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Team:Tokyo Tech/Modeling/Urea-cooler/method
From 2011.igem.org
Method
We considered 25 enzymatic reactions that affect the urea cycle as shown in Table 1 to build the model.
| Enzyme | Reaction formula | Enzyme number |
|---|---|---|
| OTC | carbamoyl phosphate + L-ornithine → L-citrulline + Pi | EC: 2.1.3.3 (argF,argI) |
| ASS | L-citrulline + L-aspartate + ATP → N-(L-arginino)succinate + AMP + PPi | EC: 6.3.4.5 (argG) |
| ASL | N-(L-arginino)succinate → fumarate + L-arginine | EC: 4.3.2.1 (argH) |
| ARG | L-arginine + H2O → L-ornithine + urea | EC: 3.5.3.1 (rocF) |
| CPS | L-glutamine + HCO3- + H2O + 2ATP → L-glutamate + carbamoyl phosphate + 2ADP + Pi | EC: 6.3.5.5 |
| GOGAT | L-glutamine + 2-oxoglutarate + NADPH + H+ → 2 L-glutamate + NADP+ | EC: 1.4.1.13 |
| GS | L-glutamate + NH3 + ATP → L-glutamine + ADP + Pi | EC: 6.3.1.2 |
| GLU | L-glutamine + H2O = L-glutamate + NH3 | EC: 3.5.1.2 |
| GDH | 2-oxoglutarate + NH3 + NADPH + H+ = L-glutamate + NADP+ + H2O | EC: 1.4.1.4 |
| AAA | acetyl-CoA + L-glutamate → CoASH + N-acetyl-L-glutamate | EC: 2.3.1.1 (argA) |
| AGK | N-acetyl-L-glutamate + ATP → N-acetyl-L-glutamate 5-phosphate + ADP | EC: 2.7.2.8 (argB) |
| AGPR | N-acetyl-L-glutamate 5-phosphate + NADPH + H+ → N-acetyl-L-glutamate 5-semialdehyde + NADP+ + Pi | EC: 1.2.1.38 (argC) |
| AOT | N-acetyl-L-glutamate 5-semialdehyde + L-glutamate → N-acetylornithine + 2-oxoglutarate | EC: 2.6.1.11 (argD) |
| AO | N-acetylornithine + H2O → L-ornithine + acetate | EC: 3.5.1.16 (argE) |
| FH | fumarate + H2O → L-malate | EC: 4.2.1.2 |
| MDH | L-malate + NAD+ → oxaloacetate + NADH + H+ | EC: 1.1.1.37 |
| AST | oxaloacetate + L-glutamate = L-asparate + 2-oxoglutarate | EC: 2.6.1.1 |
| CS | acetyl-CoA + oxaloacetate + H2O → citrate + CoASH | EC: 2.3.3.1 |
| AH | citrate → isocitrate | EC: 4.2.1.3 |
| IDH | isocitrate + NADP+ → 2-oxoglutarate + NADPH + H+ + CO2 | EC: 1.1.1.42 |
| OGDH | 2-oxoglutarate + Enzyme N6-(lipoyl)lysine → [dihydrolipoyllysine-residue succinyl transferase]S-succinyldihydrolopiyllysine + CO2 |
EC: 1.2.4.2 |
| DST | [dihydrolipoyllysine-residue succinyl transferase]S-succinyldihydrolopiyllysine +CoASH → succinyl-CoA + Enzyme N6-(dihydrolipoyl)lysine |
EC: 2.3.1.61 |
| E3 | Enzyme N6-(dihydrolipoyl)lysine + NAD+ = Enzyme N6-(lipoyl)lysine + NADH + H | EC: 1.8.1.4 |
| SCS | succinate + ADP + Pi → succinate + CoASH + ATP | EC: 6.2.1.5 |
| SDH | succinate + FAD → fumarate + CoASH + FADH2 | EC: 1.3.99.1 |
