coenzyme A biosynthesis I (prokaryotic)

MetaCyc:COA-PWY

The prokaryotic coenzyme A biosynthesis I pathway converts (R)-4'-phosphopantothenate to CoA through phosphopantothenoyl-L-cysteine, 4'-phosphopantetheine, and 3'-dephospho-CoA intermediates.

Pathway type

cofactor biosynthesis

Organism scope

Escherichia coli NCBITaxon:562

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Pathway network

27 nodes · 38 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

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
phosphopantothenate--cysteine ligase `EC:6.3.2.5`	molecular activity
phosphopantothenoylcysteine decarboxylase `EC:4.1.1.36`	molecular activity
pantetheine-phosphate adenylyltransferase `EC:2.7.7.3`	molecular activity
dephospho-CoA kinase `EC:2.7.1.24`	molecular activity
(R)-4'-phosphopantothenate `CHEBI:10986`	small molecule
L-cysteine `CHEBI:35235`	small molecule
CTP `CHEBI:37563`	small molecule
N-[(R)-4-phosphopantothenoyl]-L-cysteine `CHEBI:59458`	small molecule
CMP `CHEBI:60377`	small molecule
diphosphate `CHEBI:33019`	small molecule
H(+) `CHEBI:15378`	small molecule
(R)-4'-phosphopantetheine `CHEBI:61723`	small molecule
CO2 `CHEBI:16526`	small molecule
ATP `CHEBI:30616`	small molecule
3'-dephospho-CoA `CHEBI:57328`	small molecule
ADP `CHEBI:456216`	small molecule
CoA `CHEBI:57287`	small molecule
Phosphopantetheine adenylyltransferase `UniProtKB:P0A6I6`	protein
cytoplasm `GO:0005737`	cellular component
magnesium(2+) `CHEBI:18420`	cofactor
Dephospho-CoA kinase `UniProtKB:P0A6I9`	protein
Coenzyme A biosynthesis bifunctional protein CoaBC `UniProtKB:P0ABQ0`	protein
FMN(3-) `CHEBI:58210`	cofactor
phosphopantothenate--cysteine ligase reaction `RHEA:19398`	reaction	left to right
phosphopantothenoylcysteine decarboxylase reaction `RHEA:16794`	reaction	left to right
phosphopantetheine adenylyltransferase reaction `RHEA:19802`	reaction	left to right
dephospho-CoA kinase reaction `RHEA:18246`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
(R)-4'-phosphopantothenate `CHEBI:10986`	consumes	phosphopantothenate--cysteine ligase reaction `RHEA:19398`	RHEA:19398 Source assertion: Rhea lists CHEBI:10986 on the substrates side of RHEA:19398 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19398']/rh:substrates; rh:contains/rh:compound/rh:accession`
L-cysteine `CHEBI:35235`	consumes	phosphopantothenate--cysteine ligase reaction `RHEA:19398`	RHEA:19398 Source assertion: Rhea lists CHEBI:35235 on the substrates side of RHEA:19398 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19398']/rh:substrates; rh:contains/rh:compound/rh:accession`
CTP `CHEBI:37563`	consumes	phosphopantothenate--cysteine ligase reaction `RHEA:19398`	RHEA:19398 Source assertion: Rhea lists CHEBI:37563 on the substrates side of RHEA:19398 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19398']/rh:substrates; rh:contains/rh:compound/rh:accession`
phosphopantothenate--cysteine ligase reaction `RHEA:19398`	produces	H(+) `CHEBI:15378`	RHEA:19398 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:19398 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19398']/rh:products; rh:contains/rh:compound/rh:accession`
phosphopantothenate--cysteine ligase reaction `RHEA:19398`	produces	diphosphate `CHEBI:33019`	RHEA:19398 Source assertion: Rhea lists CHEBI:33019 on the products side of RHEA:19398 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19398']/rh:products; rh:contains/rh:compound/rh:accession`
phosphopantothenate--cysteine ligase reaction `RHEA:19398`	produces	N-[(R)-4-phosphopantothenoyl]-L-cysteine `CHEBI:59458`	RHEA:19398 Source assertion: Rhea lists CHEBI:59458 on the products side of RHEA:19398 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19398']/rh:products; rh:contains/rh:compound/rh:accession`
phosphopantothenate--cysteine ligase reaction `RHEA:19398`	produces	CMP `CHEBI:60377`	RHEA:19398 Source assertion: Rhea lists CHEBI:60377 on the products side of RHEA:19398 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19398']/rh:products; rh:contains/rh:compound/rh:accession`
H(+) `CHEBI:15378`	consumes	phosphopantothenoylcysteine decarboxylase reaction `RHEA:16794`	RHEA:16794 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:16794 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16794']/rh:substrates; rh:contains/rh:compound/rh:accession`
N-[(R)-4-phosphopantothenoyl]-L-cysteine `CHEBI:59458`	consumes	phosphopantothenoylcysteine decarboxylase reaction `RHEA:16794`	RHEA:16794 Source assertion: Rhea lists CHEBI:59458 on the substrates side of RHEA:16794 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16794']/rh:substrates; rh:contains/rh:compound/rh:accession`
phosphopantothenoylcysteine decarboxylase reaction `RHEA:16794`	produces	CO2 `CHEBI:16526`	RHEA:16794 Source assertion: Rhea lists CHEBI:16526 on the products side of RHEA:16794 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16794']/rh:products; rh:contains/rh:compound/rh:accession`
phosphopantothenoylcysteine decarboxylase reaction `RHEA:16794`	produces	(R)-4'-phosphopantetheine `CHEBI:61723`	RHEA:16794 Source assertion: Rhea lists CHEBI:61723 on the products side of RHEA:16794 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/16794']/rh:products; rh:contains/rh:compound/rh:accession`
H(+) `CHEBI:15378`	consumes	phosphopantetheine adenylyltransferase reaction `RHEA:19802`	RHEA:19802 Source assertion: Rhea lists CHEBI:15378 on the substrates side of RHEA:19802 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19802']/rh:substrates; rh:contains/rh:compound/rh:accession`
ATP `CHEBI:30616`	consumes	phosphopantetheine adenylyltransferase reaction `RHEA:19802`	RHEA:19802 Source assertion: Rhea lists CHEBI:30616 on the substrates side of RHEA:19802 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19802']/rh:substrates; rh:contains/rh:compound/rh:accession`
(R)-4'-phosphopantetheine `CHEBI:61723`	consumes	phosphopantetheine adenylyltransferase reaction `RHEA:19802`	RHEA:19802 Source assertion: Rhea lists CHEBI:61723 on the substrates side of RHEA:19802 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19802']/rh:substrates; rh:contains/rh:compound/rh:accession`
phosphopantetheine adenylyltransferase reaction `RHEA:19802`	produces	diphosphate `CHEBI:33019`	RHEA:19802 Source assertion: Rhea lists CHEBI:33019 on the products side of RHEA:19802 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19802']/rh:products; rh:contains/rh:compound/rh:accession`
phosphopantetheine adenylyltransferase reaction `RHEA:19802`	produces	3'-dephospho-CoA `CHEBI:57328`	RHEA:19802 Source assertion: Rhea lists CHEBI:57328 on the products side of RHEA:19802 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/19802']/rh:products; rh:contains/rh:compound/rh:accession`
ATP `CHEBI:30616`	consumes	dephospho-CoA kinase reaction `RHEA:18246`	RHEA:18246 Source assertion: Rhea lists CHEBI:30616 on the substrates side of RHEA:18246 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18246']/rh:substrates; rh:contains/rh:compound/rh:accession`
3'-dephospho-CoA `CHEBI:57328`	consumes	dephospho-CoA kinase reaction `RHEA:18246`	RHEA:18246 Source assertion: Rhea lists CHEBI:57328 on the substrates side of RHEA:18246 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18246']/rh:substrates; rh:contains/rh:compound/rh:accession`
dephospho-CoA kinase reaction `RHEA:18246`	produces	H(+) `CHEBI:15378`	RHEA:18246 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:18246 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18246']/rh:products; rh:contains/rh:compound/rh:accession`
dephospho-CoA kinase reaction `RHEA:18246`	produces	ADP `CHEBI:456216`	RHEA:18246 Source assertion: Rhea lists CHEBI:456216 on the products side of RHEA:18246 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18246']/rh:products; rh:contains/rh:compound/rh:accession`
dephospho-CoA kinase reaction `RHEA:18246`	produces	CoA `CHEBI:57287`	RHEA:18246 Source assertion: Rhea lists CHEBI:57287 on the products side of RHEA:18246 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/18246']/rh:products; rh:contains/rh:compound/rh:accession`
phosphopantothenate--cysteine ligase `EC:6.3.2.5`	catalyzes	phosphopantothenate--cysteine ligase reaction `RHEA:19398`	RHEA:19397 Source assertion: Rhea associates EC:6.3.2.5 with the reaction family containing RHEA:19398. Source location `rh:ec`
phosphopantothenoylcysteine decarboxylase `EC:4.1.1.36`	catalyzes	phosphopantothenoylcysteine decarboxylase reaction `RHEA:16794`	RHEA:16793 Source assertion: Rhea associates EC:4.1.1.36 with the reaction family containing RHEA:16794. Source location `rh:ec`
pantetheine-phosphate adenylyltransferase `EC:2.7.7.3`	catalyzes	phosphopantetheine adenylyltransferase reaction `RHEA:19802`	RHEA:19801 Source assertion: Rhea associates EC:2.7.7.3 with the reaction family containing RHEA:19802. Source location `rh:ec`
dephospho-CoA kinase `EC:2.7.1.24`	catalyzes	dephospho-CoA kinase reaction `RHEA:18246`	RHEA:18245 Source assertion: Rhea associates EC:2.7.1.24 with the reaction family containing RHEA:18246. Source location `rh:ec`
phosphopantothenoylcysteine decarboxylase reaction `RHEA:16794`	precedes	phosphopantetheine adenylyltransferase reaction `RHEA:19802`	MetaCyc:COA-PWY Source assertion: MetaCyc pathway ordering places RHEA:16794 before RHEA:19802 in this pathway. Shared intermediate: CHEBI:61723. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
phosphopantothenate--cysteine ligase reaction `RHEA:19398`	precedes	phosphopantothenoylcysteine decarboxylase reaction `RHEA:16794`	MetaCyc:COA-PWY Source assertion: MetaCyc pathway ordering places RHEA:19398 before RHEA:16794 in this pathway. Shared intermediate: CHEBI:59458. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
phosphopantetheine adenylyltransferase reaction `RHEA:19802`	precedes	dephospho-CoA kinase reaction `RHEA:18246`	MetaCyc:COA-PWY Source assertion: MetaCyc pathway ordering places RHEA:19802 before RHEA:18246 in this pathway. Shared intermediate: CHEBI:57328. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
Phosphopantetheine adenylyltransferase `UniProtKB:P0A6I6`	enables	phosphopantetheine adenylyltransferase reaction `RHEA:19802`	UniProtKB:P0A6I6 Source assertion: UniProt annotates UniProtKB:P0A6I6 with catalytic activity for the reaction family of RHEA:19802. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
CoA `CHEBI:57287`	inhibits	Phosphopantetheine adenylyltransferase `UniProtKB:P0A6I6`	UniProtKB:P0A6I6 Source assertion: UniProt activity-regulation annotation: Feedback inhibited by CoA, which is competitive with ATP, 4'-phosphopantetheine and 3'-dephospho-CoA. Source location `comments[commentType='ACTIVITY REGULATION'].texts`
Phosphopantetheine adenylyltransferase `UniProtKB:P0A6I6`	located_in	cytoplasm `GO:0005737`	UniProtKB:P0A6I6 Source assertion: UniProt locates UniProtKB:P0A6I6 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: ECO:0000255. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
Phosphopantetheine adenylyltransferase `UniProtKB:P0A6I6`	has_cofactor	magnesium(2+) `CHEBI:18420`	UniProtKB:P0A6I6 Source assertion: UniProt lists CHEBI:18420 as a cofactor of UniProtKB:P0A6I6 (evidence: ECO:0000269). Crystallized in the absence of Mg(2+), the catalytic metal is not bound by the protein but probably by non-esterified oxygen atoms from ATP and/or ordered H(2)O (PubMed:11812124). Source location `comments[commentType='COFACTOR'].cofactors and note`
Dephospho-CoA kinase `UniProtKB:P0A6I9`	enables	dephospho-CoA kinase reaction `RHEA:18246`	UniProtKB:P0A6I9 Source assertion: UniProt annotates UniProtKB:P0A6I9 with catalytic activity for the reaction family of RHEA:18246. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Dephospho-CoA kinase `UniProtKB:P0A6I9`	located_in	cytoplasm `GO:0005737`	UniProtKB:P0A6I9 Source assertion: UniProt locates UniProtKB:P0A6I9 in Cytoplasm (SL-0086, mapped by UniProt to GO:0005737). Annotation evidence: ECO:0000255, ECO:0000305. Source location `comments[commentType='SUBCELLULAR LOCATION'].subcellularLocations; UniProt location vocabulary GO mapping`
Coenzyme A biosynthesis bifunctional protein CoaBC `UniProtKB:P0ABQ0`	enables	phosphopantothenoylcysteine decarboxylase reaction `RHEA:16794`	UniProtKB:P0ABQ0 Source assertion: UniProt annotates UniProtKB:P0ABQ0 with catalytic activity for the reaction family of RHEA:16794. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Coenzyme A biosynthesis bifunctional protein CoaBC `UniProtKB:P0ABQ0`	enables	phosphopantothenate--cysteine ligase reaction `RHEA:19398`	UniProtKB:P0ABQ0 Source assertion: UniProt annotates UniProtKB:P0ABQ0 with catalytic activity for the reaction family of RHEA:19398. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Coenzyme A biosynthesis bifunctional protein CoaBC `UniProtKB:P0ABQ0`	has_cofactor	magnesium(2+) `CHEBI:18420`	UniProtKB:P0ABQ0 Source assertion: UniProt lists CHEBI:18420 as a cofactor of UniProtKB:P0ABQ0 (evidence: ECO:0000255, ECO:0000269). Source location `comments[commentType='COFACTOR'].cofactors and note`
Coenzyme A biosynthesis bifunctional protein CoaBC `UniProtKB:P0ABQ0`	has_cofactor	FMN(3-) `CHEBI:58210`	UniProtKB:P0ABQ0 Source assertion: UniProt lists CHEBI:58210 as a cofactor of UniProtKB:P0ABQ0 (evidence: ECO:0000255, ECO:0000269). Binds 1 FMN per subunit. Source location `comments[commentType='COFACTOR'].cofactors and note`

References

MetaCyc:COA-PWY MetaCyc coenzyme A biosynthesis I pathway (source version: 22.5)
RHEA:19397 Rhea phosphopantothenate--cysteine ligase reaction (source version: 139)
RHEA:19398 Rhea phosphopantothenoylcysteine-forming direction (source version: 139)
RHEA:16793 Rhea phosphopantothenoylcysteine decarboxylase reaction (source version: 139)
RHEA:16794 Rhea phosphopantetheine-forming direction (source version: 139)
RHEA:19801 Rhea phosphopantetheine adenylyltransferase reaction (source version: 139)
RHEA:19802 Rhea dephospho-CoA-forming direction (source version: 139)
RHEA:18245 Rhea dephospho-CoA kinase reaction (source version: 139)
RHEA:18246 Rhea coenzyme A-forming direction (source version: 139)
UniProtKB:P0A6I6 UniProtKB:P0A6I6 authority record (source version: 2026_03)
UniProtKB:P0A6I9 UniProtKB:P0A6I9 authority record (source version: 2026_03)
UniProtKB:P0ABQ0 UniProtKB:P0ABQ0 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 4 to 4; 0 directed-ID corrections; 3 protein annotations, 3 cofactor annotations and 2 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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