Serine metabolism (Homo sapiens)

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1133-Phosphoglycerate dehydrogenase deficiency(2R)-3-phosphoglyceratepyruvatePSPHGlycineglucose3-PhosphoserineSHMT2D-Glyceraldehyde 3-phosphatePSAT1DHFRSHMT1H+glycolysisPhosphatidylserineSRMg2+PHGDHMethylene-THFD-serineTYMSPLPNAD+3-PhosphohydroxypyruvateL-serineNADHglutamate2-KetoglutarateH2OPidTMPdUMPDHFTHFglycolysissphingolipidsceramidesPhosphoserine phosphatase deficiencyPhosphoserube aminotransferase deficiencyDiseaseCatalysisPathwayStimulationProteinMetaboliteConversionConnection to diseaseLegend2


This pathway shows disorders related to serine metabolism. Disorders resulting from an enzyme defect are highlighted in pink. This pathway was inspired by Chapter 5 (ed. 4) from the book of Blau (ISBN 3642403360 (978-3642403361)), Fig. 5.2.

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Ontology Terms



  1. Blau N, Duran M, Gibson KM, Dionisi-Vici C; ''Physician's Guidee to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases'''; Springer ISBN 3642403360, 2014
  2. Fan J, Teng X, Liu L, Mattaini KR, Looper RE, Vander Heiden MG, Rabinowitz JD; ''Human phosphoglycerate dehydrogenase produces the oncometabolite D-2-hydroxyglutarate.''; ACS Chem Biol, 2015 PubMed Europe PMC Scholia
  3. Foltyn VN, Bendikov I, De Miranda J, Panizzutti R, Dumin E, Shleper M, Li P, Toney MD, Kartvelishvily E, Wolosker H; ''Serine racemase modulates intracellular D-serine levels through an alpha,beta-elimination activity.''; J Biol Chem, 2005 PubMed Europe PMC Scholia


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120418view09:41, 30 November 2021Fehrhartboxed pathway node
119121view08:53, 18 June 2021FinterlyRemoved duplicate Biopax, fixed biopaxRef
119120view08:51, 18 June 2021FinterlyAdded ISBN for book citation
118577view13:36, 28 May 2021Fehrhartadapted disease node graphics to the one in the legend
117174view09:55, 18 May 2021EweitzModified title
116210view13:07, 20 April 2021EgonwRemoved spaces in two ChEBI identifiers
116200view14:13, 19 April 2021DeSlChanged TYMS UniGene to UniProt Database
116199view14:10, 19 April 2021DeSlUpdated Pw DataNodes
116198view14:02, 19 April 2021DeSlUpdated TYMS Ensembl ID to UniProt.
116197view13:49, 19 April 2021DeSlAdded Ref for unclear interaction to 3-PP-H-pyruvate
116196view13:41, 19 April 2021DeSlUpdated more Proteins to Uniprot IDs, added details on DataNodes in comments+refs
116195view13:31, 19 April 2021DeSlAdded Rhea IDs for side metabolites untill L-serine conversion
116194view13:29, 19 April 2021DeSlUpdated PSAT1 ID from Ensembl to Uniprot
116193view13:28, 19 April 2021DeSlAdded detauls on PHGDH conversion.
116192view13:20, 19 April 2021DeSlChanges NAD+ ID back to original (since CHEBI:57540 is NAD-).
116191view13:04, 19 April 2021DeSlChanged GeneProducts back to Protein DataNodes
116188view18:34, 18 April 2021YasminomarAnnotated the remaining metabolites and interactions (except for the reaction catalyzed by PHGDH) and changed some IDs to the ones given in Rhea.
114136view10:39, 23 December 2020DeSlAdded legend, updated connections to diseases to graphical lines, arrows between metabolites and PWs to translocations.
114135view10:36, 23 December 2020DeSlUpdate description.
107647view07:43, 25 October 2019DeSlUpdated layout
107634view15:35, 24 October 2019DeSlChanged complex for metabolites into group.
107633view15:34, 24 October 2019DeSlChanged complex of metabolites to group.
107632view15:34, 24 October 2019DeSlUpdated layout
107631view15:33, 24 October 2019DeSlUpdated secondary ChEBI IDs.
107540view18:13, 18 October 2019Khanspersadded xrefs
106455view09:50, 30 August 2019DeSlUpdated glycolysis PW ID
106454view09:49, 30 August 2019DeSlOntology Term : 'PSPH deficiency' added !
106453view09:49, 30 August 2019DeSlOntology Term : 'PSAT deficiency' added !
106452view09:47, 30 August 2019DeSlOntology Term : 'PHGDH deficiency' added !
106220view12:23, 16 August 2019AkutmonOntology Term : 'inherited metabolic disorder' added !
106219view12:20, 16 August 2019AkutmonOntology Term : 'serine metabolic pathway' added !
106218view12:17, 16 August 2019Akutmonchanged deaseases to labels
106217view12:14, 16 August 2019AkutmonNew pathway

External references


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NameTypeDatabase referenceComment
(2R)-3-phosphoglycerateMetaboliteCHEBI:58272 (ChEBI)
2-KetoglutarateMetaboliteCHEBI:16810 (ChEBI)
3-PhosphohydroxypyruvateMetaboliteCHEBI:18110 (ChEBI)
3-PhosphoserineMetaboliteCHEBI:57524 (ChEBI)
D-Glyceraldehyde 3-phosphateMetaboliteCHEBI:29052 (ChEBI)
D-serineMetaboliteCHEBI:35247 (ChEBI)
DHFMetaboliteCHEBI:57451 (ChEBI) aka 7,8-dihydrofolate
DHFRProteinP00374 (Uniprot-TrEMBL)
GlycineMetaboliteCHEBI:57305 (ChEBI)
H+MetaboliteCHEBI:15378 (ChEBI)
H2OMetaboliteCHEBI:15377 (ChEBI)
L-serineMetaboliteCHEBI:33384 (ChEBI)
Methylene-THFMetaboliteCHEBI:15636 (ChEBI)
Mg2+MetaboliteCHEBI:18420 (ChEBI)
NAD+MetaboliteCHEBI:15846 (ChEBI)
NADHMetaboliteCHEBI:57945 (ChEBI)
PHGDHProteinO43175 (Uniprot-TrEMBL)
PLPMetaboliteCHEBI:18405 (ChEBI)
PSAT1ProteinQ9Y617 (Uniprot-TrEMBL)
PSPHProteinP78330 (Uniprot-TrEMBL)
PhosphatidylserineMetaboliteCHEBI:18303 (ChEBI)
PiMetaboliteCHEBI:43474 (ChEBI)
SHMT1ProteinP34896 (Uniprot-TrEMBL) serine hydroxymethyltransferase 1, cytosolic
SHMT2ProteinP34897 (Uniprot-TrEMBL) serine hydroxymethyltransferase 2; mitochondrial
SRProteinQ9GZT4 (Uniprot-TrEMBL) Serine racemase
THFMetaboliteCHEBI:57453 (ChEBI)
TYMSProteinP04818 (Uniprot-TrEMBL)
ceramidesMetaboliteCHEBI:17761 (ChEBI)
dTMPMetaboliteCHEBI:63528 (ChEBI)
dUMPMetaboliteCHEBI:246422 (ChEBI)
glucoseMetaboliteCHEBI:17234 (ChEBI)
glutamateMetaboliteCHEBI:29985 (ChEBI)
glycolysisPathwayWP534 (WikiPathways)
pyruvateMetaboliteCHEBI:15361 (ChEBI)
sphingolipidsMetaboliteCHEBI:26739 (ChEBI)

Annotated Interactions

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SourceTargetTypeDatabase referenceComment
(2R)-3-phosphoglycerate3-Phosphohydroxypyruvatemim-conversion12642 (Rhea) "PHDGH catalyzes the first reaction of de novo serine biosynthesis, producing 3-phosphohydroxypyruvate by NAD+-coupled oxidation of 3-phosphoglycerate (3PG). The PHGDH reaction is reversible and, under standard conditions, thermodynamically favors the direction from 3-phosphohydroxypyruvate to 3PG. In cells engaged in serine synthesis, the reaction is driven toward 3-phosphohydroxypyruvate due to its consumption by downstream pathway steps." [PMID:25406093]
2-Ketoglutaratemim-conversion14331 (Rhea)
3-Phosphohydroxypyruvate3-Phosphoserinemim-conversion14331 (Rhea)
3-PhosphoserineL-serinemim-conversion21209 (Rhea)
DHFTHFmim-conversion15011 (Rhea)
DHFmim-conversion12105 (Rhea)
H2Omim-conversion21209 (Rhea)
L-serineD-serinemim-conversion10981 (Rhea)
L-serineGlycinemim-conversion15483 (Rhea)
Methylene-THFmim-conversion12105 (Rhea)
Methylene-THFmim-conversion15483 (Rhea)
Pimim-conversion21209 (Rhea)
THFmim-conversion15483 (Rhea)
dUMPdTMPmim-conversion12105 (Rhea)
glutamatemim-conversion14331 (Rhea)
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