Glyoxylate metabolism (Homo sapiens)

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3LumenTissue deposition and CaOx kidney stonesSLC26A1Calcium32Primary hyperoxaluria IGluconeogenesisHYPDHPXMP2Mitochondrial intermembrane spaceHOGHOGA1GRHPRPyruvateGOCytosolGlyoxylateOxalateLDHPeroxisomeCytosolGlyoxylateOxalatePyruvateL-AlanineGlycine3-hydroxypyruvateL-SerineL-Alanine3-hydroxypyruvateD-glycerateL-glycerateLDHDAO2HOGHOGFAD2GlyoxylatePXMP2PXMP2AGT2AGTAGTAGT2AGT2AGT2HOGA1HOGA1HOGA1Primary hyperoxaluria IIIPrimary hyperoxaluria IIMitochondrial matrixHydroxyproline1P5CDHAspAT1HydroxyprolineHepatocyteOxalateGlycolateGlycolateGRGOOxalateLDHLDHLDHGlycolateOxalatePrimary hyperoxaluria IIPyruvateD-glycerateGRPrimary hyperoxaluria II???


Description

Glyoxylate metabolism in hepatocytes, affected in hyperoxaluria (PH) type 1-3. Based on Physicians Guide to the Diagnosis, Treatment, and Follow-up of Inherited Metabolic Diseases by Nenad Blau Chapter 28.

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Ontology Terms

 

Bibliography

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  1. Lai C, Pursell N, Gierut J, Saxena U, Zhou W, Dills M, Diwanji R, Dutta C, Koser M, Nazef N, Storr R, Kim B, Martin-Higueras C, Salido E, Wang W, Abrams M, Dudek H, Brown BD; ''Specific Inhibition of Hepatic Lactate Dehydrogenase Reduces Oxalate Production in Mouse Models of Primary Hyperoxaluria.''; Mol Ther, 2018 PubMed Europe PMC Scholia
  2. Rokka A, Antonenkov VD, Soininen R, Immonen HL, Pirilä PL, Bergmann U, Sormunen RT, Weckström M, Benz R, Hiltunen JK; ''Pxmp2 is a channel-forming protein in Mammalian peroxisomal membrane.''; PLoS One, 2009 PubMed Europe PMC Scholia
  3. Li X, Knight J, Fargue S, Buchalski B, Guan Z, Inscho EW, Liebow A, Fitzgerald K, Querbes W, Todd Lowther, Holmes RP; ''Metabolism of (13)C5-hydroxyproline in mouse models of Primary Hyperoxaluria and its inhibition by RNAi therapeutics targeting liver glycolate oxidase and hydroxyproline dehydrogenase.''; https://europepmc.org/article/med/26655602, 2015 PubMed Europe PMC Scholia
  4. Huang A, Burke J, Bunker RD, Mok YF, Griffin MD, Baker EN, Loomes KM; ''Regulation of human 4-hydroxy-2-oxoglutarate aldolase by pyruvate and α-ketoglutarate: implications for primary hyperoxaluria type-3''; https://pubmed.ncbi.nlm.nih.gov/31696211/, 2019 PubMed Europe PMC Scholia
  5. Jiang H, Gao X, Gong J, Yang Q, Lan R, Wang T, Liu J, Yin C, Wang S, Liu Z; ''Downregulated Expression of Solute Carrier Family 26 Member 6 in NRK-52E Cells Attenuates Oxalate-Induced Intracellular Oxidative Stress.''; Oxid Med Cell Longev, 2018 PubMed Europe PMC Scholia
  6. Atlante A, Seccia TM, Marra E, Minervini GM, Vulpis V, Pirrelli A, Passarella S; ''Carrier-mediated transport controls hydroxyproline catabolism in heart mitochondria from spontaneously hypertensive rat.''; FEBS Lett, 1996 PubMed Europe PMC Scholia
  7. Wanders RJ, Waterham HR, Ferdinandusse S; ''Metabolic Interplay between Peroxisomes and Other Subcellular Organelles Including Mitochondria and the Endoplasmic Reticulum.''; Front Cell Dev Biol, 2015 PubMed Europe PMC Scholia
  8. Grant Pearce F, Hudson AO, Loomes K, Dobson RCJ; ''Dihydrodipicolinate Synthase: Structure, Dynamics, Function, and Evolution''; https://pubmed.ncbi.nlm.nih.gov/28271480/, 2017 PubMed Europe PMC Scholia
  9. Stevens JS, Al-Awqati Q; ''Lactate dehydrogenase 5: identification of a druggable target to reduce oxaluria''; https://pubmed.ncbi.nlm.nih.gov/31107247/, 2019 PubMed Europe PMC Scholia
  10. Dindo M, Ambrosini G, Oppici E, Pey AL, O'Toole PJ, Marrison JL, Morrison IEG, Butturini E, Grottelli S, Costantini C, Cellini B; ''Dimerization Drives Proper Folding of Human Alanine:Glyoxylate Aminotransferase But Is Dispensable for Peroxisomal Targeting.''; J Pers Med, 2021 PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
141961view16:18, 28 November 2025EweitzClear deprecated metadata rendering
136362view14:47, 30 January 2025DeSlUpdated lable for SPT, added lit. ref for dimerization
128248view23:55, 29 January 2024EweitzSoften and use solid-lined rounded rectangles for disease nodes
127754view13:54, 2 December 2023EgonwChEBI id for Ca2+ instead of the "Ca" atom
122169view15:00, 14 March 2022EmiliaAgasiCorrected enzyme names and added RHEA IDs to missing interactions
122080view11:45, 10 March 2022EmiliaAgasiUpdated data nodes and added sources
122079view10:58, 10 March 2022DeSlChanged elbow-connector to straight interaction for L-Alanine
122078view10:57, 10 March 2022DeSlConnecting L-serine to same anchor as L-alanine
122077view10:56, 10 March 2022DeSlConnecting L-Alanine to same anchor as enzyme
122076view10:47, 10 March 2022DeSlConnected L-Alanine and Glycine to same anchor
122064view14:00, 9 March 2022EmiliaAgasiChanged identifiers
122050view12:49, 9 March 2022EmiliaAgasiOntology Term : 'primary hyperoxaluria' added !
122049view12:48, 9 March 2022EmiliaAgasiOntology Term : 'hyperoxaluria pathway' added !
122023view10:15, 9 March 2022EmiliaAgasireactions modified
122021view10:12, 9 March 2022EmiliaAgasiCHEBI modification
122019view10:08, 9 March 2022EmiliaAgasiConnected diseases to interaction nodes and modified RHEA IDs
121940view14:39, 8 March 2022EmiliaAgasiAdded source and corrected enzyme identifier of LDH5
121919view12:40, 8 March 2022EmiliaAgasiAdded complex in legend and corrected naming error
121772view13:48, 3 March 2022DeSlCondensed pathway, updated layout of legend
121771view13:34, 3 March 2022DeSlSmall layout changes, aligning
121688view07:59, 25 February 2022EgonwRemoved the RHEA prefix
121657view13:28, 23 February 2022EmiliaAgasiAdded reference
121655view13:23, 23 February 2022EmiliaAgasiAdded missing data nodes
121632view14:57, 22 February 2022EgonwUpdated a UniProt data source
121571view14:12, 21 February 2022Alexandraboschaddition of Rhea interactions
121560view12:44, 21 February 2022Alexandraboschchanged 'basic interaction' arrows to 'MIM conversion' where applicable and chnaged translocation arrows from dashed to solid lines + added them to the legend
121547view10:19, 21 February 2022Alexandraboschaddition of Rhea interactions
121472view15:59, 17 February 2022EmiliaAgasiOntology Term : 'D-alanine metabolic pathway' added !
121471view15:57, 17 February 2022EmiliaAgasiOntology Term : 'native cell' added !
121470view15:55, 17 February 2022EmiliaAgasiOntology Term : 'inherited metabolic disorder' added !
121469view15:51, 17 February 2022EmiliaAgasiOntology Term : 'glycine metabolic pathway' added !
121468view15:50, 17 February 2022EmiliaAgasiOntology Term : 'disease pathway' added !
121467view15:49, 17 February 2022EmiliaAgasiModified description
121466view15:49, 17 February 2022EmiliaAgasiAdded different connection points for byproduct of enzymatic reactions
121465view15:45, 17 February 2022EmiliaAgasiAdded missing identifiers and secondary PH
121420view11:20, 17 February 2022EmiliaAgasiModified description
121407view10:13, 17 February 2022EmiliaAgasiOntology Term : 'primary hyperoxaluria pathway' added !
121406view10:13, 17 February 2022EmiliaAgasiOntology Term : 'primary hyperoxaluria type 2 pathway' added !
121405view10:12, 17 February 2022EmiliaAgasiOntology Term : 'primary hyperoxaluria type 1 pathway' added !
121404view10:12, 17 February 2022EmiliaAgasiOntology Term : 'primary hyperoxaluria type 2' added !
121403view10:11, 17 February 2022EmiliaAgasiOntology Term : 'primary hyperoxaluria type 3' added !
121402view10:10, 17 February 2022EmiliaAgasiOntology Term : 'primary hyperoxaluria type 1' added !
121401view10:10, 17 February 2022EmiliaAgasiOntology Term : 'hepatocyte' added !
121397view10:03, 17 February 2022EmiliaAgasiAdded additional literature
121185view15:41, 10 February 2022EmiliaAgasiMade some enzymes complexes, changed mitochondrion, added transporters, added OMIM disease links
121136view15:51, 9 February 2022EmiliaAgasiConnected all points and added interactions using Rhea, found missing identifiers, improved layout
121105view14:26, 8 February 2022EmiliaAgasiNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
1P5CDHProtein1.2.1.88 (BRENDA)
  • 1-pyrroline-5-carboxylate dehydrogenase
  • Add "EC" with EC identifier?
3-hydroxypyruvateMetaboliteCHEBI:17180 (ChEBI)
?
  • Unknown mitochondrial HPRO carrier
  • Id: R-HSA-8953316.2 (found on Reactome)
AGT2MetaboliteQ50266211 (Wikidata) Alanine-glyoxylate aminotransferase 2
AGTMetaboliteQ50266777 (Wikidata)
  • Serine-pyruvate transaminase
  • https://www.uniprot.org/uniprot/P21549
AspATProteinP00505 (Uniprot-TrEMBL) aspartate aminotransferase
CalciumMetaboliteCHEBI:22984 (ChEBI)
D-glycerateMetaboliteQ27102017 (Wikidata)
DAOProteinP14920 (Uniprot-SwissProt) D-amino acid oxidase:FAD complex
FADProteinP14920 (Uniprot-SwissProt) Flavin adenine dinucleotide
GOProteinGlycolate oxidase
GRHPRProteinQ9UBQ7 (Uniprot-SwissProt) Also called D-glycerate dehydrogenase (GDH), and hydroxypyruvate reductase
GRProteinQ9UBQ7 (Uniprot-TrEMBL) Glyoxylate reductase/hydroxypyruvate reductase
GluconeogenesisPathwayhttps://www.wikipathways.org/index.php/Pathway:WP4361
GlycineMetaboliteCHEBI:57305 (ChEBI)
GlycolateMetaboliteCHEBI:29805 (ChEBI)
GlyoxylateMetaboliteCHEBI:36655 (ChEBI)
HOGA1ProteinQ86XE5 (Uniprot-SwissProt) 4-hydroxy-2-oxoglutarate aldolase 1
HOGMetaboliteCHEBI:17742 (ChEBI)
  • What is happening here?
  • 4-hydroxy-2-oxoglutarate
HYPDHProteinQ9UF12 (Uniprot-TrEMBL) Hydroxyproline dehydrogenase
HydroxyprolineMetaboliteCHEBI:18095 (ChEBI) trans-4-hydroxy-L-proline
L-AlanineMetaboliteCHEBI:57972 (ChEBI)
L-SerineMetaboliteCHEBI:33384 (ChEBI)
L-glycerateMetaboliteQ27102017 (Wikidata)
LDHProtein1.1.1.27 (BRENDA) L-lactate dehydrogenase
OxalateMetaboliteCHEBI:30623 (ChEBI)
PXMP2ProteinQ9NR77 (Uniprot-TrEMBL) Peroxisomal membrane protein 2
PyruvateMetaboliteCHEBI:15361 (ChEBI)
SLC26A1ProteinQ9H2B4 (Uniprot-TrEMBL)

Annotated Interactions

SourceTargetTypeDatabase referenceComment
GRHPRmim-catalysisRHEA:17905 (Rhea)
GlyoxylateOxalateArrowRHEA:14837 (Rhea)
mim-catalysisRHEA:18169 (Rhea)
mim-catalysisRHEA:22852 (Rhea)
mim-catalysisRHEA:24248 (Rhea)
Retrieved from "https://oldclassic.wikipathways.org/index.php/Pathway:WP5166"
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