Trans-sulfuration, one-carbon metabolism and related pathways (Homo sapiens)

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1PHGDH3P-Glycerate3P-HydroxypyruvatePhosphoserinePSAT1PSPHTHFdUMP5,10-Methenyl-THF10-Formyl-THF5,10-Methylene-THFDihydrofolatedTMPTYMSDHFRDHFRL1MTHFD1MTHFD2MTHFD2LMTHFD1LMTHFD1LMTHFD1MTHFD2MTHFD2LMTRBHMTCBSGSSGCLCGCLMGSSPutrescineDecarboxylated SAMCysteine sulphinateOrnithineSpermineSpermidineBile acid biosynthesisH2OOxidative stress enzymesH2O2S-AdenosylhomocysteineTotal PhospholipidsL-MethionineETNK2GPX5SOD13-SulfinoalanineL-CysteineCSADCHPT1NADPHypotaurineGlutathione (GSH)DHFR2Tetrahydrofolic acidPCYT1AMAT2AGSRPhosphocholinePCYT1BEthanolamineTaurocholic acidETNK1Glutathione disulfide (GSSG)5,10-Methenyltetrahydrofolic acidCEPT1SOD3MAT1ATaurochenodesoxycholic acidGPX7CTHGlutamateCDP-cholineGSSCHDHDNMT3AO-PhosphoethanolamineBHMT2PhosphatidylethanolamineMTHFRDNM1DimethylglycineBetainePLD1SOD2GPX6PhosphatidylcholinesCHKBGAD1CDO1GAD2L-SerineTaurineGNMTNADPHBHMTSHMT1SarcosineCDP-EthanolaminePCYT2SARDHGPX4GPX2GPX1MTRGCLM10-formyldihydrofolateGPX3AHCYL1CBSL5-oxoprolineDMGDHBAAT5-Methyltetrahydrofolic acidL-CystathionineFolic acidS-AdenosylmethionineHomocysteineGlycineSHMT2CHKACholineTYMSgamma-GlutamylcysteineGCLCL-SerinePEMTGlycine2-oxobutanoate(S)-2-Aminobutanoategamma-L-Glutamyl-L-2-aminobutyrateOphthalmateBCAT1AGXT2GCLCGSSBCAT2GCLMAcetylcholineAMTMAT2BDNMT3BDNMT3LAHCYAHCYL2GlutathioneL-SerineGlycineBetainealdehydeALDH7A12


Description

This pathway shows the (one) carbon metabolism over grey and related pathways around it.

The one carbon donor pathway (WP2190) has been added to this one (additional conversions are coloured green for clarity of the origin); as well as WP3940 (overlapping content in bold), which was based on KEGG and inferred from Mus musculus pathway WP1770_96326 with a 100.0% conversion rate.

Proteins on this pathway have targeted assays available via the CPTAC Assay Portal.

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View approved pathways at the new wikipathways.org.

Quality Tags

Ontology Terms

 

Bibliography

  1. Verkerke ARP, Shi X, Abe I, Gerszten RE, Kajimura S; ''Mitochondrial choline import regulates purine nucleotide pools via SLC25A48.''; bioRxiv, 2024 PubMed Europe PMC Scholia
  2. Ducker GS, Rabinowitz JD; ''One-Carbon Metabolism in Health and Disease.''; Cell Metab, 2017 PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
135191view16:49, 7 August 2024EgonwMIM translocation across the mitochondrial membrane
135190view16:46, 7 August 2024EgonwSLC25A48 transports choline into the mitochondrion
135189view16:41, 7 August 2024EgonwCholine to betaine is a two-step reaction
123451view15:01, 27 July 2022DeSlAdded bile acid biosynthesis PW link.
123450view14:59, 27 July 2022DeSlUpdated title, removed last modified section
123449view14:58, 27 July 2022DeSlOntology Term : 'folate metabolic pathway' added !
123448view14:56, 27 July 2022DeSlOntology Term : 'folate mediated one-carbon metabolic pathway' added !
123447view14:55, 27 July 2022DeSlUpdate description
123446view14:54, 27 July 2022DeSlCompleted merger
123445view14:36, 27 July 2022DeSlMerging WP2525 with WP3940
116582view11:08, 8 May 2021EweitzModified title
106716view13:15, 17 September 2019MaintBotHMDB identifier normalization
105844view23:13, 15 August 2019KhanspersModified description
101747view05:25, 5 November 2018EgonwEquivalent CID (different protonation) but this CID is approved.
97822view15:27, 9 June 2018EgonwModified description
97786view14:10, 7 June 2018DeSlChanged arrows to catalysis MIM-type where applicable.
97785view14:05, 7 June 2018DeSlModified description
97782view14:00, 7 June 2018DeSlAdded info from One Carbon Donor PW (WP2190) in green.
97737view13:00, 7 June 2018Jessev1993Added literature reference.
97734view12:57, 7 June 2018Jessev1993Modified description
97730view12:51, 7 June 2018Jessev1993Modified description
87802view11:23, 25 July 2016MirellaKalafatiOntology Term : 'classic metabolic pathway' added !
80205view20:49, 22 May 2015KhanspersReverted to version '10:30, 7 January 2015' by Khanspers
80149view18:41, 14 May 2015KhanspersAdded mir29 family targeting and associated lit ref
78541view10:30, 7 January 2015MaintBotadded missing graphIds
72048view16:55, 24 October 2013Mkutmonupdated annotations
72039view13:49, 24 October 2013Mkutmonfixed unconnected lines
71253view20:51, 16 October 2013MaintBotAutomated update of data sources
69727view17:06, 10 July 2013Leonjohn2008Ver 1.3
69726view15:53, 10 July 2013Leonjohn2008Ver 1.2
69725view15:43, 10 July 2013Leonjohn2008Ver 1.2
69724view15:40, 10 July 2013Leonjohn2008Periodical save, work in progress
69723view15:30, 10 July 2013Leonjohn2008Periodical save, work in progress
69722view15:11, 10 July 2013Leonjohn2008Ver 1.1
69721view14:30, 10 July 2013Leonjohn2008Periodical save, work in progress
69720view14:19, 10 July 2013Leonjohn2008Periodical save, work in progress
69719view14:09, 10 July 2013Leonjohn2008Periodical save, work in progress
69718view13:45, 10 July 2013Leonjohn2008Periodical save, work in progress
69717view13:42, 10 July 2013Leonjohn2008Ver 1.1
69716view13:37, 10 July 2013Leonjohn2008V1.1
69715view13:31, 10 July 2013Leonjohn2008Ver1.1
69713view04:28, 10 July 2013Leonjohn2008Ver1.0
69712view03:57, 10 July 2013Leonjohn2008Periodical save, work in progress
69711view03:33, 10 July 2013Leonjohn2008New pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
(S)-2-AminobutanoateMetaboliteCHEBI:35619 (ChEBI)
10-Formyl-THFMetaboliteC00234 (KEGG Compound)
10-formyldihydrofolateMetaboliteHMDB0006485 (HMDB)
2-oxobutanoateMetaboliteCHEBI:16763 (ChEBI)
3-SulfinoalanineMetaboliteC00606 (KEGG Compound)
3P-GlycerateMetaboliteC00597 (KEGG Compound)
3P-HydroxypyruvateMetaboliteC03232 (KEGG Compound)
5,10-Methenyl-THFMetaboliteC00445 (KEGG Compound)
5,10-Methenyltetrahydrofolic acidMetaboliteC00445 (KEGG Compound)
5,10-Methylene-THFMetaboliteC00143 (KEGG Compound)
5-Methyltetrahydrofolic acidMetaboliteC00440 (KEGG Compound)
5-oxoprolineMetaboliteC01879 (KEGG Compound)
AGXT2GeneProductENSG00000113492 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = En:ENSMUSG00000089678
AHCYGeneProduct191 (Entrez Gene)
AHCYL1GeneProductENSG00000168710 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:229709
AHCYL2GeneProduct23382 (Entrez Gene)
ALDH7A1GeneProductENSG00000164904 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:218865
AMTGeneProduct275 (Entrez Gene)
AcetylcholineMetaboliteHMDB0000895 (HMDB)
BAATGeneProductENSG00000136881 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:12012
BCAT1GeneProductENSG00000060982 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = En:ENSMUSG00000030268
BCAT2GeneProductENSG00000105552 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = En:ENSMUSG00000030826
BHMT2GeneProductENSG00000132840 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:64918
BHMTGeneProduct635 (Entrez Gene)
BHMTGeneProductENSG00000145692 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:12116
Betaine aldehydeMetabolite15710 (ChEBI)
BetaineMetaboliteC00719 (KEGG Compound)
Bile acid biosynthesisPathwayWP5176 (WikiPathways)
CBSGeneProduct875 (Entrez Gene)
CBSLGeneProductENSG00000274276 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:12411
CDO1GeneProductENSG00000129596 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:12583
CDP-EthanolamineMetaboliteC00570 (KEGG Compound)
CDP-cholineMetaboliteC00307 (KEGG Compound)
CEPT1GeneProductENSG00000134255 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:99712
CHDHGeneProductENSG00000016391 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:218865
CHKAGeneProductENSG00000110721 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:12660
CHKBGeneProductENSG00000100288 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:12651
CHPT1GeneProductENSG00000111666 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:212862
CSADGeneProductENSG00000139631 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:246277
CTHGeneProductENSG00000116761 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:107869
CholineMetaboliteC00114 (KEGG Compound)
Cysteine sulphinateMetabolite6409687 (PubChem-compound)
DHFRGeneProduct1719 (Entrez Gene)
DHFR2GeneProductENSG00000178700 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:13361
DHFRL1GeneProduct200895 (Entrez Gene)
DMGDHGeneProductENSG00000132837 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:74129
DNM1GeneProductENSG00000106976 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:13429
DNMT3AGeneProductENSG00000119772 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:13435
DNMT3BGeneProduct1789 (Entrez Gene)
DNMT3LGeneProduct29947 (Entrez Gene)
Decarboxylated SAMMetabolite25203490 (PubChem-compound)
DihydrofolateMetaboliteC00415 (KEGG Compound)
DimethylglycineMetaboliteC01026 (KEGG Compound)
ETNK1GeneProductENSG00000139163 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:75320
ETNK2GeneProductENSG00000143845 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:214253
EthanolamineMetaboliteC00189 (KEGG Compound)
Folic acidMetaboliteC00504 (KEGG Compound)
GAD1GeneProductENSG00000128683 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:14415
GAD2GeneProductENSG00000136750 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:14417
GCLCGeneProduct2729 (Entrez Gene)
GCLCGeneProductENSG00000001084 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = En:ENSMUSG00000032350
GCLMGeneProduct2730 (Entrez Gene)
GCLMGeneProductENSG00000023909 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = En:ENSMUSG00000028124
GNMTGeneProductENSG00000124713 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:14711
GPX1GeneProductENSG00000233276 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:14775
GPX2GeneProductENSG00000176153 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:14776
GPX3GeneProductENSG00000211445 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:14778
GPX4GeneProductENSG00000167468 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:625249
GPX5GeneProductENSG00000224586 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:14780
GPX6GeneProductENSG00000198704 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:75512
GPX7GeneProductENSG00000116157 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:67305
GSRGeneProductENSG00000104687 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:14782
GSSGeneProduct2937 (Entrez Gene)
GSSGeneProductENSG00000100983 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = En:ENSMUSG00000027610
GlutamateMetaboliteC00217 (KEGG Compound)
Glutathione (GSH)MetaboliteC00051 (KEGG Compound)
Glutathione disulfide (GSSG)MetaboliteC00127 (KEGG Compound)
GlutathioneMetaboliteC00051 (KEGG Compound)
GlycineMetaboliteC00037 (KEGG Compound)
HomocysteineMetaboliteC05330 (KEGG Compound)
HypotaurineMetaboliteC00519 (KEGG Compound)
L-CystathionineMetaboliteC02291 (KEGG Compound)
L-CysteineMetaboliteC00097 (KEGG Compound)
L-MethionineMetaboliteHMDB0000696 (HMDB)
L-SerineMetaboliteC00065 (KEGG Compound)
MAT1AGeneProductENSG00000151224 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:11720
MAT2AGeneProductENSG00000168906 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:232087
MAT2BGeneProduct27430 (Entrez Gene)
MTHFD1GeneProduct4522 (Entrez Gene)
MTHFD1LGeneProduct1719 (Entrez Gene)
MTHFD1LGeneProduct25902 (Entrez Gene)
MTHFD2GeneProduct10797 (Entrez Gene)
MTHFD2LGeneProduct441024 (Entrez Gene)
MTHFRGeneProductENSG00000177000 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:17769
MTRGeneProduct4548 (Entrez Gene)
MTRGeneProductENSG00000116984 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:238505
NADPMetaboliteC00006 (KEGG Compound)
NADPHMetaboliteC00005 (KEGG Compound)
O-PhosphoethanolamineMetaboliteC00346 (KEGG Compound)
OphthalmateMetabolite7018721 (PubChem-compound)
OrnithineMetaboliteHMDB0000214 (HMDB)
PCYT1AGeneProductENSG00000161217 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:13026
PCYT1BGeneProductENSG00000102230 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:236899
PCYT2GeneProductENSG00000185813 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:68671
PEMTGeneProductENSG00000133027 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:18618
PHGDHGeneProduct26227 (Entrez Gene)
PLD1GeneProductENSG00000075651 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:18805
PSAT1GeneProduct29968 (Entrez Gene)
PSPHGeneProduct5723 (Entrez Gene)
PhosphatidylcholinesMetabolite8002-43-5 (CAS)
PhosphatidylethanolamineMetaboliteC00350 (KEGG Compound)
PhosphocholineMetaboliteCHEBI:18132 (ChEBI)
PhosphoserineMetaboliteC01005 (KEGG Compound)
PutrescineMetaboliteHMDB0001414 (HMDB)
S-AdenosylhomocysteineMetaboliteC00021 (KEGG Compound)
S-AdenosylmethionineMetaboliteC00019 (KEGG Compound)
SARDHGeneProductENSG00000123453 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:192166
SHMT1GeneProductENSG00000176974 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:20425
SHMT2GeneProductENSG00000182199 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:108037
SOD1GeneProductENSG00000142168 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:20655
SOD2GeneProductENSG00000112096 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:20656
SOD3GeneProductENSG00000109610 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:20657
SarcosineMetaboliteC00213 (KEGG Compound)
SpermidineMetaboliteHMDB0001257 (HMDB)
SpermineMetaboliteHMDB0001256 (HMDB)
THFMetaboliteC00101 (KEGG Compound)
TYMSGeneProduct7298 (Entrez Gene)
TYMSGeneProductENSG00000176890 (Ensembl) Homology Mapping from Mus musculus to Homo sapiens: Original ID = L:22171
TaurineMetaboliteC00245 (KEGG Compound)
Taurochenodesoxycholic acidMetaboliteC05465 (KEGG Compound)
Taurocholic acidMetaboliteC05122 (KEGG Compound)
Tetrahydrofolic acidMetaboliteC00101 (KEGG Compound) aka THF
Total PhospholipidsMetaboliteCHEBI:16247 (ChEBI)
dTMPMetaboliteC00364 (KEGG Compound)
dUMPMetaboliteC00365 (KEGG Compound)
gamma-GlutamylcysteineMetaboliteC00669 (KEGG Compound)
gamma-L-Glutamyl-L-2-aminobutyrateMetabolite7014903 (PubChem-compound)

Annotated Interactions

No annotated interactions

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