Difference between revisions of "Nucleosid diphosphate kinase"
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'''Nucleoside-diphosphate kinase'''s are enzymes that catalyze the exchange of phosphate groups between different nucleotides. The overall effect of NDKs is to transfer a phosphate group from a nucleoside triphosphate to a nucleoside diphosphate. Starting with ATP and UDP, the activity of NDK produces ADP and UTP. | '''Nucleoside-diphosphate kinase'''s are enzymes that catalyze the exchange of phosphate groups between different nucleotides. The overall effect of NDKs is to transfer a phosphate group from a nucleoside triphosphate to a nucleoside diphosphate. Starting with ATP and UDP, the activity of NDK produces ADP and UTP. | ||
Revision as of 16:10, 13 May 2014
Nucleoside-diphosphate kinases are enzymes that catalyze the exchange of phosphate groups between different nucleotides. The overall effect of NDKs is to transfer a phosphate group from a nucleoside triphosphate to a nucleoside diphosphate. Starting with ATP and UDP, the activity of NDK produces ADP and UTP.
Contents
Chemical equation
![ATP + UDP \leftrightarrow ADP + UTP](/wiki/images/math/0/f/4/0f49c3d951b5d9c66138c0747bc83c4a.png)
Rate equation
Random order Bi-Bi rate law is used from [1]
![\frac{ \frac{V_{max}}{K_m^{ATP}K_m^{UDP}}\left( [ATP][UDP] - \frac{[ADP][UTP]}{K_{eq}} \right) } { \left( 1 + \frac{[ATP]}{K_{m}^{ATP}} \right)\left( 1 + \frac{[UDP]}{K_{m}^{UDP}} \right) + \left( 1 + \frac{[ADP]}{K_{m}^{ADP}} \right)\left( 1 + \frac{[UTP]}{K_{m}^{UTP}} \right) -1 }](/wiki/images/math/9/e/6/9e6a0b14129bad329a3c09d3c7a69f43.png)
Parameter values
- A mean body weight is defined as 75Kg in Konig et. al [1]. The
is calculated by multiplying the reported value with body weight.
Parameter | Value | Units | Organism | Remarks |
---|---|---|---|---|
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Human Liver | |
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mM | Rat liver | |
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mM | Rat liver | |
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mM | Rat tissue | |
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mM | Rat liver | |
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Dimensionless |
Parameters with uncertainty
- In the paper by Walter (1980) et. al. [3] two values of
,
and
have been reported; one for cytosolic kinase and the other for membrane-associated kinase. As in our model we are not differentiating between cytosolic and membrane-associated kinase, we would consider both those values and calculate the uncertainty from them.
- Similarly two values of
has been reported in Fukuchi (1994) et. al. [4]; for
kinase and
kinase. Taking average of those kinase gives a value of
- Two values of
is also reported in Fukuchi (1994) et. al. [4]; 126 (4.20
multiplied with 30 mg) and 138 (4.60
multiplied with 30 mg)
. Taking average gives
.
- Standard free energy
is reported to be zero kJ/mol. Therefore the value of Keq is assumed to be constant.
Parameter | Value | Units | Organism | Remarks |
---|---|---|---|---|
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Rat lever | |
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mM | ||
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mM | ||
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mM | ||
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mM | ||
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Dimensionless |
References
- ↑ 1.0 1.1 M. König, S. Bulik, H.G. Holzhütter (2012), Quantifying the contribution of the liver to glucose homeostasis: a detailed kinetic model of human hepatic glucose metabolism, PLoS Comput. Biol., 8 (6), p. e1002577
- ↑ Villar-Palasi C & Larner J (1960). Levels of activity of the enzymes of the glycogen cycle in rat tissues. Arch Biochem Biophys 86, 270–273.
- ↑ 3.0 3.1 3.2 3.3 Walter P and Blobel G. (1980), Purification of a membrane-associated protein complex required for protein translocation across the endoplasmic reticulum, Proc. Natl. Acad. Sci. 77:7112-7116
- ↑ 4.0 4.1 4.2 Fukuchi, T., Shimada, N., Hanai, N., Ishikawa, N., Watanabe, K., and Kimura, N. (1994) Recombinant rat nucleoside diphosphate kinase isoforms (
and
): purification, properties and application to immunological detection of native isoforms in rat tissues. Biochim. Biophys. Acta 1205, 113–122