L-serine biosynthesis I

MetaCyc:SERSYN-PWY

The phosphorylated L-serine biosynthesis pathway converts (2R)-3-phosphoglycerate to L-serine through 3-phosphooxypyruvate and O-phospho-L-serine.

Pathway type

amino acid biosynthesis

Organism scope

Escherichia coli NCBITaxon:562

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Pathway network

26 nodes · 28 asserted directed edges

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Chemical / cofactor
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Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Escherichia coli `NCBITaxon:562`	taxon
phosphoglycerate dehydrogenase `EC:1.1.1.95`	molecular activity
phosphoserine transaminase `EC:2.6.1.52`	molecular activity
phosphoserine phosphatase `EC:3.1.3.3`	molecular activity
(2R)-3-phosphoglycerate `CHEBI:58272`	small molecule
NAD(+) `CHEBI:57540`	small molecule
3-phosphooxypyruvate `CHEBI:18110`	small molecule
NADH `CHEBI:57945`	small molecule
H+ `CHEBI:15378`	small molecule
L-glutamate `CHEBI:29985`	small molecule
O-phospho-L-serine `CHEBI:57524`	small molecule
2-oxoglutarate `CHEBI:16810`	small molecule
H2O `CHEBI:15377`	small molecule
L-serine `CHEBI:33384`	small molecule
phosphate `CHEBI:43474`	small molecule
D-3-phosphoglycerate dehydrogenase `UniProtKB:P0A9T0`	protein
Phosphoserine phosphatase `UniProtKB:P0AGB0`	protein
magnesium(2+) `CHEBI:18420`	cofactor
manganese(2+) `CHEBI:29035`	cofactor
cobalt(2+) `CHEBI:48828`	cofactor
zinc(2+) `CHEBI:29105`	cofactor
Phosphoserine aminotransferase `UniProtKB:P23721`	protein
cytoplasm `GO:0005737`	cellular component
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
biosynthetic phosphoglycerate dehydrogenase reaction `RHEA:12642`	reaction	left to right
biosynthetic phosphoserine transaminase reaction `RHEA:14331`	reaction	right to left
L-phosphoserine phosphatase reaction `RHEA:21209`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
NAD(+) `CHEBI:57540`	consumes	biosynthetic phosphoglycerate dehydrogenase reaction `RHEA:12642`	RHEA:12642 Source assertion: Rhea lists CHEBI:57540 on the substrates side of RHEA:12642 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/12642']/rh:substrates; rh:contains/rh:compound/rh:accession`
(2R)-3-phosphoglycerate `CHEBI:58272`	consumes	biosynthetic phosphoglycerate dehydrogenase reaction `RHEA:12642`	RHEA:12642 Source assertion: Rhea lists CHEBI:58272 on the substrates side of RHEA:12642 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/12642']/rh:substrates; rh:contains/rh:compound/rh:accession`
biosynthetic phosphoglycerate dehydrogenase reaction `RHEA:12642`	produces	H+ `CHEBI:15378`	RHEA:12642 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:12642 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/12642']/rh:products; rh:contains/rh:compound/rh:accession`
biosynthetic phosphoglycerate dehydrogenase reaction `RHEA:12642`	produces	3-phosphooxypyruvate `CHEBI:18110`	RHEA:12642 Source assertion: Rhea lists CHEBI:18110 on the products side of RHEA:12642 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/12642']/rh:products; rh:contains/rh:compound/rh:accession`
biosynthetic phosphoglycerate dehydrogenase reaction `RHEA:12642`	produces	NADH `CHEBI:57945`	RHEA:12642 Source assertion: Rhea lists CHEBI:57945 on the products side of RHEA:12642 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/12642']/rh:products; rh:contains/rh:compound/rh:accession`
3-phosphooxypyruvate `CHEBI:18110`	consumes	biosynthetic phosphoserine transaminase reaction `RHEA:14331`	RHEA:14331 Source assertion: Rhea lists CHEBI:18110 on the substrates side of RHEA:14331 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14331']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-glutamate `CHEBI:29985`	consumes	biosynthetic phosphoserine transaminase reaction `RHEA:14331`	RHEA:14331 Source assertion: Rhea lists CHEBI:29985 on the substrates side of RHEA:14331 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14331']/rh:substrates; rh:contains/rh:compound/rh:accession`
biosynthetic phosphoserine transaminase reaction `RHEA:14331`	produces	2-oxoglutarate `CHEBI:16810`	RHEA:14331 Source assertion: Rhea lists CHEBI:16810 on the products side of RHEA:14331 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14331']/rh:products; rh:contains/rh:compound/rh:accession`
biosynthetic phosphoserine transaminase reaction `RHEA:14331`	produces	O-phospho-L-serine `CHEBI:57524`	RHEA:14331 Source assertion: Rhea lists CHEBI:57524 on the products side of RHEA:14331 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/14331']/rh:products; rh:contains/rh:compound/rh:accession`
H2O `CHEBI:15377`	consumes	L-phosphoserine phosphatase reaction `RHEA:21209`	RHEA:21209 Source assertion: Rhea lists CHEBI:15377 on the substrates side of RHEA:21209 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21209']/rh:substrates; rh:contains/rh:compound/rh:accession`
O-phospho-L-serine `CHEBI:57524`	consumes	L-phosphoserine phosphatase reaction `RHEA:21209`	RHEA:21209 Source assertion: Rhea lists CHEBI:57524 on the substrates side of RHEA:21209 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21209']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-phosphoserine phosphatase reaction `RHEA:21209`	produces	L-serine `CHEBI:33384`	RHEA:21209 Source assertion: Rhea lists CHEBI:33384 on the products side of RHEA:21209 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21209']/rh:products; rh:contains/rh:compound/rh:accession`
L-phosphoserine phosphatase reaction `RHEA:21209`	produces	phosphate `CHEBI:43474`	RHEA:21209 Source assertion: Rhea lists CHEBI:43474 on the products side of RHEA:21209 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/21209']/rh:products; rh:contains/rh:compound/rh:accession`
phosphoglycerate dehydrogenase `EC:1.1.1.95`	catalyzes	biosynthetic phosphoglycerate dehydrogenase reaction `RHEA:12642`	RHEA:12641 Source assertion: Rhea associates EC:1.1.1.95 with the reaction family containing RHEA:12642. Source location `rh:ec`
phosphoserine transaminase `EC:2.6.1.52`	catalyzes	biosynthetic phosphoserine transaminase reaction `RHEA:14331`	RHEA:14329 Source assertion: Rhea associates EC:2.6.1.52 with the reaction family containing RHEA:14331. Source location `rh:ec`
phosphoserine phosphatase `EC:3.1.3.3`	catalyzes	L-phosphoserine phosphatase reaction `RHEA:21209`	RHEA:21208 Source assertion: Rhea associates EC:3.1.3.3 with the reaction family containing RHEA:21209. Source location `rh:ec`
biosynthetic phosphoglycerate dehydrogenase reaction `RHEA:12642`	precedes	biosynthetic phosphoserine transaminase reaction `RHEA:14331`	MetaCyc:SERSYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:12642 before RHEA:14331 in this pathway. Shared intermediate: CHEBI:18110. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
biosynthetic phosphoserine transaminase reaction `RHEA:14331`	precedes	L-phosphoserine phosphatase reaction `RHEA:21209`	MetaCyc:SERSYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:14331 before RHEA:21209 in this pathway. Shared intermediate: CHEBI:57524. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
D-3-phosphoglycerate dehydrogenase `UniProtKB:P0A9T0`	enables	biosynthetic phosphoglycerate dehydrogenase reaction `RHEA:12642`	UniProtKB:P0A9T0 Source assertion: UniProt annotates UniProtKB:P0A9T0 with catalytic activity for the reaction family of RHEA:12642. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
L-serine `CHEBI:33384`	inhibits	D-3-phosphoglycerate dehydrogenase `UniProtKB:P0A9T0`	UniProtKB:P0A9T0 Source assertion: UniProt activity-regulation annotation: Displays feedback inhibition by L-serine. Inhibited by glycine Source location `comments[commentType='ACTIVITY REGULATION'].texts`
Phosphoserine phosphatase `UniProtKB:P0AGB0`	enables	L-phosphoserine phosphatase reaction `RHEA:21209`	UniProtKB:P0AGB0 Source assertion: UniProt annotates UniProtKB:P0AGB0 with catalytic activity for the reaction family of RHEA:21209. Annotation evidence: curated source annotation; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Phosphoserine phosphatase `UniProtKB:P0AGB0`	has_cofactor	magnesium(2+) `CHEBI:18420`	UniProtKB:P0AGB0 Source assertion: UniProt lists CHEBI:18420 as a cofactor of UniProtKB:P0AGB0 (evidence: ECO:0000269). Binds 1 Mg(2+) ion per subunit. Can also use other divalent metal cations as Mn(2+), Co(2+) and Zn(2+). Source location `comments[commentType='COFACTOR'].cofactors and note`
Phosphoserine phosphatase `UniProtKB:P0AGB0`	has_cofactor	manganese(2+) `CHEBI:29035`	UniProtKB:P0AGB0 Source assertion: UniProt lists CHEBI:29035 as a cofactor of UniProtKB:P0AGB0 (evidence: ECO:0000269). Binds 1 Mg(2+) ion per subunit. Can also use other divalent metal cations as Mn(2+), Co(2+) and Zn(2+). Source location `comments[commentType='COFACTOR'].cofactors and note`
Phosphoserine phosphatase `UniProtKB:P0AGB0`	has_cofactor	cobalt(2+) `CHEBI:48828`	UniProtKB:P0AGB0 Source assertion: UniProt lists CHEBI:48828 as a cofactor of UniProtKB:P0AGB0 (evidence: ECO:0000269). Binds 1 Mg(2+) ion per subunit. Can also use other divalent metal cations as Mn(2+), Co(2+) and Zn(2+). Source location `comments[commentType='COFACTOR'].cofactors and note`
Phosphoserine phosphatase `UniProtKB:P0AGB0`	has_cofactor	zinc(2+) `CHEBI:29105`	UniProtKB:P0AGB0 Source assertion: UniProt lists CHEBI:29105 as a cofactor of UniProtKB:P0AGB0 (evidence: ECO:0000269). Binds 1 Mg(2+) ion per subunit. Can also use other divalent metal cations as Mn(2+), Co(2+) and Zn(2+). Source location `comments[commentType='COFACTOR'].cofactors and note`
Phosphoserine aminotransferase `UniProtKB:P23721`	enables	biosynthetic phosphoserine transaminase reaction `RHEA:14331`	UniProtKB:P23721 Source assertion: UniProt annotates UniProtKB:P23721 with catalytic activity for the reaction family of RHEA:14331. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Phosphoserine aminotransferase `UniProtKB:P23721`	located_in	cytoplasm `GO:0005737`	UniProtKB:P23721 Source assertion: UniProt locates UniProtKB:P23721 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: curated source annotation. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
Phosphoserine aminotransferase `UniProtKB:P23721`	has_cofactor	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P23721 Source assertion: UniProt lists CHEBI:597326 as a cofactor of UniProtKB:P23721 (evidence: ECO:0000269). Binds 1 pyridoxal phosphate per subunit. Source location `comments[commentType='COFACTOR'].cofactors and note`

References

MetaCyc:SERSYN-PWY MetaCyc L-serine biosynthesis I pathway (source version: 22.5)
RHEA:12642 Rhea biosynthetic phosphoglycerate dehydrogenase direction (source version: 139)
RHEA:14331 Rhea biosynthetic phosphoserine transaminase direction (source version: 139)
RHEA:21209 Rhea L-phosphoserine phosphatase direction (source version: 139)
PMID:14086727 Pizer, Journal of Biological Chemistry, 1963
RHEA:12641 RHEA:12641 authority record (source version: 139)
RHEA:14329 RHEA:14329 authority record (source version: 139)
RHEA:21208 RHEA:21208 authority record (source version: 139)
UniProtKB:P0A9T0 UniProtKB:P0A9T0 authority record (source version: 2026_03)
UniProtKB:P0AGB0 UniProtKB:P0AGB0 authority record (source version: 2026_03)
UniProtKB:P23721 UniProtKB:P23721 authority record (source version: 2026_03)

Curation history

2026-10-05T06:25:52Z codex
- EDIT — Review causal chemistry and add sourced molecular context
  Reviewed the entire record against MetaCyc 22.5 native pathway XML (including nested pathways), Rhea 139 explicit sides and directions, ENZYME 02-Sep-2026, PubMed records, and reviewed UniProt 2026_03 annotations within the record's taxon scope. Replaced generated structured-source quotations with source_assertion and source_locator. Typed molecular activities and participants. Reaction count 3 to 3; 0 directed-ID corrections; 3 protein annotations, 5 cofactor annotations and 1 sourced locations. All Rhea reaction substrate/product sets checked against independent Rhea authority; native pathway leaf coverage and source exceptions recorded in reports/causal_graph_review/metacyc-review.json. Full source URLs, versions and byte hashes are in metacyc-sources.json. All 50 MetaCyc records passed native schema validation; six targeted chemistry/evidence regression tests passed. Missing protein or cofactor annotations are not treated as biological absence; qualifications and exclusions are preserved in the ledger.
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