low affinity sites of (KM of 88 μM and 1.8 mM, respectively)23. This is consistent with the published Kd of 30 μM for the coenzyme24.
One catalytic turnover of UDP-GlcA produces two molecules of NADH per cycle
α describes the mode of mixed inhibition (Equation 8). An α < 1 in the NAD+ saturation curves show that UDP-Xyl binds preferentially to the allosteric binding, and secondarily to the coenzyme binding site.
The number of independent data points used in nonlinear regression (see Methods).