TCA cycle (plant) (Oryza sativa)

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1-6, 1078, 911mitochondrial matrixOGDH complexH+SCS dimerNADHCO2SDH complexCoA-SHCoQSUCCAH+SUCC-CoAIDH (NAD) complexMALNADHAc-CoACO2NAD+FUM1(LOC_Os03g21950.1)CoA-SHPiPYRNADHCoA-SHATPFUMAH+OAMDHNAD+H+ISCITADPACOH2ONAD+CoA-SHH2OCSYMalate dehydrogenase(decarboxylating)CIT2OGNAD+QH2NADHCO27


Description

Developed by Gramene.org Source:Plant Reactome.

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Bibliography

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  1. Araújo WL, Nunes-Nesi A, Nikoloski Z, Sweetlove LJ, Fernie AR.; ''Metabolic control and regulation of the tricarboxylic acid cycle in photosynthetic and heterotrophic plant tissues.''; PubMed Europe PMC Scholia
  2. Tronconi MA, Maurino VG, Andreo CS, Drincovich MF.; ''Three different and tissue-specific NAD-malic enzymes generated by alternative subunit association in Arabidopsis thaliana.''; PubMed Europe PMC Scholia
  3. Sweetlove LJ, Beard KF, Nunes-Nesi A, Fernie AR, Ratcliffe RG.; ''Not just a circle: flux modes in the plant TCA cycle.''; PubMed Europe PMC Scholia
  4. Tronconi MA, Gerrard Wheeler MC, Maurino VG, Drincovich MF, Andreo CS.; ''NAD-malic enzymes of Arabidopsis thaliana display distinct kinetic mechanisms that support differences in physiological control.''; PubMed Europe PMC Scholia
  5. Grover SD, Canellas PF, Wedding RT.; ''Purification of NAD malic enzyme from potato and investigation of some physical and kinetic properties.''; PubMed Europe PMC Scholia
  6. Millar AH, Whelan J, Soole KL, Day DA.; ''Organization and regulation of mitochondrial respiration in plants.''; PubMed Europe PMC Scholia
  7. Abiko T, Obara M, Ushioda A, Hayakawa T, Hodges M, Yamaya T.; ''Localization of NAD-isocitrate dehydrogenase and glutamate dehydrogenase in rice roots: candidates for providing carbon skeletons to NADH-glutamate synthase.''; PubMed Europe PMC Scholia
  8. Figueroa P, Léon G, Elorza A, Holuigue L, Araya A, Jordana X.; ''The four subunits of mitochondrial respiratory complex II are encoded by multiple nuclear genes and targeted to mitochondria in Arabidopsis thaliana.''; PubMed Europe PMC Scholia
  9. Figueroa P, León G, Elorza A, Holuigue L, Jordana X.; ''Three different genes encode the iron-sulfur subunit of succinate dehydrogenase in Arabidopsis thaliana.''; PubMed Europe PMC Scholia
  10. Day DA, Hanson JB.; ''Pyruvate and malate transport and oxidation in corn mitochondria.''; PubMed Europe PMC Scholia
  11. Studart-Guimarães C, Gibon Y, Frankel N, Wood CC, Zanor MI, Fernie AR, Carrari F.; ''Identification and characterisation of the alpha and beta subunits of succinyl CoA ligase of tomato.''; PubMed Europe PMC Scholia

History

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CompareRevisionActionTimeUserComment
127040view19:35, 25 July 2023KhanspersOntology Term : 'citric acid cycle pathway' added !
127039view19:34, 25 July 2023KhanspersOntology Term : 'classic metabolic pathway' added !
127038view19:29, 25 July 2023KhanspersModified description
117424view10:44, 21 May 2021EweitzModified title
82151view12:38, 9 September 2015Anweshafixing title, data source, & tagging incomplete pathways
82073view14:42, 8 September 2015Anweshafixing title, data source, & tagging incomplete pathways
80524view14:49, 25 June 2015AnweshaNew pathway

External references

DataNodes

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NameTypeDatabase referenceComment
2OGMetaboliteCHEBI:30915 (ChEBI)
ACOProtein1121696 (Reactome) Facilitates the conversion of 2-isopropylmalate to 3-isopropylmalate.
ADPMetaboliteCHEBI:16761 (ChEBI)
ATPMetaboliteCHEBI:15422 (ChEBI)
Ac-CoAMetaboliteCHEBI:15351 (ChEBI)
CITMetaboliteCHEBI:30769 (ChEBI)
CO2MetaboliteCHEBI:16526 (ChEBI)
CSYProtein1121841 (Reactome) Catalyzes the conversion of Acetyl-CoA to Citric acid.
CoA-SHMetaboliteCHEBI:15346 (ChEBI)
CoQMetaboliteCHEBI:16389 (ChEBI)
FUM1 (LOC_Os03g21950.1)ProteinQ10LR5 (Uniprot-TrEMBL) Catalyzes the convertion of fumaric acid into malate.
FUMAMetaboliteCHEBI:18012 (ChEBI)
H+MetaboliteCHEBI:15378 (ChEBI)
H2OMetaboliteCHEBI:15377 (ChEBI)
IDH (NAD) complexComplex1173231 (Reactome) Catalyzes the conversion from isocitrate to 2-oxoglutarate.
ISCITMetaboliteCHEBI:151 (ChEBI)
MALMetaboliteCHEBI:30797 (ChEBI)
MDHProtein1122020 (Reactome)
Malate dehydrogenase (decarboxylating)Protein5146764 (Reactome) Catalyzes the conversion of (S)-malate to pyruvate.
NAD+MetaboliteCHEBI:15846 (ChEBI)
NADHMetaboliteCHEBI:16908 (ChEBI)
OAMetaboliteCHEBI:30744 (ChEBI)
OGDH complexComplex1173227 (Reactome) Catalyzes the conversion of 2-oxoglutarate into succinyl-CoA.
PYRMetaboliteCHEBI:32816 (ChEBI)
PiMetaboliteCHEBI:18367 (ChEBI)
QH2MetaboliteCHEBI:17976 (ChEBI)
SCS dimerComplex1173262 (Reactome) Catalyzes the conversion of Succinyl-CoA to Succinate.
SDH complexComplex1173274 (Reactome) Catalyzes the conversion of Succinate to Fumaric acid.
SUCC-CoAMetaboliteCHEBI:15380 (ChEBI)
SUCCAMetaboliteCHEBI:15741 (ChEBI)

Annotated Interactions

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SourceTargetTypeDatabase referenceComment
1119632 (Reactome) Mitochondrial aconitase reversibly converts citrate to isocitrate via a cis-aconitate intermediate. Two candidate rice aconitase enzymes have been identified by similarity to Arabidopsis thaliana proteins.
1120092 (Reactome) Citrate synthase in the mitochondrial matrix catalyzes the reaction of oxaloacetate, acetyl-CoA, and H2O to form citrate and CoA-SH. Rice citrate synthase has not been characterized experimentally. Two candidate citrate synthase proteins predicted from analysis of the rice genomic DNA sequence have been identified and distinguished from potential peroxisomal citrate synthase isoforms based on sequence similarity to Arabidospsis thaliana proteins.
1120194 (Reactome) Mitochondrial isocitrate dehydrogenase catalyzes the reaction of isocitrate and NAD+ to form 2-oxoglutarate, CO2 and NADH + H+. The enzyme is a complex of regulatory and catalytic subunits, and has been characterized experimentally in rice as a component of the process by which inorganic nitrogen is assimilated and used for amino acid biosynthesis in root cells (Akibo et al. 2005).
1120286 (Reactome) The succinate dehydrogenase complex catalyzes the reaction of succinate and ubiquinone to form fumarate and ubiquinol. The electrons yielded in this reaction ultimately enter mitochondrial electron transport via FAD. The rice complex has not been studied experimentally; the identities of its components are inferred by homology from those of the better-studied Arabidopsis thaliana complex (Figueroa et al. 2001, 2002).
1120492 (Reactome) The mitochondrial OGDH complex catalyzes the reaction of 2-oxoglutarate, coA-SH, and NAD+ to form succinyl-CoA, CO2, andNADH + H+. Putative rice OGDH E1, E2, and E3 subunit proteins have been identified based on sequence similarity with Arabidopsis thaliana orthologues. The stoichiometry of the rice complex is unknown.
1120787 (Reactome) Mitochondrial malate dehydrogenase catalyzes the reversible reaction of malate and NAD+ to form oxaloacetate and NADH + H+. The rice enzymes that catalyze this reaction have not been studied experimentally but two candidate proteins have been identified on the basis of sequence similarity to malate dehydrogenase enzymes of other, better-studied plant species.
1121548 (Reactome) Mitochondrial fumarate hydratase (FUM1) catalyzes the reversible reaction of fumarate and H2) to form malate. The rice FUM1 enzyme has not been characterized experimentally; its properties are inferred from those of better-studied plant orthologues.
1121627 (Reactome) Mitochndrial SCS (succinyl-CoA ligase) catalyzes the reaction of succinyl-CoA, ADP, and orthophosphate to form succinate, ATP, and CoA-SH. The rice enzyme has not been experimentally characterized but is inferred to be a heterodimer by orthology to well-studied tomato proteins (Studart-Guimaraes et al. 2005).
2OG1120492 (Reactome)
2OGArrow1120194 (Reactome)
5146774 (Reactome) Pyruvate is converted into Acetyl-CoA.
5146775 (Reactome) Malate is converted into pyruvate through the catalytic activity of Malate dehydrogenase (decarboxylating)
ACOmim-catalysis1119632 (Reactome)
ADP1121627 (Reactome)
ATPArrow1121627 (Reactome)
Ac-CoA1120092 (Reactome)
Ac-CoAArrow5146774 (Reactome)
CIT1119632 (Reactome)
CITArrow1120092 (Reactome)
CO2Arrow1120194 (Reactome)
CO2Arrow1120492 (Reactome)
CO2Arrow5146774 (Reactome)
CO2Arrow5146775 (Reactome)
CSYmim-catalysis1120092 (Reactome)
CoA-SH1120492 (Reactome)
CoA-SH5146774 (Reactome)
CoA-SHArrow1120092 (Reactome)
CoA-SHArrow1121627 (Reactome)
CoQ1120286 (Reactome)
FUM1 (LOC_Os03g21950.1)mim-catalysis1121548 (Reactome)
FUMA1121548 (Reactome)
FUMAArrow1120286 (Reactome)
H+Arrow1120194 (Reactome)
H+Arrow1120492 (Reactome)
H+Arrow1120787 (Reactome)
H+Arrow5146774 (Reactome)
H+Arrow5146775 (Reactome)
H2O1120092 (Reactome)
H2O1121548 (Reactome)
IDH (NAD) complexmim-catalysis1120194 (Reactome)
ISCIT1120194 (Reactome)
ISCITArrow1119632 (Reactome)
MAL1120787 (Reactome)
MAL5146775 (Reactome)
MALArrow1121548 (Reactome)
MDHmim-catalysis1120787 (Reactome)
Malate dehydrogenase (decarboxylating)mim-catalysis5146775 (Reactome)
NAD+1120194 (Reactome)
NAD+1120492 (Reactome)
NAD+1120787 (Reactome)
NAD+5146774 (Reactome)
NAD+5146775 (Reactome)
NADHArrow1120194 (Reactome)
NADHArrow1120492 (Reactome)
NADHArrow1120787 (Reactome)
NADHArrow5146774 (Reactome)
NADHArrow5146775 (Reactome)
OA1120092 (Reactome)
OAArrow1120787 (Reactome)
OGDH complexmim-catalysis1120492 (Reactome)
PYR5146774 (Reactome)
PYRArrow5146775 (Reactome)
Pi1121627 (Reactome)
QH2Arrow1120286 (Reactome)
SCS dimermim-catalysis1121627 (Reactome)
SDH complexmim-catalysis1120286 (Reactome)
SUCC-CoA1121627 (Reactome)
SUCC-CoAArrow1120492 (Reactome)
SUCCA1120286 (Reactome)
SUCCAArrow1121627 (Reactome)
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