D-xylose degradation I

MetaCyc:XYLCAT-PWY

D-xylose degradation I isomerizes alpha-D-xylose to alpha-D-xylulofuranose, then phosphorylates D-xylulose with ATP to form D-xylulose 5-phosphate for entry into the pentose phosphate pathway.

Pathway type

carbohydrate degradation

Organism scope

Escherichia coli NCBITaxon:562

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Pathway network

15 nodes · 14 asserted directed edges

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Chemical / cofactor
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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
xylose isomerase `EC:5.3.1.5`	molecular activity
xylulokinase `EC:2.7.1.17`	molecular activity
alpha-D-xylose `CHEBI:28518`	small molecule
alpha-D-xylulofuranose `CHEBI:188998`	small molecule
D-xylulose `CHEBI:17140`	small molecule
ATP `CHEBI:30616`	small molecule
D-xylulose 5-phosphate `CHEBI:57737`	small molecule
ADP `CHEBI:456216`	small molecule
H(+) `CHEBI:15378`	small molecule
Xylose isomerase `UniProtKB:P00944`	protein
cytoplasm `GO:0005737`	cellular component
magnesium(2+) `CHEBI:18420`	cofactor
Xylulose kinase `UniProtKB:P09099`	protein
xylulokinase reaction `RHEA:10965`	reaction	left to right
xylose isomerase reaction `RHEA:22817`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
D-xylulose `CHEBI:17140`	consumes	xylulokinase reaction `RHEA:10965`	RHEA:10965 Source assertion: Rhea lists CHEBI:17140 on the substrates side of RHEA:10965 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/10965']/rh:substrates; rh:contains/rh:compound/rh:accession`
ATP `CHEBI:30616`	consumes	xylulokinase reaction `RHEA:10965`	RHEA:10965 Source assertion: Rhea lists CHEBI:30616 on the substrates side of RHEA:10965 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/10965']/rh:substrates; rh:contains/rh:compound/rh:accession`
xylulokinase reaction `RHEA:10965`	produces	H(+) `CHEBI:15378`	RHEA:10965 Source assertion: Rhea lists CHEBI:15378 on the products side of RHEA:10965 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/10965']/rh:products; rh:contains/rh:compound/rh:accession`
xylulokinase reaction `RHEA:10965`	produces	ADP `CHEBI:456216`	RHEA:10965 Source assertion: Rhea lists CHEBI:456216 on the products side of RHEA:10965 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/10965']/rh:products; rh:contains/rh:compound/rh:accession`
xylulokinase reaction `RHEA:10965`	produces	D-xylulose 5-phosphate `CHEBI:57737`	RHEA:10965 Source assertion: Rhea lists CHEBI:57737 on the products side of RHEA:10965 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/10965']/rh:products; rh:contains/rh:compound/rh:accession`
alpha-D-xylose `CHEBI:28518`	consumes	xylose isomerase reaction `RHEA:22817`	RHEA:22817 Source assertion: Rhea lists CHEBI:28518 on the substrates side of RHEA:22817 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22817']/rh:substrates; rh:contains/rh:compound/rh:accession`
xylose isomerase reaction `RHEA:22817`	produces	alpha-D-xylulofuranose `CHEBI:188998`	RHEA:22817 Source assertion: Rhea lists CHEBI:188998 on the products side of RHEA:22817 in this directed reaction. Source location `rdf:Description[@rdf:about='http://rdf.rhea-db.org/22817']/rh:products; rh:contains/rh:compound/rh:accession`
xylose isomerase `EC:5.3.1.5`	catalyzes	xylose isomerase reaction `RHEA:22817`	RHEA:22816 Source assertion: Rhea associates EC:5.3.1.5 with the reaction family containing RHEA:22817. Source location `rh:ec`
xylulokinase `EC:2.7.1.17`	catalyzes	xylulokinase reaction `RHEA:10965`	RHEA:10964 Source assertion: Rhea associates EC:2.7.1.17 with the reaction family containing RHEA:10965. Source location `rh:ec`
xylose isomerase reaction `RHEA:22817`	precedes	xylulokinase reaction `RHEA:10965`	MetaCyc:XYLCAT-PWY Source assertion: MetaCyc pathway ordering places RHEA:22817 before RHEA:10965 in this pathway. The source ordering may bridge anomer-specific and broader substrate classes. Source location `Pathway/reaction-ordering and reaction-layout; Rhea-to-MetaCyc cross-references`
Xylose isomerase `UniProtKB:P00944`	enables	xylose isomerase reaction `RHEA:22817`	UniProtKB:P00944 Source assertion: UniProt annotates UniProtKB:P00944 with catalytic activity for the reaction family of RHEA:22817. Annotation evidence: ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`
Xylose isomerase `UniProtKB:P00944`	located_in	cytoplasm `GO:0005737`	UniProtKB:P00944 Source assertion: UniProt locates UniProtKB:P00944 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`
Xylose isomerase `UniProtKB:P00944`	has_cofactor	magnesium(2+) `CHEBI:18420`	UniProtKB:P00944 Source assertion: UniProt lists CHEBI:18420 as a cofactor of UniProtKB:P00944 (evidence: ECO:0000250). Binds 2 magnesium ions per subunit. Source location `comments[commentType='COFACTOR'].cofactors and note`
Xylulose kinase `UniProtKB:P09099`	enables	xylulokinase reaction `RHEA:10965`	UniProtKB:P09099 Source assertion: UniProt annotates UniProtKB:P09099 with catalytic activity for the reaction family of RHEA:10965. Annotation evidence: ECO:0000255, ECO:0000269; organism taxon: NCBITaxon:83333. Source location `comments[commentType='CATALYTIC ACTIVITY'].reaction.reactionCrossReferences`

References

MetaCyc:XYLCAT-PWY MetaCyc D-xylose degradation I (source version: 22.5)
RHEA:22816 Rhea xylose isomerase reaction (source version: 139)
RHEA:22819 Rhea bidirectional xylose isomerase reaction (source version: 139)
RHEA:10964 Rhea xylulokinase reaction (source version: 139)
RHEA:10965 Rhea D-xylulose-5-phosphate-forming direction (source version: 139)
RHEA:22817 RHEA:22817 authority record (source version: 139)
UniProtKB:P00944 UniProtKB:P00944 authority record (source version: 2026_03)
UniProtKB:P09099 UniProtKB:P09099 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; 1 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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