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Revision as of 18:40, 5 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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