KEGG   PATHWAY: ppa00020
Entry
ppa00020                    Pathway                                
Name
Citrate cycle (TCA cycle) - Komagataella phaffii
Description
The citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form of acetate, derived from glycolysis and pyruvate oxidation for carbohydrates and from beta oxidation of fatty acids. The two-carbon acetyl group in acetyl-CoA is transferred to the four-carbon compound of oxaloacetate to form the six-carbon compound of citrate. In a series of reactions two carbons in citrate are oxidized to CO2 and the reaction pathway supplies NADH for use in the oxidative phosphorylation and other metabolic processes. The pathway also supplies important precursor metabolites including 2-oxoglutarate. At the end of the cycle the remaining four-carbon part is transformed back to oxaloacetate. According to the genome sequence data, many organisms seem to lack genes for the full cycle [MD:M00009], but contain genes for specific segments [MD:M00010 M00011].
Class
Metabolism; Carbohydrate metabolism
Pathway map
ppa00020  Citrate cycle (TCA cycle)
ppa00020

Module
ppa_M00003  Gluconeogenesis, oxaloacetate => fructose-6P [PATH:ppa00020]
ppa_M00009  Citrate cycle (TCA cycle, Krebs cycle) [PATH:ppa00020]
ppa_M00010  Citrate cycle, first carbon oxidation, oxaloacetate => 2-oxoglutarate [PATH:ppa00020]
ppa_M00011  Citrate cycle, second carbon oxidation, 2-oxoglutarate => oxaloacetate [PATH:ppa00020]
ppa_M00307  Pyruvate oxidation, pyruvate => acetyl-CoA [PATH:ppa00020]
Other DBs
GO: 0006099
Organism
Komagataella phaffii [GN:ppa]
Gene
PAS_chr1-1_0475  hypothetical protein [KO:K01647] [EC:2.3.3.1]
PAS_chr1-3_0104  Aconitase, required for the tricarboxylic acid (TCA) cycle and also independently required for mitoc [KO:K01681] [EC:4.2.1.3]
PAS_chr1-1_0233  Mitochondrial NADP-specific isocitrate dehydrogenase, catalyzes the oxidation of isocitrate [KO:K00031] [EC:1.1.1.42]
PAS_chr2-1_0580  Cytosolic NADP-specific isocitrate dehydrogenase [KO:K00031] [EC:1.1.1.42]
PAS_chr2-1_0120  Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase, which catalyzes the oxidation of [KO:K00030] [EC:1.1.1.41]
PAS_chr4_0580  Subunit of mitochondrial NAD(+)-dependent isocitrate dehydrogenase [KO:K00030] [EC:1.1.1.41]
PAS_chr2-1_0089  Component of the mitochondrial alpha-ketoglutarate dehydrogenase complex, which catalyzes a key step [KO:K00164] [EC:1.2.4.2]
PAS_chr1-3_0094  Dihydrolipoyl transsuccinylase, component of the mitochondrial alpha-ketoglutarate dehydrogenase [KO:K00658] [EC:2.3.1.61]
PAS_chr2-2_0048  Dihydrolipoamide dehydrogenase [KO:K00382] [EC:1.8.1.4]
PAS_chr3_0831  Alpha subunit of succinyl-CoA ligase [KO:K01899] [EC:6.2.1.4 6.2.1.5]
PAS_chr2-2_0407  Beta subunit of succinyl-CoA ligase, which is a mitochondrial enzyme of the TCA cycle [KO:K01900] [EC:6.2.1.4 6.2.1.5]
PAS_chr4_0733  Flavoprotein subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p) [KO:K00234] [EC:1.3.5.1]
PAS_chr3_1111  Iron-sulfur protein subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p) [KO:K00235] [EC:1.3.5.1]
PAS_chr1-4_0487  hypothetical protein [KO:K00236]
PAS_chr3_0424  Membrane anchor subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p) [KO:K00237]
PAS_chr2-2_0283  Membrane anchor subunit of succinate dehydrogenase (Sdh1p, Sdh2p, Sdh3p, Sdh4p) [KO:K00237]
PAS_chr3_0647  Fumarase, converts fumaric acid to L-malic acid in the TCA cycle [KO:K01679] [EC:4.2.1.2]
PAS_chr2-1_0238  Mitochondrial malate dehydrogenase, catalyzes interconversion of malate and oxaloacetate [KO:K00026] [EC:1.1.1.37]
PAS_chr4_0815  Mitochondrial malate dehydrogenase, catalyzes interconversion of malate and oxaloacetate [KO:K00026] [EC:1.1.1.37]
PAS_chr2-2_0024  Pyruvate carboxylase isoform, cytoplasmic enzyme that converts pyruvate to oxaloacetate [KO:K01958] [EC:6.4.1.1]
PAS_FragB_0061  Phosphoenolpyruvate carboxykinase [KO:K01610] [EC:4.1.1.49]
PAS_chr2-2_0294  E1 alpha subunit of the pyruvate dehydrogenase (PDH) complex [KO:K00161] [EC:1.2.4.1]
PAS_chr1-4_0593  E1 beta subunit of the pyruvate dehydrogenase (PDH) complex [KO:K00162] [EC:1.2.4.1]
PAS_chr1-1_0050  Dihydrolipoamide acetyltransferase component (E2) of pyruvate dehydrogenase complex [KO:K00627] [EC:2.3.1.12]
Compound
C00022  Pyruvate
C00024  Acetyl-CoA
C00026  2-Oxoglutarate
C00036  Oxaloacetate
C00042  Succinate
C00068  Thiamin diphosphate
C00074  Phosphoenolpyruvate
C00091  Succinyl-CoA
C00122  Fumarate
C00149  (S)-Malate
C00158  Citrate
C00311  Isocitrate
C00417  cis-Aconitate
C05125  2-(alpha-Hydroxyethyl)thiamine diphosphate
C05379  Oxalosuccinate
C05381  3-Carboxy-1-hydroxypropyl-ThPP
C15972  Enzyme N6-(lipoyl)lysine
C15973  Enzyme N6-(dihydrolipoyl)lysine
C16254  [Dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine
C16255  [Dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine
Reference
  Authors
Nishizuka Y (ed).
  Title
[Metabolic Maps] (In Japanese)
  Journal
Tokyo Kagaku Dojin (1980)
Reference
  Authors
Nishizuka Y, Seyama Y, Ikai A, Ishimura Y, Kawaguchi A (eds).
  Title
[Cellular Functions and Metabolic Maps] (In Japanese)
  Journal
Tokyo Kagaku Dojin (1997)
Reference
  Authors
Michal G.
  Title
Biochemical Pathways
  Journal
Wiley (1999)
Related
pathway
ppa00010  Glycolysis / Gluconeogenesis
ppa00053  Ascorbate and aldarate metabolism
ppa00061  Fatty acid biosynthesis
ppa00062  Fatty acid elongation
ppa00071  Fatty acid degradation
ppa00190  Oxidative phosphorylation
ppa00220  Arginine biosynthesis
ppa00250  Alanine, aspartate and glutamate metabolism
ppa00280  Valine, leucine and isoleucine degradation
ppa00350  Tyrosine metabolism
ppa00470  D-Amino acid metabolism
ppa00630  Glyoxylate and dicarboxylate metabolism
KO pathway
ko00020   
LinkDB

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