adenine and adenosine salvage I

MetaCyc:P121-PWY

The complete two-reaction pathway converts adenosine to AMP through adenine. The E. coli K-12 DeoD homohexamer phosphorolyzes adenosine to adenine and alpha-D-ribose 1-phosphate; the Apt homodimer transfers phosphoribosyl from supplied PRPP to adenine, forming AMP and diphosphate. This is the phosphorolysis route defined by P121-PWY, distinct from the four-step IMP-producing salvage III route and the nucleoside-hydrolase route. E. coli enzyme identity and activity are supported separately from the native pathway definition, whose listed species do not include E. coli. K-12 native enzyme annotations are distinguished from experiments in K-12 derivatives and recombinant enzyme assays. Magnesium supports Apt activity; native annotation also lists manganese as an alternative, without claiming simultaneous occupancy. Apt is intracellular, with reported membrane association dependent on preparation. Phosphate is a DeoD substrate. The graph selects the salvage directions of reversible chemistry and does not establish this branch as the dominant route under all growth conditions. Transport, PRPP synthesis, alternative nucleoside hydrolysis, and downstream AMP phosphorylation lie outside the exact two-step boundary.

Pathway type

nucleotide salvage

Organism scope

Escherichia coli K-12 NCBITaxon:83333

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Pathway network

18 nodes · 20 asserted directed edges

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Reaction / activity
Chemical / cofactor
Protein / complex
Cell / process context
Taxon
Pathway
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 K-12 `NCBITaxon:83333`	taxon
adenosine `CHEBI:16335`	small molecule
adenine `CHEBI:16708`	small molecule
diphosphate(3-) `CHEBI:33019`	small molecule
hydrogenphosphate `CHEBI:43474`	small molecule
adenosine 5'-monophosphate(2-) `CHEBI:456215`	small molecule
alpha-D-ribose 1-phosphate(2-) `CHEBI:57720`	small molecule
5-O-phosphonato-alpha-D-ribofuranosyl diphosphate(5-) `CHEBI:58017`	small molecule
magnesium(2+) `CHEBI:18420`	cofactor
manganese(2+) `CHEBI:29035`	cofactor
cytoplasm `GO:0005737`	cellular component
Adenine phosphoribosyltransferase `UniProtKB:P69503`	protein
Purine nucleoside phosphorylase DeoD-type `UniProtKB:P0ABP8`	protein
purine nucleoside phosphorylase `MetaCyc:DEOD-CPLX`	complex
adenine phosphoribosyltransferase `MetaCyc:ADENPRIBOSYLTRAN-CPLX`	complex
adenosine + phosphate => alpha-D-ribose 1-phosphate + adenine `RHEA:27643`	molecular activity	left to right
5-phospho-alpha-D-ribose 1-diphosphate + adenine => AMP + diphosphate `RHEA:16611`	molecular activity	right to left

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
adenosine `CHEBI:16335`	consumes	adenosine + phosphate => alpha-D-ribose 1-phosphate + adenine `RHEA:27643`	RHEA:27643 Source assertion: RHEA:27643 substrates contain CHEBI:16335 with coefficient 1; the compound is adenosine. Source location `rh:27643 rh:substrates <http://rdf.rhea-db.org/27642_L>; <http://rdf.rhea-db.org/27642_L> rh:contains1 <http://rdf.rhea-db.org/Participant_27642_compound_2547>; <http://rdf.rhea-db.org/Participant_27642_compound_2547> rh:compound <http://rdf.rhea-db.org/Compound_2547>; rh:accession/rh:formula/rh:charge`
hydrogenphosphate `CHEBI:43474`	consumes	adenosine + phosphate => alpha-D-ribose 1-phosphate + adenine `RHEA:27643`	RHEA:27643 Source assertion: RHEA:27643 substrates contain CHEBI:43474 with coefficient 1; the compound is hydrogenphosphate. Source location `rh:27643 rh:substrates <http://rdf.rhea-db.org/27642_L>; <http://rdf.rhea-db.org/27642_L> rh:contains1 <http://rdf.rhea-db.org/Participant_27642_compound_5518>; <http://rdf.rhea-db.org/Participant_27642_compound_5518> rh:compound <http://rdf.rhea-db.org/Compound_5518>; rh:accession/rh:formula/rh:charge`
adenosine + phosphate => alpha-D-ribose 1-phosphate + adenine `RHEA:27643`	produces	alpha-D-ribose 1-phosphate(2-) `CHEBI:57720`	RHEA:27643 Source assertion: RHEA:27643 products contain CHEBI:57720 with coefficient 1; the compound is alpha-D-ribose 1-phosphate(2-). Source location `rh:27643 rh:products <http://rdf.rhea-db.org/27642_R>; <http://rdf.rhea-db.org/27642_R> rh:contains1 <http://rdf.rhea-db.org/Participant_27642_compound_2276>; <http://rdf.rhea-db.org/Participant_27642_compound_2276> rh:compound <http://rdf.rhea-db.org/Compound_2276>; rh:accession/rh:formula/rh:charge`
adenosine + phosphate => alpha-D-ribose 1-phosphate + adenine `RHEA:27643`	produces	adenine `CHEBI:16708`	RHEA:27643 Source assertion: RHEA:27643 products contain CHEBI:16708 with coefficient 1; the compound is adenine. Source location `rh:27643 rh:products <http://rdf.rhea-db.org/27642_R>; <http://rdf.rhea-db.org/27642_R> rh:contains1 <http://rdf.rhea-db.org/Participant_27642_compound_4174>; <http://rdf.rhea-db.org/Participant_27642_compound_4174> rh:compound <http://rdf.rhea-db.org/Compound_4174>; rh:accession/rh:formula/rh:charge`
adenosine + phosphate => alpha-D-ribose 1-phosphate + adenine `RHEA:27643`	part_of	`MetaCyc:P121-PWY`	MetaCyc:P121-PWY Source assertion: P121-PWY includes ADENPHOSPHOR-RXN and selects native layout direction L2R. Source location `Pathway[@frameid="P121-PWY"]/reaction-list/Reaction[@frameid="ADENPHOSPHOR-RXN"]; reaction-layout[Reaction/@frameid="ADENPHOSPHOR-RXN"]/direction` MetaCyc:ADENPHOSPHOR-RXN Source assertion: ADENPHOSPHOR-RXN links to Rhea 27645 bidirectional; native chemical sides and physiological orientation are retained separately. Source location `Reaction[@frameid="ADENPHOSPHOR-RXN"]/dblink[dblink-db="RHEA"]; left; right; reaction-direction` RHEA:27643 Source assertion: Rhea master 27642 contains directed reaction 27643; the selected left-to-right member supplies the normalized chemical equation. Source location `rh:27642 rh:directionalReaction rh:27643; rh:27643 rh:substrates/rh:products/rh:equation`
5-O-phosphonato-alpha-D-ribofuranosyl diphosphate(5-) `CHEBI:58017`	consumes	5-phospho-alpha-D-ribose 1-diphosphate + adenine => AMP + diphosphate `RHEA:16611`	RHEA:16611 Source assertion: RHEA:16611 substrates contain CHEBI:58017 with coefficient 1; the compound is 5-O-phosphonato-alpha-D-ribofuranosyl diphosphate(5-). Source location `rh:16611 rh:substrates <http://rdf.rhea-db.org/16609_R>; <http://rdf.rhea-db.org/16609_R> rh:contains1 <http://rdf.rhea-db.org/Participant_16609_compound_4203>; <http://rdf.rhea-db.org/Participant_16609_compound_4203> rh:compound <http://rdf.rhea-db.org/Compound_4203>; rh:accession/rh:formula/rh:charge`
adenine `CHEBI:16708`	consumes	5-phospho-alpha-D-ribose 1-diphosphate + adenine => AMP + diphosphate `RHEA:16611`	RHEA:16611 Source assertion: RHEA:16611 substrates contain CHEBI:16708 with coefficient 1; the compound is adenine. Source location `rh:16611 rh:substrates <http://rdf.rhea-db.org/16609_R>; <http://rdf.rhea-db.org/16609_R> rh:contains1 <http://rdf.rhea-db.org/Participant_16609_compound_4174>; <http://rdf.rhea-db.org/Participant_16609_compound_4174> rh:compound <http://rdf.rhea-db.org/Compound_4174>; rh:accession/rh:formula/rh:charge`
5-phospho-alpha-D-ribose 1-diphosphate + adenine => AMP + diphosphate `RHEA:16611`	produces	adenosine 5'-monophosphate(2-) `CHEBI:456215`	RHEA:16611 Source assertion: RHEA:16611 products contain CHEBI:456215 with coefficient 1; the compound is adenosine 5'-monophosphate(2-). Source location `rh:16611 rh:products <http://rdf.rhea-db.org/16609_L>; <http://rdf.rhea-db.org/16609_L> rh:contains1 <http://rdf.rhea-db.org/Participant_16609_compound_2590>; <http://rdf.rhea-db.org/Participant_16609_compound_2590> rh:compound <http://rdf.rhea-db.org/Compound_2590>; rh:accession/rh:formula/rh:charge`
5-phospho-alpha-D-ribose 1-diphosphate + adenine => AMP + diphosphate `RHEA:16611`	produces	diphosphate(3-) `CHEBI:33019`	RHEA:16611 Source assertion: RHEA:16611 products contain CHEBI:33019 with coefficient 1; the compound is diphosphate(3-). Source location `rh:16611 rh:products <http://rdf.rhea-db.org/16609_L>; <http://rdf.rhea-db.org/16609_L> rh:contains1 <http://rdf.rhea-db.org/Participant_16609_compound_2106>; <http://rdf.rhea-db.org/Participant_16609_compound_2106> rh:compound <http://rdf.rhea-db.org/Compound_2106>; rh:accession/rh:formula/rh:charge`
5-phospho-alpha-D-ribose 1-diphosphate + adenine => AMP + diphosphate `RHEA:16611`	part_of	`MetaCyc:P121-PWY`	MetaCyc:P121-PWY Source assertion: P121-PWY includes ADENPRIBOSYLTRAN-RXN and selects native layout direction R2L. Source location `Pathway[@frameid="P121-PWY"]/reaction-list/Reaction[@frameid="ADENPRIBOSYLTRAN-RXN"]; reaction-layout[Reaction/@frameid="ADENPRIBOSYLTRAN-RXN"]/direction` MetaCyc:ADENPRIBOSYLTRAN-RXN Source assertion: ADENPRIBOSYLTRAN-RXN links to Rhea 16609 master; native chemical sides and physiological orientation are retained separately. Source location `Reaction[@frameid="ADENPRIBOSYLTRAN-RXN"]/dblink[dblink-db="RHEA"]; left; right; reaction-direction` RHEA:16611 Source assertion: Rhea master 16609 contains directed reaction 16611; the selected right-to-left member supplies the normalized chemical equation. Source location `rh:16609 rh:directionalReaction rh:16611; rh:16611 rh:substrates/rh:products/rh:equation`
Purine nucleoside phosphorylase DeoD-type `UniProtKB:P0ABP8`	part_of	purine nucleoside phosphorylase `MetaCyc:DEOD-CPLX`	MetaCyc:DEOD-CPLX Source assertion: Native DEOD-CPLX contains six DEOD-MONOMER subunits. Source location `Protein[@frameid="DEOD-CPLX"]/component[Protein/@frameid="DEOD-MONOMER"]/coefficient` MetaCyc:DEOD-MONOMER Source assertion: Native DEOD-MONOMER unification cross-reference identifies UniProt P0ABP8. Source location `Protein[@frameid="DEOD-MONOMER"]/dblink[dblink-db="UNIPROT"]/dblink-oid` UniProtKB:P0ABP8 Source assertion: The reviewed subunit comment describes a homohexamer, organized as a trimer of homodimers, with experimental references. Source location `comments[commentType="SUBUNIT"].texts` PMID:30337572 Source assertion: The E. coli enzyme is a homohexamer; each dimer contributes residues to its neighboring active site, and the trimer-of-dimers assembly stabilizes catalytically productive conformations. Source location `PMC6193948 Introduction; Results, concluding mechanistic paragraph; Fig. 4`
purine nucleoside phosphorylase `MetaCyc:DEOD-CPLX`	catalyzes	adenosine + phosphate => alpha-D-ribose 1-phosphate + adenine `RHEA:27643`	MetaCyc:DEOD-CPLX Source assertion: DEOD-CPLX catalyzes ADENPHOSPHOR-ENZRXN, linked to ADENPHOSPHOR-RXN. Source location `Protein[@frameid="DEOD-CPLX"]/catalyzes/Enzymatic-Reaction[@frameid="ADENPHOSPHOR-ENZRXN"]/reaction` UniProtKB:P0ABP8 Source assertion: The reviewed catalytic activity assigns adenosine phosphorolysis to RHEA:27642, supported by experimental PubMed evidence; direction here follows P121-PWY. Source location `comments[commentType="CATALYTIC ACTIVITY"].reaction[reactionCrossReferences/id="RHEA:27642"]` PMID:30337572 Source assertion: Wild-type E. coli purine nucleoside phosphorylase was assayed with natural substrate adenosine and phosphate; mutant and substrate-analogue results are distinguished from the wild-type assay. Source location `PMC6193948 Results, Catalytic and kinetic properties; Table 1 and Fig. 2`
Adenine phosphoribosyltransferase `UniProtKB:P69503`	part_of	adenine phosphoribosyltransferase `MetaCyc:ADENPRIBOSYLTRAN-CPLX`	MetaCyc:ADENPRIBOSYLTRAN-CPLX Source assertion: The native E. coli MG1655 Apt complex contains two ADENPRIBOSYLTRAN-MONOMER subunits. Source location `Protein[@frameid="ADENPRIBOSYLTRAN-CPLX"]/component[Protein/@frameid="ADENPRIBOSYLTRAN-MONOMER"]/coefficient; species/Organism/@frameid` MetaCyc:ADENPRIBOSYLTRAN-MONOMER Source assertion: The native Apt subunit has UniProt P69503 as a unification cross-reference. Source location `Protein[@frameid="ADENPRIBOSYLTRAN-MONOMER"]/dblink[dblink-db="UNIPROT"]/dblink-oid` UniProtKB:P69503 Source assertion: Reviewed subunit annotation states homodimer; no experimental evidence code is attached to this particular comment. Source location `comments[commentType="SUBUNIT"].texts`
adenine phosphoribosyltransferase `MetaCyc:ADENPRIBOSYLTRAN-CPLX`	catalyzes	5-phospho-alpha-D-ribose 1-diphosphate + adenine => AMP + diphosphate `RHEA:16611`	MetaCyc:ADENPRIBOSYLTRAN-CPLX Source assertion: Native Apt complex catalyzes ADENPRIBOSYLTRAN-ENZRXN, which links to ADENPRIBOSYLTRAN-RXN. Source location `Protein[@frameid="ADENPRIBOSYLTRAN-CPLX"]/catalyzes/Enzymatic-Reaction/reaction` MetaCyc:ADENPRIBOSYLTRAN-RXN Source assertion: The native reaction is physiologically right-to-left: adenine plus PRPP forms AMP plus diphosphate. Source location `Reaction[@frameid="ADENPRIBOSYLTRAN-RXN"]/right; left; reaction-direction` UniProtKB:P69503 Source assertion: Reviewed catalytic activity assigns RHEA:16609 under HAMAP MF_00004 inference; this annotation is not presented as a direct assay. Source location `comments[commentType="CATALYTIC ACTIVITY"].reaction.reactionCrossReferences; reaction.evidences` PMID:21111048 Source assertion: Recombinant E. coli APRT expressed in BL21(AI) was purified and assayed with adenine and PRPP in a coupled assay. This demonstrates activity of the recombinant construct, not whole-pathway wild-type flux. Source location `PMC4125576 Methods, expression/purification and APRT assay; Results, Determination of enzyme activities; Fig. 3c; Table 1`
adenine phosphoribosyltransferase `MetaCyc:ADENPRIBOSYLTRAN-CPLX`	has_cofactor	magnesium(2+) `CHEBI:18420`	MetaCyc:ADENPRIBOSYLTRAN-ENZRXN Source assertion: The native Apt enzymatic reaction lists Mg2+ as cofactor, citing Hochstadt-Ozer and Stadtman 1971; that paper was not independently available in full text here. Source location `Enzymatic-Reaction[@frameid="ADENPRIBOSYLTRAN-ENZRXN"]/cofactor[Compound/@frameid="MG+2"]` PMID:21111048 Source assertion: The recombinant APRT coupled activity assay included 10 mM MgCl2, 1.5 mM PRPP and 1.5 mM adenine hydrochloride at pH 7.8; the assay does not establish in vivo metal occupancy. Source location `PMC4125576 Methods, Activity assays/APRT, paragraph beginning "The spectrophotometric assay"`
adenine phosphoribosyltransferase `MetaCyc:ADENPRIBOSYLTRAN-CPLX`	has_cofactor	manganese(2+) `CHEBI:29035`	MetaCyc:ADENPRIBOSYLTRAN-ENZRXN Source assertion: The native enzymatic reaction lists Mn2+ as an alternative to Mg2+. This is source annotation, not a claim of simultaneous binding or a separately inspected manganese assay. Source location `Enzymatic-Reaction[@frameid="ADENPRIBOSYLTRAN-ENZRXN"]/alternative-cofactor[cofactor/Compound/@frameid="MG+2"]/alternate/Compound[@frameid="MN+2"]`
Adenine phosphoribosyltransferase `UniProtKB:P69503`	located_in	cytoplasm `GO:0005737`	UniProtKB:P69503 Source assertion: The reviewed entry locates Apt in the cytoplasm; the location comment has no attached experimental evidence code. Source location `comments[commentType="SUBCELLULAR LOCATION"].subcellularLocations.location` PMID:365172 Source assertion: The inspected abstract places adenine phosphoribosyltransferase intracellularly and reports no significant association with purified membrane fractions, distinguishing localization from preparation-dependent membrane association. Source location `Europe PMC resultList.result[id="365172"].abstractText`
adenosine + phosphate => alpha-D-ribose 1-phosphate + adenine `RHEA:27643`	provides_input_for	5-phospho-alpha-D-ribose 1-diphosphate + adenine => AMP + diphosphate `RHEA:16611`	MetaCyc:P121-PWY Source assertion: The native pathway orders ADENPHOSPHOR-RXN before ADENPRIBOSYLTRAN-RXN and shows ADENINE as the connecting native compound. Source location `Pathway[@frameid="P121-PWY"]/reaction-ordering[Reaction/@frameid="ADENPRIBOSYLTRAN-RXN"]/predecessor-reactions; reaction-layout/right-primaries` RHEA:27643 Source assertion: RHEA:27643 products contain CHEBI:16708 with coefficient 1; the compound is adenine. Source location `rh:27643 rh:products <http://rdf.rhea-db.org/27642_R>; <http://rdf.rhea-db.org/27642_R> rh:contains1 <http://rdf.rhea-db.org/Participant_27642_compound_4174>; <http://rdf.rhea-db.org/Participant_27642_compound_4174> rh:compound <http://rdf.rhea-db.org/Compound_4174>; rh:accession/rh:formula/rh:charge` RHEA:16611 Source assertion: RHEA:16611 substrates contain CHEBI:16708 with coefficient 1; the compound is adenine. Source location `rh:16611 rh:substrates <http://rdf.rhea-db.org/16609_R>; <http://rdf.rhea-db.org/16609_R> rh:contains1 <http://rdf.rhea-db.org/Participant_16609_compound_4174>; <http://rdf.rhea-db.org/Participant_16609_compound_4174> rh:compound <http://rdf.rhea-db.org/Compound_4174>; rh:accession/rh:formula/rh:charge` PMID:765747 Source assertion: The E. coli salvage scheme places purine nucleoside phosphorylase between adenosine and adenine and adenine phosphoribosyltransferase between adenine and AMP; experiments use the K-12 derivatives listed in Table 1. Source location `p. 85, Fig. 1; pp. 86-87, Methods and Table 1`
Adenine phosphoribosyltransferase `UniProtKB:P69503`	part_of	Escherichia coli K-12 `NCBITaxon:83333`	UniProtKB:P69503 Source assertion: The reviewed entry identifies Escherichia coli strain K12, taxon 83333, with ordered locus b0469. Source location `organism.taxonId; organism.scientificName; genes.orderedLocusNames`
Purine nucleoside phosphorylase DeoD-type `UniProtKB:P0ABP8`	part_of	Escherichia coli K-12 `NCBITaxon:83333`	UniProtKB:P0ABP8 Source assertion: The reviewed entry identifies Escherichia coli strain K12, taxon 83333, with ordered locus b4384. Source location `organism.taxonId; organism.scientificName; genes.orderedLocusNames`

References

MetaCyc:P121-PWY MetaCyc P121-PWY native full XML (source version: MetaCyc 22.5 native XML)
MetaCyc:ADENPHOSPHOR-RXN MetaCyc ADENPHOSPHOR-RXN native full XML (source version: MetaCyc 22.5 native XML)
MetaCyc:ADENPRIBOSYLTRAN-RXN MetaCyc ADENPRIBOSYLTRAN-RXN native full XML (source version: MetaCyc 22.5 native XML)
MetaCyc:DEOD-CPLX MetaCyc DEOD-CPLX native full XML (source version: MetaCyc 22.5 native XML)
MetaCyc:DEOD-MONOMER MetaCyc DEOD-MONOMER native full XML (source version: MetaCyc 22.5 native XML)
MetaCyc:ADENPRIBOSYLTRAN-CPLX MetaCyc ADENPRIBOSYLTRAN-CPLX native full XML (source version: MetaCyc 22.5 native XML)
MetaCyc:ADENPRIBOSYLTRAN-MONOMER MetaCyc ADENPRIBOSYLTRAN-MONOMER native full XML (source version: MetaCyc 22.5 native XML)
MetaCyc:ADENPRIBOSYLTRAN-ENZRXN MetaCyc ADENPRIBOSYLTRAN-ENZRXN native full XML (source version: MetaCyc 22.5 native XML)
UniProtKB:P69503 Adenine phosphoribosyltransferase (source version: UniProt release 2026_03; 02-September-2026)
UniProtKB:P0ABP8 Purine nucleoside phosphorylase DeoD-type (source version: UniProt release 2026_03; 02-September-2026)
RHEA:27643 Rhea directed reaction 27643 (source version: Rhea 142; 2026-09-02; full RDF artifact)
RHEA:16611 Rhea directed reaction 16611 (source version: Rhea 142; 2026-09-02; full RDF artifact)
PMID:30337572 Crystallographic snapshots of ligand binding to hexameric purine nucleoside phosphorylase and kinetic studies give insight into the mechanism of catalysis. (source version: 2018 primary full text, PMC BioC XML)
PMID:21111048 Expression, purification and analysis of the activity of enzymes from the pentose phosphate pathway. (source version: 2011 primary full text, PMC BioC XML)
PMID:765747 Location on the chromosome of Escherichia coli of genes governing purine metabolism. (source version: 1975 primary full PDF, 7 pages)
PMID:365172 The location of purine phosphoribosyltransferase activities in Escherichia coli. (source version: 1978 primary abstract in Europe PMC exact PMID batch; full text not inspected)

Curation history

2026-10-11T05:30:39Z codex
- CREATE — Add the complete adenosine phosphorolysis and adenine salvage route to AMP
  MetaCyc:P121-PWY; two reactions, 20 edges. Native pathway boundary is separated from E. coli K-12 enzyme/primary evidence because the inspected native species list does not list E. coli. DeoD homohexamer, Apt homodimer, conditional metal and localization evidence, selected reversible chemistry, and distinctions from salvage III and hydrolase alternatives are retained. Exact source bodies, identifier ledgers, source-to-graph coverage and author replays are retained under research/pathway_additions/2026-10-11-next-192 and its declared external cache. Ignored and hidden files were included in duplicate searches with explicit exclusions. Independent scientific review and full frozen-corpus gates remain pending at this event; final results belong in the cohort receipt.
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