L-threonine biosynthesis

MetaCyc:HOMOSER-THRESYN-PWY

L-threonine biosynthesis converts L-homoserine to L-threonine through O-phospho-L-homoserine.

Pathway type

amino acid biosynthesis

Organism scope

Escherichia coli NCBITaxon:562

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Pathway network

16 nodes · 16 asserted directed edges

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Reaction / activity
Chemical / cofactor
Protein / complex
Other participant
Cell / process context
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
homoserine kinase `EC:2.7.1.39`	molecular activity
threonine synthase `EC:4.2.3.1`	molecular activity
L-homoserine `CHEBI:57476`	small molecule
ATP `CHEBI:30616`	small molecule
O-phospho-L-homoserine `CHEBI:57590`	small molecule
ADP `CHEBI:456216`	small molecule
H+ `CHEBI:15378`	small molecule
H2O `CHEBI:15377`	small molecule
L-threonine `CHEBI:57926`	small molecule
phosphate `CHEBI:43474`	small molecule
Homoserine kinase `UniProtKB:P00547`	protein
cytoplasm `GO:0005737`	cellular component
Threonine synthase `UniProtKB:P00934`	protein
pyridoxal 5'-phosphate(2-) `CHEBI:597326`	cofactor
homoserine kinase reaction `RHEA:13986`	reaction	left to right
L-threonine synthase reaction `RHEA:10841`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
ATP `CHEBI:30616`	consumes	homoserine kinase reaction `RHEA:13986`	RHEA:13986 Source assertion: Rhea lists CHEBI:30616 on the substrates side of RHEA:13986 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13986']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-homoserine `CHEBI:57476`	consumes	homoserine kinase reaction `RHEA:13986`	RHEA:13986 Source assertion: Rhea lists CHEBI:57476 on the substrates side of RHEA:13986 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13986']/rh:substrates; rh:contains/rh:compound/rh:accession`
homoserine kinase reaction `RHEA:13986`	produces	H+ `CHEBI:15378`	RHEA:13986 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:13986 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13986']/rh:products; rh:contains/rh:compound/rh:accession`
homoserine kinase reaction `RHEA:13986`	produces	ADP `CHEBI:456216`	RHEA:13986 Source assertion: Rhea lists CHEBI:456216 on the products side of RHEA:13986 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13986']/rh:products; rh:contains/rh:compound/rh:accession`
homoserine kinase reaction `RHEA:13986`	produces	O-phospho-L-homoserine `CHEBI:57590`	RHEA:13986 Source assertion: Rhea lists CHEBI:57590 on the products side of RHEA:13986 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/13986']/rh:products; rh:contains/rh:compound/rh:accession`
H2O `CHEBI:15377`	consumes	L-threonine synthase reaction `RHEA:10841`	RHEA:10841 Source assertion: Rhea lists CHEBI:15377 on the substrates side of RHEA:10841 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/10841']/rh:substrates; rh:contains/rh:compound/rh:accession`
O-phospho-L-homoserine `CHEBI:57590`	consumes	L-threonine synthase reaction `RHEA:10841`	RHEA:10841 Source assertion: Rhea lists CHEBI:57590 on the substrates side of RHEA:10841 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/10841']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-threonine synthase reaction `RHEA:10841`	produces	phosphate `CHEBI:43474`	RHEA:10841 Source assertion: Rhea lists CHEBI:43474 on the products side of RHEA:10841 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/10841']/rh:products; rh:contains/rh:compound/rh:accession`
L-threonine synthase reaction `RHEA:10841`	produces	L-threonine `CHEBI:57926`	RHEA:10841 Source assertion: Rhea lists CHEBI:57926 on the products side of RHEA:10841 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/10841']/rh:products; rh:contains/rh:compound/rh:accession`
homoserine kinase `EC:2.7.1.39`	catalyzes	homoserine kinase reaction `RHEA:13986`	RHEA:13985 Source assertion: Rhea associates EC:2.7.1.39 with the reaction family containing RHEA:13986. Source location `rh:ec` PMID:8973190 Homoserine kinase, an enzyme in the aspartate pathway of amino acid biosynthesis in Escherichia coli, catalyzes the conversion of L-homoserine to L-homoserine phosphate. Source location `PubMed Abstract`
threonine synthase `EC:4.2.3.1`	catalyzes	L-threonine synthase reaction `RHEA:10841`	RHEA:10840 Source assertion: Rhea associates EC:4.2.3.1 with the reaction family containing RHEA:10841. Source location `rh:ec`
homoserine kinase reaction `RHEA:13986`	precedes	L-threonine synthase reaction `RHEA:10841`	MetaCyc:HOMOSER-THRESYN-PWY Source assertion: MetaCyc pathway ordering places RHEA:13986 before RHEA:10841 in this pathway. Shared intermediate: CHEBI:57590. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
Homoserine kinase `UniProtKB:P00547`	enables	homoserine kinase reaction `RHEA:13986`	UniProtKB:P00547 Source assertion: UniProt annotates UniProtKB:P00547 with catalytic activity for the reaction family of RHEA:13986. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Homoserine kinase `UniProtKB:P00547`	located_in	cytoplasm `GO:0005737`	UniProtKB:P00547 Source assertion: UniProt locates UniProtKB:P00547 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: ECO:0000305. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
Threonine synthase `UniProtKB:P00934`	enables	L-threonine synthase reaction `RHEA:10841`	UniProtKB:P00934 Source assertion: UniProt annotates UniProtKB:P00934 with catalytic activity for the reaction family of RHEA:10841. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Threonine synthase `UniProtKB:P00934`	has_cofactor	pyridoxal 5'-phosphate(2-) `CHEBI:597326`	UniProtKB:P00934 Source assertion: UniProt lists CHEBI:597326 as a cofactor of UniProtKB:P00934 (evidence: ECO:0000269). Source location `comments[commentType='COFACTOR'].cofactors and note`

References

MetaCyc:HOMOSER-THRESYN-PWY MetaCyc L-threonine biosynthesis pathway (source version: 22.5)
RHEA:13986 Rhea biosynthetic homoserine kinase direction (source version: 139)
RHEA:10840 Rhea L-threonine synthase reaction (source version: 139)
RHEA:10841 Rhea left-to-right L-threonine synthase direction (source version: 139)
PMID:8973190 Huo and Viola, Biochemistry, 1996
RHEA:13985 RHEA:13985 authority record (source version: 139)
UniProtKB:P00547 UniProtKB:P00547 authority record (source version: 2026_03)
UniProtKB:P00934 UniProtKB:P00934 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 2 to 2; 0 directed-ID corrections; 2 protein annotations, 1 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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