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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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<div align="center"> | <div align="center"> | ||
<table border="1" id="table3"> | <table border="1" id="table3"> | ||
| - | <caption>Table 3 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 | + | <td>carbamoyl phosphate + L-ornithine → 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 | + | <td>L-citrulline + L-aspartate + ATP → 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 | + | <td>N-(L-arginino)succinate → 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 + H<sub>2</sub>O | + | <td>L-arginine + H<sub>2</sub>O → 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 + HCO<sub>3</sub><sup>-</sup> + H<sub>2</sub>O + 2ATP | + | <td>L-glutamine + HCO<sub>3</sub><sup>-</sup> + H<sub>2</sub>O + 2ATP → 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<sup>+</sup> | + | <td>L-glutamine + 2-oxoglutarate + NADPH + H<sup>+</sup> → 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 + NH<sub>3</sub> + ATP | + | <td>L-glutamate + NH<sub>3</sub> + ATP → L-glutamine + ADP + Pi</td> |
<td>EC: 6.3.1.2</td> | <td>EC: 6.3.1.2</td> | ||
</tr> | </tr> | ||
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<tr> | <tr> | ||
<td>AAA</td> | <td>AAA</td> | ||
| - | <td>acetyl-CoA + L-glutamate | + | <td>acetyl-CoA + L-glutamate → 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 | + | <td>N-acetyl-L-glutamate + ATP → 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<sup>+</sup> | + | <td>N-acetyl-L-glutamate 5-phosphate + NADPH + H<sup>+</sup> → 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 | + | <td>N-acetyl-L-glutamate 5-semialdehyde + L-glutamate → 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 + H<sub>2</sub>O | + | <td>N-acetylornithine + H<sub>2</sub>O → 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 + H<sub>2</sub>O | + | <td>fumarate + H<sub>2</sub>O → 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<sup>+</sup> | + | <td>L-malate + NAD<sup>+</sup> → 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 + H<sub>2</sub>O | + | <td>acetyl-CoA + oxaloacetate + H<sub>2</sub>O → 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 | + | <td>citrate → 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+ | + | <td>isocitrate + NADP+ → 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 /> | + | <td>2-oxoglutarate + Enzyme N6-(lipoyl)lysine <br />→ [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 /> | + | <td>[dihydrolipoyllysine-residue succinyl transferase]S-succinyldihydrolopiyllysine +CoASH <br />→ succinyl-CoA + Enzyme N6-(dihydrolipoyl)lysine</td> |
<td>EC: 2.3.1.61</td> | <td>EC: 2.3.1.61</td> | ||
</tr> | </tr> | ||
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<tr> | <tr> | ||
<td>SCS</td> | <td>SCS</td> | ||
| - | <td>succinate + ADP + Pi | + | <td>succinate + ADP + Pi → 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 | + | <td>succinate + FAD → fumarate + CoASH + FADH<sub>2</sub></td> |
<td>EC: 1.3.99.1</td> | <td>EC: 1.3.99.1</td> | ||
</tr> | </tr> | ||
| Line 501: | 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 | + | by the symbols = and →, respectively. |
</p> | </p> | ||
| Line 507: | Line 514: | ||
<div align="center" sytle="margin-top:30px;"> | <div align="center" sytle="margin-top:30px;"> | ||
<table border="1" id="table4"> | <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> | ||
| Line 515: | Line 524: | ||
<tr> | <tr> | ||
<td>1</td> | <td>1</td> | ||
| - | <td>Acetyl-CoA + ADP + Pi + 2H<sub>2</sub>O + NADP<sup>+</sup> + 2NAD<sup>+</sup> + FAD | + | <td>Acetyl-CoA + ADP + Pi + 2H<sub>2</sub>O + NADP<sup>+</sup> + 2NAD<sup>+</sup> + FAD → 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 + H<sub>2</sub>O | + | <td>ATP + H<sub>2</sub>O → ADP + Pi</td> |
<td>GLU, GS</td> | <td>GLU, GS</td> | ||
</tr> | </tr> | ||
<tr> | <tr> | ||
<td>3</td> | <td>3</td> | ||
| - | <td>ATP + H<sub>2</sub>O | + | <td>ATP + H<sub>2</sub>O →ADP + Pi</td> |
<td>-GDH, GOGAT, GS</td> | <td>-GDH, GOGAT, GS</td> | ||
</tr> | </tr> | ||
| Line 535: | Line 544: | ||
<tr> | <tr> | ||
<td>5</td> | <td>5</td> | ||
| - | <td>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 3ATP + H<sub>2</sub>O + NADPH + NAD<sup>+</sup> | + | <td>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 3ATP + H<sub>2</sub>O + NADPH + NAD<sup>+</sup> → 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>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 3ATP + H<sub>2</sub>O + NADPH + NAD<sup>+</sup> | + | <td>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 3ATP + H<sub>2</sub>O + NADPH + NAD<sup>+</sup> → 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>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 4ATP + 2H<sub>2</sub>O + NADPH + NAD<sup>+</sup> | + | <td>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 4ATP + 2H<sub>2</sub>O + NADPH + NAD<sup>+</sup> → 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>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 5ATP + 3H<sub>2</sub>O + NADPH + NAD<sup>+</sup> | + | <td>2NH<sub>3</sub> + HCO<sub>3</sub><sup>-</sup> + 5ATP + 3H<sub>2</sub>O + NADPH + NAD<sup>+</sup> → 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> | ||
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<div align="center" style="margin-top:30px;"> | <div align="center" style="margin-top:30px;"> | ||
<table border="1" id="table5"> | <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 566: | Line 577: | ||
<tr> | <tr> | ||
<td>1</td> | <td>1</td> | ||
| - | <td>L-glutamine + acetyl-CoA + ATP + H<sub>2</sub>O + 2 NADPH + 2 H<sup>+</sup><br /> | + | <td>L-glutamine + acetyl-CoA + ATP + H<sub>2</sub>O + 2 NADPH + 2 H<sup>+</sup><br /> → L-ornithine + CoASH + acetate + ADP + Pi + 2 NADP<sup>+</sup></td> |
<td>GOGAT, AAA, AGK,<br /> 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 H<sub>2</sub>O + NADPH + H<sup>+</sup><br /> | + | <td>2 L-glutamine + acetyl-CoA + ATP +3 H<sub>2</sub>O + NADPH + H<sup>+</sup><br /> → L-ornithine + 2-oxoglutarate + 2 NH<sub>3</sub> + CoASH + acetate + ADP + Pi + NADP<sup>+</sup></td> |
<td>2GLU, AAA, AGK, AGPR,<br /> 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 NH<sub>3</sub> + acetyl-CoA + ATP + 3 NADPH + 3 H<sup>+</sup> <br /> | + | <td>2-oxoglutarate + 2 NH<sub>3</sub> + acetyl-CoA + ATP + 3 NADPH + 3 H<sup>+</sup> <br /> → L-ornithine + CoASH + acetate + ADP + Pi + H<sub>2</sub>O + 3 NADP<sup>+</sup></td> |
<td>2 GDH, AAA, AGK,<br /> 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 + HCO<sub>3</sub><sup>-</sup> + 4 ATP + 4 H<sub>2</sub>O + NADPH + H<sup>+</sup> <br /> | + | <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 /> → L-arginine + fumarate + 2 2-oxoglutarate + CoASH + acetate + 3 ADP + AMP + 3 Pi + PPi + NADP<sup>+</sup></td> |
<td>2GLU, AST, OTC, ASS,<br /> ASL, CPS, AAA,<br /> 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 NH<sub>3</sub> + acety-CoA + HCO<sub>3</sub><sup>-</sup> + 4 ATP + 3NADPH + 3H<sup>+</sup> <br /> | + | <td>oxaloacetate + L-glutamine + 2 NH<sub>3</sub> + acety-CoA + HCO<sub>3</sub><sup>-</sup> + 4 ATP + 3NADPH + 3H<sup>+</sup> <br /> → L-arginine + fumarate + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 3 NADP<sup>+</sup></td> |
<td>2GDH, AST, OTC,<br /> ASS, ASL, CPS,<br /> AAA, AGK, AGPR,<br /> 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 + 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 /> | + | <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 /> →L-arginine + fumarate + CoASH + acetate + 3ADP + AMP + 3Pi + PPi + 2NADP<sup>+</sup></td> |
<td>AST, OTC, ASS, ASL,<br /> CPS, AAA, AGK,<br /> 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 + HCO<sub>3</sub><sup>-</sup> + 3 ATP + 3 H<sub>2</sub>O + NADPH + H<sup>+</sup><br /> | + | <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 /> → L-citrulline + 2-oxoglutarate + NH<sub>3</sub> + CoASH + acetate + 3 ADP + 3 Pi + NADP<sup>+</sup> </td> |
<td>GLU, OTC, CPS,<br /> AAA, AGK, AGPR,<br /> 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 + 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 /> | + | <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 /> → L-citrulline + CoASH + acetate + 3 ADP + 3 Pi + 2 NADP<sup>+</sup></td> |
<td>GDH, OTC, CPS, AAA, <br /> 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 + HCO<sub>3</sub><sup>-</sup> + 4ATP + 4H<sub>2</sub>O + NADPH + H<sup>+</sup><br /> | + | <td>oxaloacetate + 3 L-glutamine + acetyl-CoA + HCO<sub>3</sub><sup>-</sup> + 4ATP + 4H<sub>2</sub>O + NADPH + H<sup>+</sup><br />→ 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,<br /> ASS, CPS, AAA,<br /> 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 NH<sub>3</sub> + acetyl-CoA + HCO<sub>3</sub><sup>-</sup> + 4ATP + 3NADPH + 3H<sup>+</sup><br /> | + | <td>oxaloacetate + L-glutamine + 2 NH<sub>3</sub> + acetyl-CoA + HCO<sub>3</sub><sup>-</sup> + 4ATP + 3NADPH + 3H<sup>+</sup><br /> → N-(L-arginino)succinate + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 3 NADP<sup>+</sup></td> |
<td>2GDH, AST, OTC,<br /> ASS, CPS, AAA,<br /> 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 + HCO<sub>3</sub><sup>-</sup> + 4 ATP + 2 H<sub>2</sub>O + 2 NADPH + 2H<sup>+</sup><br /> | + | <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 /> → N-(L-arginino)succinate + 2-Oxoglutarate + CoASH + acetate + 3 ADP + AMP + 3Pi + PPi + 2 NADP<sup>+</sup> </td> |
<td>AST, OTC, ASS,<br /> CPS, GOGAT, AAA,<br /> AGK, AGPR, ATO, AO</td> | <td>AST, OTC, ASS,<br /> CPS, GOGAT, AAA,<br /> AGK, AGPR, ATO, AO</td> | ||
</tr> | </tr> | ||
| Line 622: | Line 633: | ||
</div> | </div> | ||
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| - | |||
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Latest revision as of 14:54, 28 October 2011
Urea Modeling : Tables
| 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.
| 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 |
| 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 |
