Team:Tokyo Tech/Modeling/Urea-cooler/method

From 2011.igem.org

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<h1> Method </h1>
<h1> Method </h1>
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<p>We considered 25 enzymatic reactions that affect the urea cycle as shown in Table 1 to build the model.
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<p>We considered 25 enzymatic reactions that affect the urea cycle as shown in Table 1 to build the model.<br />
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<table border="1">
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<caption>Table 1 25 enzymatic reactions we considered when we built the model.</caption>
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<tr>
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<th>Enzyme</th>
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<th>Reaction formula</th>
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<th>Enzyme number</th>
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</tr>
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<tr>
 +
<td>OTC</td>
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<td>carbamoyl phosphate + L-ornithine → L-citrulline + Pi</td>
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<td>EC: 2.1.3.3 (argF,argI)</td>
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</tr>
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<tr>
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<td>ASS</td>
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<td>L-citrulline + L-aspartate + ATP → N-(L-arginino)succinate + AMP + PPi</td>
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<td>EC: 6.3.4.5 (argG)</td>
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</tr>
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<tr>
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<td>ASL</td>
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<td>N-(L-arginino)succinate → fumarate + L-arginine</td>
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<td>EC: 4.3.2.1 (argH)</td>
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</tr>
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<tr>
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<td>ARG</td>
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<td>L-arginine + H2O → L-ornithine + urea</td>
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<td>EC: 3.5.3.1 (rocF)</td>
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</tr>
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<tr>
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<td>CPS</td>
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<td>L-glutamine + HCO3- + H2O + 2ATP → L-glutamate + carbamoyl phosphate + 2ADP + Pi</td>
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<td>EC: 6.3.5.5</td>
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</tr>
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<tr>
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<td>GOGAT</td>
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<td>L-glutamine + 2-oxoglutarate + NADPH + H+ → 2 L-glutamate + NADP+</td>
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<td>EC: 1.4.1.13</td>
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</tr>
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<tr>
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<td>GS</td>
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<td>L-glutamate + NH3 + ATP → L-glutamine + ADP + Pi</td>
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<td>EC: 6.3.1.2</td>
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</tr>
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<tr>
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<td>GLU</td>
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<td>L-glutamine + H2O = L-glutamate + NH3</td>
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<td>EC: 3.5.1.2</td>
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</tr>
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<tr>
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<td>GDH</td>
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<td>2-oxoglutarate + NH3 + NADPH + H+ = L-glutamate + NADP+ + H2O</td>
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<td>EC: 1.4.1.4</td>
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</tr>
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<tr>
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<td>AAA</td>
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<td>acetyl-CoA + L-glutamate → CoASH + N-acetyl-L-glutamate</td>
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<td>EC: 2.3.1.1 (argA)</td>
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</tr>
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<tr>
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<td>AGK</td>
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<td>N-acetyl-L-glutamate + ATP → N-acetyl-L-glutamate 5-phosphate + ADP</td>
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<td>EC: 2.7.2.8 (argB)</td>
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</tr>
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<tr>
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<td>AGPR</td>
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<td>N-acetyl-L-glutamate 5-phosphate + NADPH + H+ → N-acetyl-L-glutamate 5-semialdehyde + NADP+ + Pi</td>
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<td>EC: 1.2.1.38 (argC)</td>
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</tr>
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<tr>
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<td>AOT</td>
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<td>N-acetyl-L-glutamate 5-semialdehyde + L-glutamate → N-acetylornithine + 2-oxoglutarate</td>
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<td>EC: 2.6.1.11 (argD)</td>
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</tr>
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<tr>
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<td>AO</td>
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<td>N-acetylornithine + H2O → L-ornithine + acetate</td>
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<td>EC: 3.5.1.16 (argE)</td>
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</tr>
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<tr>
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<td>FH</td>
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<td>fumarate + H2O → L-malate</td>
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<td>EC: 4.2.1.2</td>
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</tr>
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<tr>
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<td>MDH</td>
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<td>L-malate + NAD+ → oxaloacetate + NADH + H+</td>
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<td>EC: 1.1.1.37</td>
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</tr>
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<tr>
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<td>AST</td>
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<td>oxaloacetate + L-glutamate = L-asparate + 2-oxoglutarate</td>
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<td>EC: 2.6.1.1</td>
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</tr>
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<tr>
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<td>CS</td>
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<td>acetyl-CoA + oxaloacetate + H2O → citrate + CoASH</td>
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<td>EC: 2.3.3.1</td>
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</tr>
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<tr>
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<td>AH</td>
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<td>citrate → isocitrate</td>
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<td>EC: 4.2.1.3</td>
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</tr>
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<tr>
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<td>IDH</td>
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<td>isocitrate + NADP+ → 2-oxoglutarate + NADPH + H+ + CO2</td>
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<td>EC: 1.1.1.42</td>
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</tr>
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<tr>
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<td>OGDH</td>
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<td>2-oxoglutarate + Enzyme N6-(lipoyl)lysine <br />→ [dihydrolipoyllysine-residue succinyl transferase]S-succinyldihydrolopiyllysine + CO2</td>
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<td>EC: 1.2.4.2</td>
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</tr>
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<tr>
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<td>DST</td>
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<td>[dihydrolipoyllysine-residue succinyl transferase]S-succinyldihydrolopiyllysine +CoASH <br />→ succinyl-CoA + Enzyme N6-(dihydrolipoyl)lysine</td>
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<td>EC: 2.3.1.61</td>
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</tr>
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<tr>
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<td>E3</td>
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<td>Enzyme N6-(dihydrolipoyl)lysine + NAD+ = Enzyme N6-(lipoyl)lysine + NADH + H</td>
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<td>EC: 1.8.1.4</td>
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</tr>
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<tr>
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<td>SCS</td>
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<td>succinate + ADP + Pi → succinate + CoASH + ATP</td>
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<td>EC: 6.2.1.5</td>
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</tr>
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<tr>
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<td>SDH</td>
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<td>succinate + FAD → fumarate + CoASH + FADH2</td>
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<td>EC: 1.3.99.1</td>
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</tr>
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</table>
</p>
</p>

Revision as of 09:50, 4 October 2011

Tokyo Tech 2011

Tokyo Tech 2011

Method

We considered 25 enzymatic reactions that affect the urea cycle as shown in Table 1 to build the model.

Table 1 25 enzymatic reactions we considered when we built 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

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