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

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<h1> Urea Modeling : Tables </h1>
<h1> Urea Modeling : Tables </h1>
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<p>
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<div align="center">
<div align="center">
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<table border="1">
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<table border="1" id="table3">
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<caption>Table 1 25 enzymatic reactions we considered when we built the model.</caption>
+
<caption>
 +
Table 3 25 enzymatic reactions we considered when we built the model.
 +
</caption>
<tr>
<tr>
<th>Enzyme</th>
<th>Enzyme</th>
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<tr>
<tr>
<td>OTC</td>
<td>OTC</td>
-
<td>carbamoyl phosphate + L-ornithine → L-citrulline + Pi</td>
+
<td>carbamoyl phosphate + L-ornithine &rarr; L-citrulline + Pi</td>
-
<td>EC: 2.1.3.3 (argF,argI)</td>
+
<td>EC: 2.1.3.3 (<span class="gene">argF</span>,<span class="gene">argI</span>)</td>
</tr>
</tr>
<tr>
<tr>
<td>ASS</td>
<td>ASS</td>
-
<td>L-citrulline + L-aspartate + ATP → N-(L-arginino)succinate + AMP + PPi</td>
+
<td>L-citrulline + L-aspartate + ATP &rarr; N-(L-arginino)succinate + AMP + PPi</td>
-
<td>EC: 6.3.4.5 (argG)</td>
+
<td>EC: 6.3.4.5 (<span class="gene">argG</span>)</td>
</tr>
</tr>
<tr>
<tr>
<td>ASL</td>
<td>ASL</td>
-
<td>N-(L-arginino)succinate → fumarate + L-arginine</td>
+
<td>N-(L-arginino)succinate &rarr; fumarate + L-arginine</td>
-
<td>EC: 4.3.2.1 (argH)</td>
+
<td>EC: 4.3.2.1 (<span class="gene">argH</span>)</td>
</tr>
</tr>
<tr>
<tr>
<td>ARG</td>
<td>ARG</td>
-
<td>L-arginine + H2O → L-ornithine + urea</td>
+
<td>L-arginine + H<sub>2</sub>O &rarr; L-ornithine + urea</td>
-
<td>EC: 3.5.3.1 (rocF)</td>
+
<td>EC: 3.5.3.1 (<span class="gene">rocF</span>)</td>
</tr>
</tr>
<tr>
<tr>
<td>CPS</td>
<td>CPS</td>
-
<td>L-glutamine + HCO3- + H2O + 2ATP → L-glutamate + carbamoyl phosphate + 2ADP + Pi</td>
+
<td>L-glutamine + HCO<sub>3</sub><sup>-</sup> + H<sub>2</sub>O + 2ATP &rarr; L-glutamate + carbamoyl phosphate + 2ADP + Pi</td>
<td>EC: 6.3.5.5</td>
<td>EC: 6.3.5.5</td>
</tr>
</tr>
<tr>
<tr>
<td>GOGAT</td>
<td>GOGAT</td>
-
<td>L-glutamine + 2-oxoglutarate + NADPH + H+ → 2 L-glutamate + NADP+</td>
+
<td>L-glutamine + 2-oxoglutarate + NADPH + H<sup>+</sup> &rarr; 2 L-glutamate + NADP<sup>+</sup></td>
<td>EC: 1.4.1.13</td>
<td>EC: 1.4.1.13</td>
</tr>
</tr>
<tr>
<tr>
<td>GS</td>
<td>GS</td>
-
<td>L-glutamate + NH3 + ATP → L-glutamine + ADP + Pi</td>
+
<td>L-glutamate + NH<sub>3</sub> + ATP &rarr; L-glutamine + ADP + Pi</td>
<td>EC: 6.3.1.2</td>
<td>EC: 6.3.1.2</td>
</tr>
</tr>
<tr>
<tr>
<td>GLU</td>
<td>GLU</td>
-
<td>L-glutamine + H2O = L-glutamate + NH3</td>
+
<td>L-glutamine + H<sub>2</sub>O = L-glutamate + NH<sub>3</sub></td>
<td>EC: 3.5.1.2</td>
<td>EC: 3.5.1.2</td>
</tr>
</tr>
<tr>
<tr>
<td>GDH</td>
<td>GDH</td>
-
<td>2-oxoglutarate + NH3 + NADPH + H+ = L-glutamate + NADP+ + H2O</td>
+
<td>2-oxoglutarate + NH<sub>3</sub> + NADPH + H<sup>+</sup> = L-glutamate + NADP<sup>+</sup> + H<sub>2</sub>O</td>
<td>EC: 1.4.1.4</td>
<td>EC: 1.4.1.4</td>
</tr>
</tr>
<tr>
<tr>
<td>AAA</td>
<td>AAA</td>
-
<td>acetyl-CoA + L-glutamate → CoASH + N-acetyl-L-glutamate</td>
+
<td>acetyl-CoA + L-glutamate &rarr; CoASH + N-acetyl-L-glutamate</td>
-
<td>EC: 2.3.1.1 (argA)</td>
+
<td>EC: 2.3.1.1 (<span class="gene">argA</span>)</td>
</tr>
</tr>
<tr>
<tr>
<td>AGK</td>
<td>AGK</td>
-
<td>N-acetyl-L-glutamate + ATP → N-acetyl-L-glutamate 5-phosphate + ADP</td>
+
<td>N-acetyl-L-glutamate + ATP &rarr; N-acetyl-L-glutamate 5-phosphate + ADP</td>
-
<td>EC: 2.7.2.8 (argB)</td>
+
<td>EC: 2.7.2.8 (<span class="gene">argB</span>)</td>
</tr>
</tr>
<tr>
<tr>
<td>AGPR</td>
<td>AGPR</td>
-
<td>N-acetyl-L-glutamate 5-phosphate + NADPH + H+ → N-acetyl-L-glutamate 5-semialdehyde + NADP+ + Pi</td>
+
<td>N-acetyl-L-glutamate 5-phosphate + NADPH + H<sup>+</sup> &rarr; N-acetyl-L-glutamate 5-semialdehyde + NADP<sup>+</sup> + Pi</td>
-
<td>EC: 1.2.1.38 (argC)</td>
+
<td>EC: 1.2.1.38 (<span class="gene">argC</span>)</td>
</tr>
</tr>
<tr>
<tr>
<td>AOT</td>
<td>AOT</td>
-
<td>N-acetyl-L-glutamate 5-semialdehyde + L-glutamate → N-acetylornithine + 2-oxoglutarate</td>
+
<td>N-acetyl-L-glutamate 5-semialdehyde + L-glutamate &rarr; N-acetylornithine + 2-oxoglutarate</td>
-
<td>EC: 2.6.1.11 (argD)</td>
+
<td>EC: 2.6.1.11 (<span class="gene">argD</span>)</td>
</tr>
</tr>
<tr>
<tr>
<td>AO</td>
<td>AO</td>
-
<td>N-acetylornithine + H2O → L-ornithine + acetate</td>
+
<td>N-acetylornithine + H<sub>2</sub>O &rarr; L-ornithine + acetate</td>
-
<td>EC: 3.5.1.16 (argE)</td>
+
<td>EC: 3.5.1.16 (<span class="gene">argE</span>)</td>
</tr>
</tr>
<tr>
<tr>
<td>FH</td>
<td>FH</td>
-
<td>fumarate + H2O → L-malate</td>
+
<td>fumarate + H<sub>2</sub>O &rarr; L-malate</td>
<td>EC: 4.2.1.2</td>
<td>EC: 4.2.1.2</td>
</tr>
</tr>
<tr>
<tr>
<td>MDH</td>
<td>MDH</td>
-
<td>L-malate + NAD+ → oxaloacetate + NADH + H+</td>
+
<td>L-malate + NAD<sup>+</sup> &rarr; oxaloacetate + NADH + H<sup>+</sup></td>
<td>EC: 1.1.1.37</td>
<td>EC: 1.1.1.37</td>
</tr>
</tr>
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<tr>
<tr>
<td>CS</td>
<td>CS</td>
-
<td>acetyl-CoA + oxaloacetate + H2O → citrate + CoASH</td>
+
<td>acetyl-CoA + oxaloacetate + H<sub>2</sub>O &rarr; citrate + CoASH</td>
<td>EC: 2.3.3.1</td>
<td>EC: 2.3.3.1</td>
</tr>
</tr>
<tr>
<tr>
<td>AH</td>
<td>AH</td>
-
<td>citrate → isocitrate</td>
+
<td>citrate &rarr; isocitrate</td>
<td>EC: 4.2.1.3</td>
<td>EC: 4.2.1.3</td>
</tr>
</tr>
<tr>
<tr>
<td>IDH</td>
<td>IDH</td>
-
<td>isocitrate + NADP+ → 2-oxoglutarate + NADPH + H+ + CO2</td>
+
<td>isocitrate + NADP+ &rarr; 2-oxoglutarate + NADPH + H<sup>+</sup> + CO<sub>2</sub></td>
<td>EC: 1.1.1.42</td>
<td>EC: 1.1.1.42</td>
</tr>
</tr>
<tr>
<tr>
<td>OGDH</td>
<td>OGDH</td>
-
<td>2-oxoglutarate + Enzyme N6-(lipoyl)lysine <br />→ [dihydrolipoyllysine-residue succinyl transferase]S-succinyldihydrolopiyllysine + CO2</td>
+
<td>2-oxoglutarate + Enzyme N6-(lipoyl)lysine <br />&rarr; [dihydrolipoyllysine-residue succinyl transferase]S-succinyldihydrolopiyllysine + CO<sub>2</sub></td>
<td>EC: 1.2.4.2</td>
<td>EC: 1.2.4.2</td>
</tr>
</tr>
<tr>
<tr>
<td>DST</td>
<td>DST</td>
-
<td>[dihydrolipoyllysine-residue succinyl transferase]S-succinyldihydrolopiyllysine +CoASH <br />→ succinyl-CoA + Enzyme N6-(dihydrolipoyl)lysine</td>
+
<td>[dihydrolipoyllysine-residue succinyl transferase]S-succinyldihydrolopiyllysine +CoASH <br />&rarr; succinyl-CoA + Enzyme N6-(dihydrolipoyl)lysine</td>
<td>EC: 2.3.1.61</td>
<td>EC: 2.3.1.61</td>
</tr>
</tr>
<tr>
<tr>
<td>E3</td>
<td>E3</td>
-
<td>Enzyme N6-(dihydrolipoyl)lysine + NAD+ = Enzyme N6-(lipoyl)lysine + NADH + H</td>
+
<td>Enzyme N6-(dihydrolipoyl)lysine + NAD<sup>+</sup> = Enzyme N6-(lipoyl)lysine + NADH + H<sup>+</sup></td>
<td>EC: 1.8.1.4</td>
<td>EC: 1.8.1.4</td>
</tr>
</tr>
<tr>
<tr>
<td>SCS</td>
<td>SCS</td>
-
<td>succinate + ADP + Pi → succinate + CoASH + ATP</td>
+
<td>succinate + ADP + Pi &rarr; succinate + CoASH + ATP</td>
<td>EC: 6.2.1.5</td>
<td>EC: 6.2.1.5</td>
</tr>
</tr>
<tr>
<tr>
<td>SDH</td>
<td>SDH</td>
-
<td>succinate + FAD → fumarate + CoASH + FADH2</td>
+
<td>succinate + FAD &rarr; fumarate + CoASH + FADH<sub>2</sub></td>
<td>EC: 1.3.99.1</td>
<td>EC: 1.3.99.1</td>
</tr>
</tr>
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AAT, amino-acid N-acetyltransferase;  
AAT, amino-acid N-acetyltransferase;  
AGK, acetylglutamate kinase;  
AGK, acetylglutamate kinase;  
-
AGPR, N-acetyl-γ-glutamylphosphate reductase;  
+
AGPR, N-acetyl-&gamma;-glutamylphosphate reductase;  
AOT, acetylornithine transaminase;  
AOT, acetylornithine transaminase;  
AO, acetylornithine deacetylase;  
AO, acetylornithine deacetylase;  
Line 475: Line 508:
SDH, succinate dehydrogenase<br />
SDH, succinate dehydrogenase<br />
Reversible and irreversible reactions are indicated, in the reaction equations,  
Reversible and irreversible reactions are indicated, in the reaction equations,  
-
by the symbols = and →, respectively.
+
by the symbols = and &rarr;, respectively.
</p>
</p>
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<div align="center">
+
<div align="center" sytle="margin-top:30px;">
-
<table border="1">
+
<table border="1" id="table4">
-
<caption>Table 4 Reaction formulas leaded by the concept of elementary flux mode</caption>
+
<caption>
 +
Table 4 Reaction formulas leaded by the concept of elementary flux mode
 +
</caption>
<tr>
<tr>
<th>Mode</th>
<th>Mode</th>
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<tr>
<tr>
<td>1</td>
<td>1</td>
-
<td>Acetyl-CoA + ADP + Pi + 2H2O + NADP+ + 2NAD+ + FAD → CoASH + ATP + NADPH + 2NADH + 3H+ + FADH2 + 2CO2</td>
+
<td>Acetyl-CoA + ADP + Pi + 2H<sub>2</sub>O + NADP<sup>+</sup> + 2NAD<sup>+</sup> + FAD &rarr; CoASH + ATP + NADPH + 2NADH + 3H<sup>+</sup> + FADH<sub>2</sub> + 2CO<sub>2</sub></td>
<td>FH, MDH, CS, AH, IDH, OGDH, DST, E3, SCS, SDH</td>
<td>FH, MDH, CS, AH, IDH, OGDH, DST, E3, SCS, SDH</td>
</tr>
</tr>
<tr>
<tr>
<td>2</td>
<td>2</td>
-
<td>ATP + H2O → ADP + Pi</td>
+
<td>ATP + H<sub>2</sub>O &rarr; ADP + Pi</td>
<td>GLU, GS</td>
<td>GLU, GS</td>
</tr>
</tr>
<tr>
<tr>
<td>3</td>
<td>3</td>
-
<td>ATP + H2O →ADP + Pi</td>
+
<td>ATP + H<sub>2</sub>O &rarr;ADP + Pi</td>
<td>-GDH, GOGAT, GS</td>
<td>-GDH, GOGAT, GS</td>
</tr>
</tr>
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<tr>
<tr>
<td>5</td>
<td>5</td>
-
<td>2NH3 + HCO3- + 3ATP + H2O + NADPH + NAD+ → Urea + 2ADP + AMP + 2Pi + PPi + NADP+ + NADH</td>
+
<td>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 3ATP + H<sub>2</sub>O + NADPH + NAD<sup>+</sup> &rarr; Urea + 2ADP + AMP + 2Pi + PPi + NADP<sup>+</sup> + NADH</td>
<td>-GLU, GDH, AST, OTC, ASS, ASL, ARG, CPS, FH, MDH</td>
<td>-GLU, GDH, AST, OTC, ASS, ASL, ARG, CPS, FH, MDH</td>
</tr>
</tr>
<tr>
<tr>
<td>6</td>
<td>6</td>
-
<td>2NH3 + HCO3- + 3ATP + H2O + NADPH + NAD+ → Urea + 2ADP + AMP + 2Pi + PPi + NADP+ + NADH</td>
+
<td>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 3ATP + H<sub>2</sub>O + NADPH + NAD<sup>+</sup> &rarr; Urea + 2ADP + AMP + 2Pi + PPi + NADP<sup>+</sup> + NADH</td>
<td>-2GLU, AST, OTC, ASS, ASL, ARG, CPS, GOGAT, FH, MDH</td>
<td>-2GLU, AST, OTC, ASS, ASL, ARG, CPS, GOGAT, FH, MDH</td>
</tr>
</tr>
<tr>
<tr>
<td>7</td>
<td>7</td>
-
<td>2NH3 + HCO3- + 4ATP + 2H2O + NADPH + NAD+ → Urea + 3ADP + AMP + 3Pi + PPi + NADP+ + NADH</td>
+
<td>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 4ATP + 2H<sub>2</sub>O + NADPH + NAD<sup>+</sup> &rarr; Urea + 3ADP + AMP + 3Pi + PPi + NADP<sup>+</sup> + NADH</td>
<td>GDH, AST, OTC, ASS, ASL, ARG, CPS, GS, FH, MDH</td>
<td>GDH, AST, OTC, ASS, ASL, ARG, CPS, GS, FH, MDH</td>
</tr>
</tr>
<tr>
<tr>
<td>8</td>
<td>8</td>
-
<td>2NH3 + HCO3- + 5ATP + 3H2O + NADPH + NAD+ → Urea + 4ADP + AMP + 4Pi + PPi + NADP+ + NADH</td>
+
<td>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 5ATP + 3H<sub>2</sub>O + NADPH + NAD<sup>+</sup> &rarr; Urea + 4ADP + AMP + 4Pi + PPi + NADP<sup>+</sup> + NADH</td>
<td>AST, OTC, ASS, ASL, ARG, CPS, GOGAT, 2GS, FH, MDH</td>
<td>AST, OTC, ASS, ASL, ARG, CPS, GOGAT, 2GS, FH, MDH</td>
</tr>
</tr>
Line 530: Line 565:
</div>
</div>
-
<div align="center">
+
<div align="center" style="margin-top:30px;">
-
<table border="1">
+
<table border="1" id="table5">
-
<caption>Table 5 Reaction formulas of producing four components of the urea cycle modes from L-glutamine and intermediates of TCA cycle</caption>
+
<caption>
 +
Table 5 Reaction formulas of producing four components of the urea cycle modes from L-glutamine and intermediates of TCA cycle
 +
</caption>
<tr>
<tr>
<th>Mode </th>
<th>Mode </th>
Line 540: Line 577:
<tr>
<tr>
<td>1</td>
<td>1</td>
-
<td>L-glutamine + acetyl-CoA + ATP + H2O +  2 NADPH + 2 H+<br /> → L-ornithine + CoASH + acetate + ADP + Pi + 2 NADP+</td>
+
<td>L-glutamine + acetyl-CoA + ATP + H<sub>2</sub>O +  2 NADPH + 2 H<sup>+</sup><br /> &rarr; L-ornithine + CoASH + acetate + ADP + Pi + 2 NADP<sup>+</sup></td>
-
<td>GOGAT, AAA, AGK, AGPR, ATO, AO</td>
+
<td>GOGAT, AAA, AGK,<br /> AGPR, ATO, AO</td>
</tr>
</tr>
<tr>
<tr>
<td>2</td>
<td>2</td>
-
<td>2 L-glutamine + acetyl-CoA + ATP +3 H2O +  NADPH +  H+<br /> → L-ornithine + 2-oxoglutarate + 2 NH3 + CoASH + acetate + ADP + Pi + NADP+</td>
+
<td>2 L-glutamine + acetyl-CoA + ATP +3 H<sub>2</sub>O +  NADPH +  H<sup>+</sup><br /> &rarr; L-ornithine + 2-oxoglutarate + 2 NH<sub>3</sub> + CoASH + acetate + ADP + Pi + NADP<sup>+</sup></td>
-
<td>2GLU, AAA, AGK, AGPR, ATO, AO</td>
+
<td>2GLU, AAA, AGK, AGPR,<br /> ATO, AO</td>
</tr>
</tr>
<tr>
<tr>
<td>3</td>
<td>3</td>
-
<td>2-oxoglutarate + 2 NH3 + acetyl-CoA + ATP + 3 NADPH + 3 H+ <br /> → L-ornithine + CoASH + acetate + ADP + Pi + H2O + 3 NADP+</td>
+
<td>2-oxoglutarate + 2 NH<sub>3</sub> + acetyl-CoA + ATP + 3 NADPH + 3 H<sup>+</sup> <br /> &rarr; L-ornithine + CoASH + acetate + ADP + Pi + H<sub>2</sub>O + 3 NADP<sup>+</sup></td>
-
<td>2 GDH, AAA, AGK, AGPR, ATO, AO</td>
+
<td>2 GDH, AAA, AGK,<br /> AGPR, ATO, AO</td>
</tr>
</tr>
<tr>
<tr>
<td>4</td>
<td>4</td>
-
<td>oxaloacetate + 3 L-glutamine +  acetyl-CoA +  HCO3- + 4 ATP + 4 H2O + NADPH +  H+ <br /> → L-arginine + fumarate + 2 2-oxoglutarate + CoASH + acetate + 3 ADP + AMP + 3 Pi + PPi +  NADP+</td>
+
<td>oxaloacetate + 3 L-glutamine +  acetyl-CoA +  HCO<sub>3</sub><sup>-</sup> + 4 ATP + 4 H<sub>2</sub>O + NADPH +  H<sup>+</sup> <br /> &rarr; L-arginine + fumarate + 2 2-oxoglutarate + CoASH + acetate + 3 ADP + AMP + 3 Pi + PPi +  NADP<sup>+</sup></td>
-
<td>2GLU, AST, OTC, ASS, ASL, CPS, AAA, AGK, AGPR, ATO, AO</td>
+
<td>2GLU, AST, OTC, ASS,<br /> ASL, CPS, AAA,<br /> AGK, AGPR, ATO, AO</td>
</tr>
</tr>
<tr>
<tr>
<td>5</td>
<td>5</td>
-
<td>oxaloacetate + L-glutamine + 2 NH3 + acety-CoA + HCO3- + 4 ATP  + 3NADPH + 3H+ <br /> → L-arginine + fumarate + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 3 NADP+</td>
+
<td>oxaloacetate + L-glutamine + 2 NH<sub>3</sub> + acety-CoA + HCO<sub>3</sub><sup>-</sup> + 4 ATP  + 3NADPH + 3H<sup>+</sup> <br /> &rarr; L-arginine + fumarate + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 3 NADP<sup>+</sup></td>
-
<td>2GDH, AST, OTC, ASS, ASL, CPS, AAA, AGK, AGPR, ATO, AO</td>
+
<td>2GDH, AST, OTC,<br /> ASS, ASL, CPS,<br /> AAA, AGK, AGPR,<br /> ATO, AO</td>
</tr>
</tr>
<tr>
<tr>
<td>6</td>
<td>6</td>
-
<td>oxaloacetate + 2 L-glutamine + NH3 + acetyl-CoA + HCO3- + 4ATP + 2 H2O + 2 NADPH + 2 H+<br /> →L-arginine + fumarate + CoASH + acetate + 3ADP + AMP + 3Pi + PPi + 2NADP+</td>
+
<td>oxaloacetate + 2 L-glutamine + NH<sub>3</sub> + acetyl-CoA + HCO<sub>3</sub><sup>-</sup> + 4ATP + 2 H<sub>2</sub>O + 2 NADPH + 2 H<sup>+</sup><br /> &rarr;L-arginine + fumarate + CoASH + acetate + 3ADP + AMP + 3Pi + PPi + 2NADP<sup>+</sup></td>
-
<td>AST, OTC, ASS, ASL, CPS, AAA, AGK, AGPR, ATO, GOGAT, AO</td>
+
<td>AST, OTC, ASS, ASL,<br /> CPS, AAA, AGK,<br /> AGPR, ATO, GOGAT, AO</td>
</tr>
</tr>
<tr>
<tr>
<td>7</td>
<td>7</td>
-
<td>2 L-glutamine + acetyl-CoA + HCO3- + 3 ATP + 3 H2O + NADPH + H+<br /> → L-citrulline + 2-oxoglutarate + NH3 + CoASH + acetate + 3 ADP + 3 Pi + NADP+ </td>
+
<td>2 L-glutamine + acetyl-CoA + HCO<sub>3</sub><sup>-</sup> + 3 ATP + 3 H<sub>2</sub>O + NADPH + H<sup>+</sup><br /> &rarr; L-citrulline + 2-oxoglutarate + NH<sub>3</sub> + CoASH + acetate + 3 ADP + 3 Pi + NADP<sup>+</sup> </td>
-
<td>GLU, OTC, CPS,  AAA, AGK, AGPR, ATO, AO</td>
+
<td>GLU, OTC, CPS,<br /> AAA, AGK, AGPR,<br /> ATO, AO</td>
</tr>
</tr>
<tr>
<tr>
<td>8</td>
<td>8</td>
-
<td>L-glutamine + NH3 + acetyl-CoA + HCO3- + 3 ATP + H2O + 2 NADPH +2 H+<br /> → L-citrulline + CoASH + acetate + 3 ADP + 3 Pi + 2 NADP+</td>
+
<td>L-glutamine + NH<sub>3</sub> + acetyl-CoA + HCO<sub>3</sub><sup>-</sup> + 3 ATP + H<sub>2</sub>O + 2 NADPH +2 H<sup>+</sup><br /> &rarr; L-citrulline + CoASH + acetate + 3 ADP + 3 Pi + 2 NADP<sup>+</sup></td>
-
<td>GDH, OTC, CPS,  AAA, AGK, AGPR, ATO, AO</td>
+
<td>GDH, OTC, CPS,  AAA, <br /> AGK, AGPR, ATO, AO</td>
</tr>
</tr>
<tr>
<tr>
<td>9</td>
<td>9</td>
-
<td>oxaloacetate + 3 L-glutamine + acetyl-CoA + HCO3- + 4ATP + 4H2O + NADPH + H+<br />→ N-(L-arginino)succinate + 2 2-oxoglutarate + 2 NH3 + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + NADP+</td>
+
<td>oxaloacetate + 3 L-glutamine + acetyl-CoA + HCO<sub>3</sub><sup>-</sup> + 4ATP + 4H<sub>2</sub>O + NADPH + H<sup>+</sup><br />&rarr; N-(L-arginino)succinate + 2 2-oxoglutarate + 2 NH<sub>3</sub> + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi <br />+ NADP<sup>+</sup></td>
-
<td>2GLU, AST, OTC, ASS, CPS, AAA, AGK, AGPR, ATO, AO</td>
+
<td>2GLU, AST, OTC,<br /> ASS, CPS, AAA,<br /> AGK, AGPR, ATO, AO</td>
</tr>
</tr>
<tr>
<tr>
<td>10</td>
<td>10</td>
-
<td>oxaloacetate + L-glutamine + 2 NH3 + acetyl-CoA + HCO3- + 4ATP + 3NADPH + 3H+<br /> → N-(L-arginino)succinate  + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 3 NADP+</td>
+
<td>oxaloacetate + L-glutamine + 2 NH<sub>3</sub> + acetyl-CoA + HCO<sub>3</sub><sup>-</sup> + 4ATP + 3NADPH + 3H<sup>+</sup><br /> &rarr; N-(L-arginino)succinate  + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 3 NADP<sup>+</sup></td>
-
<td>2GDH,  AST, OTC, ASS, CPS, AAA, AGK, AGPR, ATO, AO</td>
+
<td>2GDH,  AST, OTC,<br /> ASS, CPS, AAA,<br /> AGK, AGPR, ATO, AO</td>
</tr>
</tr>
<tr>
<tr>
<td>11</td>
<td>11</td>
-
<td>oxaloacetate + 2L-glutamine + acetyl CoA + HCO3- + 4 ATP + 2 H2O + 2 NADPH + 2H+<br /> → N-(L-arginino)succinate  + 2-Oxoglutarate +  CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 2 NADP+ </td>
+
<td>oxaloacetate + 2L-glutamine + acetyl CoA + HCO<sub>3</sub><sup>-</sup> + 4 ATP + 2 H<sub>2</sub>O + 2 NADPH + 2H<sup>+</sup><br /> &rarr; N-(L-arginino)succinate  + 2-Oxoglutarate +  CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 2 NADP<sup>+</sup> </td>
-
<td>AST, OTC, ASS, CPS, GOGAT, AAA, AGK, AGPR, ATO, AO</td>
+
<td>AST, OTC, ASS,<br /> CPS, GOGAT, AAA,<br /> AGK, AGPR, ATO, AO</td>
</tr>
</tr>
</table>
</table>
</div>
</div>
-
<div align="center">
 
-
<table border="1">
 
-
<caption>Table 6 Reaction formulas of the L-aspartate producing modes from L-glutamine and intermediates of TCA cycle</caption>
 
-
<tr>
 
-
<th>Mode</th>
 
-
<th>Reaction formula</th>
 
-
<th>Participating steps</th>
 
-
</tr>
 
-
<tr>
 
-
<td>1</td>
 
-
<td>oxaloacetate + L-glutamine +  H2O → L-aspartate + 2-oxoglutarate + NH3</td>
 
-
<td>GLU, AST</td>
 
-
</tr>
 
-
<tr>
 
-
<td>2</td>
 
-
<td>oxaloacetate +  NH3 + NADPH + H+  → L-aspartate + H2O + NADP+</td>
 
-
<td>GDH, AST</td>
 
-
</tr>
 
-
<tr>
 
-
<td>3</td>
 
-
<td>2 oxaloacetate + L-glutamine + NADPH + H+  → 2 L-aspartate + 2-oxoglutarate + NADP+</td>
 
-
<td>2AST, GOGAT</td>
 
-
</tr>
 
-
</table>
 
-
</div>
 
-
 
-
 
-
</p>
 
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Latest revision as of 14:54, 28 October 2011

Tokyo Tech 2011

Urea Modeling : Tables

Table 3 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

*Abbreviations of enzymes: OTC, ornithine transcarbamoylase; ASS, argininosuccinate synthase; ASL, argininosuccinate lyase; ARG, arginase; CPS, carbamoyl phosphate synthetase; GOGAT, glutamate synthase; GS, glutamine synthetase; GLU, glutaminase; GDH, glutamate dehydrogenase; AAT, amino-acid N-acetyltransferase; AGK, acetylglutamate kinase; AGPR, N-acetyl-γ-glutamylphosphate reductase; AOT, acetylornithine transaminase; AO, acetylornithine deacetylase; FH, fumarate hydratase; MDH, malate dehydrogenase; AST, asparate aminotransferase; CS, citrate (Si)-synthase; AH, aconitate hydratase; IDH, isocitrate dehydrogenase; OGDH, oxoglutarate dehydrogenase; DST, dihydrolipoyllysine-residue succinyltransferase; E3, dihydrolipoyl dehydrogenase; SCS, succinyl-CoA synthetase; SDH, succinate dehydrogenase
Reversible and irreversible reactions are indicated, in the reaction equations, by the symbols = and →, respectively.

Table 4 Reaction formulas leaded by the concept of elementary flux mode
Mode Reaction formula Participating steps
1 Acetyl-CoA + ADP + Pi + 2H2O + NADP+ + 2NAD+ + FAD → CoASH + ATP + NADPH + 2NADH + 3H+ + FADH2 + 2CO2 FH, MDH, CS, AH, IDH, OGDH, DST, E3, SCS, SDH
2 ATP + H2O → ADP + Pi GLU, GS
3 ATP + H2O →ADP + Pi -GDH, GOGAT, GS
4 nothing -GLU, -GDH, GOGAT
5 2NH3 + HCO3- + 3ATP + H2O + NADPH + NAD+ → Urea + 2ADP + AMP + 2Pi + PPi + NADP+ + NADH -GLU, GDH, AST, OTC, ASS, ASL, ARG, CPS, FH, MDH
6 2NH3 + HCO3- + 3ATP + H2O + NADPH + NAD+ → Urea + 2ADP + AMP + 2Pi + PPi + NADP+ + NADH -2GLU, AST, OTC, ASS, ASL, ARG, CPS, GOGAT, FH, MDH
7 2NH3 + HCO3- + 4ATP + 2H2O + NADPH + NAD+ → Urea + 3ADP + AMP + 3Pi + PPi + NADP+ + NADH GDH, AST, OTC, ASS, ASL, ARG, CPS, GS, FH, MDH
8 2NH3 + HCO3- + 5ATP + 3H2O + NADPH + NAD+ → Urea + 4ADP + AMP + 4Pi + PPi + NADP+ + NADH AST, OTC, ASS, ASL, ARG, CPS, GOGAT, 2GS, FH, MDH
Table 5 Reaction formulas of producing four components of the urea cycle modes from L-glutamine and intermediates of TCA cycle
Mode Reaction formula Participating steps
1 L-glutamine + acetyl-CoA + ATP + H2O + 2 NADPH + 2 H+
→ L-ornithine + CoASH + acetate + ADP + Pi + 2 NADP+		 GOGAT, AAA, AGK,
AGPR, ATO, AO
2 2 L-glutamine + acetyl-CoA + ATP +3 H2O + NADPH + H+
→ L-ornithine + 2-oxoglutarate + 2 NH3 + CoASH + acetate + ADP + Pi + NADP+		 2GLU, AAA, AGK, AGPR,
ATO, AO
3 2-oxoglutarate + 2 NH3 + acetyl-CoA + ATP + 3 NADPH + 3 H+
→ L-ornithine + CoASH + acetate + ADP + Pi + H2O + 3 NADP+		 2 GDH, AAA, AGK,
AGPR, ATO, AO
4 oxaloacetate + 3 L-glutamine + acetyl-CoA + HCO3- + 4 ATP + 4 H2O + NADPH + H+
→ L-arginine + fumarate + 2 2-oxoglutarate + CoASH + acetate + 3 ADP + AMP + 3 Pi + PPi + NADP+		 2GLU, AST, OTC, ASS,
ASL, CPS, AAA,
AGK, AGPR, ATO, AO
5 oxaloacetate + L-glutamine + 2 NH3 + acety-CoA + HCO3- + 4 ATP + 3NADPH + 3H+
→ L-arginine + fumarate + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 3 NADP+		 2GDH, AST, OTC,
ASS, ASL, CPS,
AAA, AGK, AGPR,
ATO, AO
6 oxaloacetate + 2 L-glutamine + NH3 + acetyl-CoA + HCO3- + 4ATP + 2 H2O + 2 NADPH + 2 H+
→L-arginine + fumarate + CoASH + acetate + 3ADP + AMP + 3Pi + PPi + 2NADP+		 AST, OTC, ASS, ASL,
CPS, AAA, AGK,
AGPR, ATO, GOGAT, AO
7 2 L-glutamine + acetyl-CoA + HCO3- + 3 ATP + 3 H2O + NADPH + H+
→ L-citrulline + 2-oxoglutarate + NH3 + CoASH + acetate + 3 ADP + 3 Pi + NADP+ 		GLU, OTC, CPS,
AAA, AGK, AGPR,
ATO, AO
8 L-glutamine + NH3 + acetyl-CoA + HCO3- + 3 ATP + H2O + 2 NADPH +2 H+
→ L-citrulline + CoASH + acetate + 3 ADP + 3 Pi + 2 NADP+		 GDH, OTC, CPS, AAA,
AGK, AGPR, ATO, AO
9 oxaloacetate + 3 L-glutamine + acetyl-CoA + HCO3- + 4ATP + 4H2O + NADPH + H+
→ N-(L-arginino)succinate + 2 2-oxoglutarate + 2 NH3 + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi
+ NADP+		 2GLU, AST, OTC,
ASS, CPS, AAA,
AGK, AGPR, ATO, AO
10 oxaloacetate + L-glutamine + 2 NH3 + acetyl-CoA + HCO3- + 4ATP + 3NADPH + 3H+
→ N-(L-arginino)succinate + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 3 NADP+		 2GDH, AST, OTC,
ASS, CPS, AAA,
AGK, AGPR, ATO, AO
11 oxaloacetate + 2L-glutamine + acetyl CoA + HCO3- + 4 ATP + 2 H2O + 2 NADPH + 2H+
→ N-(L-arginino)succinate + 2-Oxoglutarate + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 2 NADP+ 		AST, OTC, ASS,
CPS, GOGAT, AAA,
AGK, AGPR, ATO, AO

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