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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
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Caulobacter crescentus CB15 Pathway: TCA cycle I (prokaryotic)

If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Locations of Mapped Genes:

Synonyms: tricarboxylic acid cycle, citric acid cycle, Krebs cycle, Szent-Gyorgyi-Krebs cycle, TCA cycle I (2-oxoglutarate dehydrogenase)

Superclasses: Generation of Precursor Metabolites and Energy TCA cycle

Pathway Summary from MetaCyc:
General Background

The TCA pathway is a catabolic pathway of aerobic respiration that generates both energy and reducing power. In addition, it is also the first step in generating precursors for biosynthesis. The pathway is very common, and a variation of it exists in practically all aerobic living organisms [Krebs37, Krebs38, Krebs45].

The input to the cycle is acetyl-CoA, an activated form of acetate that is generated by the degradation of carbohydrates, fats and proteins. A common source of acetyl-coA is pyruvate, which is generated by glycolysis and converted to acetyl-CoA by the pyruvate dehydrogenase complex.

In every turn the TCA cycle converts one molecule of acetyl-CoA into two CO2 molecules, reduces a total of four molecules of either NAD+, NADP+, or quinone to NADH, NADPH and quinol, respectively, and phosphorylates one molecule of GDP to GTP.

The reduced molecules of NADH/NADPH/quinol that are formed by the TCA cycle serve as electron donors for oxidative phosphorylation (see for example aerobic respiration I (cytochrome c)). In that process the electrons flow to a terminal acceptor, powering on their way proton pumps that trasport protons across the cytoplasmic or mitochondrial membranes, generating a proton motive force (PMF). As the protons return to their original location, they power ATPase enzymes that phosphorylate ADP molecules to ATP. The total energy gained from the complete breakdown of one molecule of glucose by glycolysis, the TCA cycle, and oxidative phosphorylation equals about 30 ATP molecules in eukaryotes.

The name of the TCA (short for tricarboxylic acid) cycle is derived from the fact that the first step in the pathway is attachment of acetyl-coA to citrate, an acid with three carboxylate groups. The pathway is also known as the citric acid cycle, and as the Szent-Gyorgyi-Krebs cycle (or just the Krebs cycle), named after the scientists who described it.

Some organisms possess a truncated version of the TCA cycle, known as the glyoxylate cycle, that converts acetyl-CoA to biosynthetic intermediates without the loss of CO2 [Walsh84, Nimmo87, Holms87].

About This Pathway

This is a common variation of the pathway that occurs in many bacteria and archaea. There are a few small differences between this prokaryotic version of the cycle and the version found in most eukaryotes (see TCA cycle II (plants and fungi)). In this pathway, an NADP-dependent enzyme (EC 1.1.1.42) catalyzes the dehydrogenation of D-threo-isocitrate to 2-oxoglutarate, while eukaryotes employ an NAD+-dependent enzyme (EC 1.1.1.41). Another difference is that while in most eukaryotes the conversion of (S)-malate to oxaloacetate is catalyzed only by an NAD-dependent enzyme (EC 1.1.1.37), prokaryotes that employ this variation of the TCA cycle possess an alternative quinone-dependent enzyme (EC 1.1.5.4).

While the pathway is most common in heterotrophic bacteria and arachaea, there is evidence for its presence in some facultatively autotrophic archaea when growing under heterotrophic conditions.

In Escherichia coli, when acetate is the carbon source, citrate synthase is rate-limiting for the TCA cycle [Walsh85, Walsh87].

Superpathways: superpathway of glyoxylate bypass and TCA

Variants: superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass

Pathway Evidence Glyph:

Key to pathway glyph edge colors: ?

  An enzyme catalyzing this reaction is present in this organism
  The reaction and any enzyme that catalyzes it (if one has been identified) is unique to this pathway


References

Holms87: Holms WH (1987). "Control of flux through the citric acid cycle and the glyoxylate bypass in Escherichia coli." Biochem Soc Symp 1987;54;17-31. PMID: 3332993

Krebs37: Krebs HA, Johnson WA (1937). "Acetopyruvic acid (αγ-diketovaleric acid) as an intermediate metabolite in animal tissues." Biochem J 31(5);772-9. PMID: 16746397

Krebs38: Krebs HA, Salvin E, Johnson WA (1938). "The formation of citric and α-ketoglutaric acids in the mammalian body." Biochem J 32(1);113-7. PMID: 16746585

Krebs45: Krebs HA, Eggleston LV (1945). "Metabolism of acetoacetate in animal tissues. 1." Biochem J 39(5);408-19. PMID: 16747930

Nimmo87: Nimmo HG, Borthwick AC, el-Mansi EM, Holms WH, MacKintosh C, Nimmo GA (1987). "Regulation of the enzymes at the branchpoint between the citric acid cycle and the glyoxylate bypass in Escherichia coli." Biochem Soc Symp 1987;54;93-101. PMID: 3333001

Walsh84: Walsh K, Koshland DE (1984). "Determination of flux through the branch point of two metabolic cycles. The tricarboxylic acid cycle and the glyoxylate shunt." J Biol Chem 1984;259(15);9646-54. PMID: 6378912

Walsh85: Walsh K, Koshland DE (1985). "Characterization of rate-controlling steps in vivo by use of an adjustable expression vector." Proc Natl Acad Sci U S A 1985;82(11);3577-81. PMID: 3889909

Walsh87: Walsh K, Schena M, Flint AJ, Koshland DE (1987). "Compensatory regulation in metabolic pathways--responses to increases and decreases in citrate synthase levels." Biochem Soc Symp 1987;54;183-95. PMID: 3332995

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Kawamukai02: Kawamukai M (2002). "Biosynthesis, bioproduction and novel roles of ubiquinone." J Biosci Bioeng 94(6);511-7. PMID: 16233343


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Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, biocyc12.