5'-deoxyadenosine degradation I

MetaCyc:PWY-8130

This exact MetaCyc pathway converts 5'-deoxyadenosine plus inorganic phosphate to adenine, dihydroxyacetone phosphate (DHAP) and acetaldehyde in three reactions. MtnP phosphorolysis produces 5-deoxy-α-D-ribose 1-phosphate and adenine; MtnA isomerizes the sugar phosphate to 5-deoxy-D-ribulose 1-phosphate; Ald2 cleaves it to DHAP and acetaldehyde. The graph retains all nine native chemical-side occurrences and both intermediate transfers. Its phosphate-consuming entry distinguishes it from the hydrolysis-plus-kinase route PWY-8131. Free 5-deoxyribose, ATP, ADP and hydrolytic water are not additional steps or participants in this route. Metabolite continuity does not imply physical substrate channeling. Direct whole-route physiological evidence concerns Rhodospirillum rubrum ATCC 11170. In the 2020 study, anaerobic feeding with [5′-³H]-5′-deoxyadenosine and chromatographic product analysis showed that mtnP deletion blocked entry, mtnA deletion arrested conversion at 5-deoxyribose 1-phosphate, and ald2 deletion arrested it at 5-deoxyribulose 1-phosphate. Mutants accumulated extracellular 5′-deoxyadenosine during both aerobic and anaerobic growth, and plasmid complementation restored abundance toward the wild-type level. The paper's twofold comparison is 5′-deoxyadenosine versus MTA abundance across strains; it is not a twofold mutant-versus-wild-type effect. The species taxon records the native assembly assignment, while the strain taxon anchors experimental physiology. Neither the MetaCyc Bacteria range nor its Rhodopseudomonas palustris species listing is extended here into demonstrated whole-route physiology in all those organisms. RXN-14304 carries the native PHYSIOL-LEFT-TO-RIGHT direction. RXN-21315 and RXN-21316 are native REVERSIBLE reactions, although the pathway layout and all three activity frames use the degradative left-to-right orientation. These source contexts remain distinct. Rhea release 142 independently supports the three reaction families and all nine sides; the native entry cross-reference RHEA:24872 is the bidirectional member of the RHEA:24869 family, whereas UniProt's physiological entry direction uses RHEA:24870. No exact directional equivalence is asserted between those contexts. Full native-to-ChEBI InChI comparisons establish all seven chemical identities, including the specific phosphate charge states and α-D sugar-phosphate structure. Formal atom and charge balance is not a measurement of intracellular protonation or a fresh experimental determination of stereochemistry. The reviewed current proteins are Q2RXH9/MtnP (Rru_A0361), Q2RXI0/MtnA (Rru_A0360) and Q2RXI1/Ald2 (Rru_A0359), all assigned to strain ATCC 11170. Native gene/product links and reciprocal UniProt cross-references establish these identities. The graph preserves MtnP's native MONOMER-17874 chain and its exact mapping from Q2RXH9, rather than adding a second biological chain for the same protein. The 2012 paper reverses the A0360/A0361 enzyme names in one passage; the corroborated mapping from its earlier passage, native genes and current UniProt is used. That paper establishes the adjacent MTA/isoprenoid mechanism and provides the earlier biochemical context; it is not used as proof of the complete 5′-deoxyadenosine DHAP route. MtnP catalysis is assigned to native CPLX-8605. Its component slot contains two CPLX-8604 subassemblies, each of which contains three MONOMER-17874 chains, with reciprocal membership links. CPLX-8604 nevertheless has the issuer label S-methyl-5′-thioadenosine phosphorylase dimer. That label/composition conflict is preserved without renaming the source entity or treating the isolated chain as an independently demonstrated catalyst. UniProt describes a homohexamer assembled as a dimer of homotrimers, but the evidence is the HAMAP inference code ECO:0000255; it is not a direct measurement of physiological assembly stoichiometry in this record. The 2020 purified-enzyme reconstitution used R. rubrum proteins expressed from pET28 in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. It is an in vitro recombinant experiment even though one Results sentence calls reconstitution in vivo. This assay is separate from native-host isotope feeding and deletion experiments. Exact MtnP affinity-tag identity and orientation are not established by the accessible Methods. Native MtnA commentary attributes a His10 construct, and native Ald2 commentary attributes a His6 construct and anaerobic purification to older work; these remain database-attributed construct details, not confirmation from unavailable supporting files or a fresh complete reading of the 2017 paper. The MtnA activity frame distinguishes earlier purified heterologous and mutant evidence from partially purified heterologous evidence assigned to 2020. Its conflicting general protein commentary does not erase that finer evidence tier. Native activity slots and the 2020 Table 1 report substrate-specific Km/kcat pairs of 40 micromolar/6.7 s−1 for MtnP with 5′-deoxyadenosine, 171 micromolar/0.18 s−1 for MtnA with 5-deoxyribose 1-phosphate, and 229 micromolar/1.94 s−1 for Ald2 with 5-deoxyribulose 1-phosphate. Table 1 marks the first two pairs as literature values, and UniProt attributes them to the 2012 paper, while the native kinetic slots cite 2020. All these attribution tiers are retained. The accessible 2012 main text delegates detailed enzymology to inaccessible SI. Values are assay-specific, not cellular flux constants. The retained BioC Ald2 catalytic-efficiency entry disagrees arithmetically with its Km and kcat; that disputed efficiency is neither propagated nor silently corrected. Ald2 requires a divalent metal in the reported activity assays. Co2+ and Ni2+ gave the highest activity among the tested R. rubrum reconstitution conditions. The two cofactor edges describe alternative recombinant apoenzyme preparations: EDTA treatment and dialysis preceded separate 0.1 mM metal incubations for one hour. They do not assert simultaneous metal occupancy or identify the native cellular metal. UniProt's one-cobalt-per-subunit statement is by similarity and is not treated as measured stoichiometry. Mixed Mg2+/Co2+ conditions in a coupled MtnA assay also do not establish an independently required cofactor for every enzyme in that coupled system. The same R. rubrum enzymes act on methylthio substrates in methionine salvage, but those substrates and downstream sulfur reactions define adjacent routes. The final two reactions are shared with PWY-8131; its E. coli ATCC 25922 physiology and Bacillus component assays do not establish phosphorolytic entry in those organisms. The R. rubrum work supports degradation and carbon salvage chemistry, including further conversion of acetaldehyde to ethanol or acetate, without adding unassigned downstream enzyme nodes or claiming growth with 5′-deoxyadenosine as the sole carbon source. Potential detoxification and broad taxonomic distribution remain source-discussion context rather than unqualified demonstrated outcomes for every strain. Both complete primary main texts were read from their retained NCBI BioC originals, including available main-text table and figure captions. The 2012 SI attempts yielded failed or unusable responses, and its original figure bodies were not available. The 2020 supporting PDF/spreadsheet and original figure images remained inaccessible through the tested routes. No claim relies solely on those unavailable materials. Current ChEBI 144504 has inconsistent definition prose; its ribulose label and complete structure establish identity. Native MtnA commentary also misstates the older MTA mutant's arrest metabolite; the primary 2012 experiment and the separate 2020 5′-deoxyadenosine experiment are kept distinct. Broader source leads remain open; this draft does not establish source exhaustion or public-release licensing clearance.

Pathway type
metabolic
Organism scope

Read the source YAML

Pathway network

23 nodes · 21 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.

Pathway network: 5'-deoxyadenosine degradation I 23 nodes · 21 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. MetaCyc:RXN-14304 — part_of → MetaCyc:PWY-8130; This native reaction is explicitly listed in the exact three-event pathway. Whole-route physiological scope is the tested ATCC 11170 strain; this edge does not describe the heterologous expression host.; Evidence: MetaCyc:PWY-8130, MetaCyc:RXN-14304, PMID:31950558, PMID:31950558, PMID:31950558, NCBITaxon:269796part of CHEBI:17319 — consumes → MetaCyc:RXN-14304; One stoichiometric occurrence on the native written left side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.; Evidence: MetaCyc:RXN-14304, MetaCyc:CH33ADO, CHEBI:17319, RHEA:24869consumes CHEBI:43474 — consumes → MetaCyc:RXN-14304; One stoichiometric occurrence on the native written left side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.; Evidence: MetaCyc:RXN-14304, MetaCyc:Pi, CHEBI:43474, RHEA:24869consumes MetaCyc:RXN-14304 — produces → CHEBI:58749; One stoichiometric occurrence on the native written right side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.; Evidence: MetaCyc:RXN-14304, MetaCyc:CPD-15199, CHEBI:58749, RHEA:24869produces MetaCyc:RXN-14304 — produces → CHEBI:16708; One stoichiometric occurrence on the native written right side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.; Evidence: MetaCyc:RXN-14304, MetaCyc:ADENINE, CHEBI:16708, RHEA:24869produces MetaCyc:RXN-21315 — part_of → MetaCyc:PWY-8130; This native reaction is explicitly listed in the exact three-event pathway. Whole-route physiological scope is the tested ATCC 11170 strain; this edge does not describe the heterologous expression host.; Evidence: MetaCyc:PWY-8130, MetaCyc:RXN-21315, PMID:31950558, PMID:31950558, PMID:31950558, NCBITaxon:269796part of CHEBI:58749 — consumes → MetaCyc:RXN-21315; One stoichiometric occurrence on the native written left side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.; Evidence: MetaCyc:RXN-21315, MetaCyc:CPD-15199, CHEBI:58749, RHEA:61296consumes MetaCyc:RXN-21315 — produces → CHEBI:144504; One stoichiometric occurrence on the native written right side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.; Evidence: MetaCyc:RXN-21315, MetaCyc:CPD-23219, CHEBI:144504, RHEA:61296produces MetaCyc:RXN-21316 — part_of → MetaCyc:PWY-8130; This native reaction is explicitly listed in the exact three-event pathway. Whole-route physiological scope is the tested ATCC 11170 strain; this edge does not describe the heterologous expression host.; Evidence: MetaCyc:PWY-8130, MetaCyc:RXN-21316, PMID:31950558, PMID:31950558, PMID:31950558, NCBITaxon:269796part of CHEBI:144504 — consumes → MetaCyc:RXN-21316; One stoichiometric occurrence on the native written left side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.; Evidence: MetaCyc:RXN-21316, MetaCyc:CPD-23219, CHEBI:144504, RHEA:61300consumes MetaCyc:RXN-21316 — produces → CHEBI:57642; One stoichiometric occurrence on the native written right side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.; Evidence: MetaCyc:RXN-21316, MetaCyc:DIHYDROXY-ACETONE-PHOSPHATE, CHEBI:57642, RHEA:61300produces MetaCyc:RXN-21316 — produces → CHEBI:15343; One stoichiometric occurrence on the native written right side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.; Evidence: MetaCyc:RXN-21316, MetaCyc:ACETALD, CHEBI:15343, RHEA:61300produces MetaCyc:RXN-14304 — provides_input_for → MetaCyc:RXN-21315; The shared intermediate is 5-deoxy-α-D-ribose 1-phosphate. This records chemical continuity and native ordering, not physical channeling.; Evidence: MetaCyc:PWY-8130, MetaCyc:PWY-8130provides input for MetaCyc:RXN-21315 — provides_input_for → MetaCyc:RXN-21316; The shared intermediate is 5-deoxy-D-ribulose 1-phosphate. This records chemical continuity and native ordering, not physical channeling.; Evidence: MetaCyc:PWY-8130, MetaCyc:PWY-8130provides input for MetaCyc:CPLX-8604 — part_of → MetaCyc:CPLX-8605; The native component coefficient is 2. This preserves the native topology; CPLX-8604 retains its conflicting dimer label. Physiological stoichiometry has not been directly measured by the sources inspected here. Native assembly species assignment; the physiological strain scope is recorded separately.; Evidence: MetaCyc:CPLX-8605, MetaCyc:CPLX-8604, UniProtKB:Q2RXH9, MetaCyc:CPLX-8605, NCBITaxon:1085part of MetaCyc:MONOMER-17874 — part_of → MetaCyc:CPLX-8604; The native component coefficient is 3. This preserves the native topology; CPLX-8604 retains its conflicting dimer label. Physiological stoichiometry has not been directly measured by the sources inspected here. The current reviewed protein is assigned to strain ATCC 11170; recombinant expression in E. coli does not change its biological origin.; Evidence: MetaCyc:CPLX-8604, MetaCyc:MONOMER-17874, UniProtKB:Q2RXH9, UniProtKB:Q2RXH9, UniProtKB:Q2RXH9part of MetaCyc:CPLX-8605 — catalyzes → MetaCyc:RXN-14304; subject experimental construct: pET28-expressed R. rubrum recombinant protein purified from E. coli Rosetta(DE3) pLysS by nickel chromatography; exact affinity-tag identity/orientation for MtnP is not established by accessible Methods. Native assembly identity is preserved separately.; Evidence PMID:31950558: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography. (//passage[41]); Purified heterologous evidence is assigned to both 2012 and 2020; the 2020 table marks these kinetic values as literature measurements. The qualifier restricts the recombinant assay support; separate native-host evidence supports whole-route physiology.; Evidence: MetaCyc:ENZRXN-29275, MetaCyc:ENZRXN-29275, MetaCyc:ENZRXN-29275, MetaCyc:ENZRXN-29275, MetaCyc:ENZRXN-29275, PMID:31950558, PMID:31950558, UniProtKB:Q2RXH9, PMID:31950558, UniProtKB:Q2RXH9catalyzes UniProtKB:Q2RXI0 — catalyzes → MetaCyc:RXN-21315; subject experimental construct: Recombinant R. rubrum MtnA expressed in E. coli; native commentary attributes a His10 construct, while the 2020 Methods give pET28/Rosetta(DE3) pLysS nickel purification. Exact tag orientation is unresolved; native 2020 evidence is partially purified.; Evidence PMID:31950558: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography. (//passage[41]); Evidence MetaCyc:MONOMER-17870: Native commentary attributes a His10 construct expressed in E. coli; the complete activity frame separately preserves partially purified heterologous evidence for 2020. (/ptools-xml/Protein[@frameid='MONOMER-17870']/comment); Earlier purified heterologous and mutant evidence is distinct from the partially purified heterologous tier assigned to 2020. The qualifier restricts the recombinant assay support; separate native-host evidence supports whole-route physiology. The current reviewed protein is assigned to strain ATCC 11170; recombinant expression in E. coli does not change its biological origin.; Evidence: MetaCyc:ENZRXN-29274, MetaCyc:ENZRXN-29274, MetaCyc:ENZRXN-29274, MetaCyc:ENZRXN-29274, MetaCyc:ENZRXN-29274, PMID:31950558, PMID:31950558, UniProtKB:Q2RXI0, PMID:31950558, UniProtKB:Q2RXI0, UniProtKB:Q2RXI0, UniProtKB:Q2RXI0catalyzes UniProtKB:Q2RXI1 — catalyzes → MetaCyc:RXN-21316; subject experimental construct: Recombinant R. rubrum Ald2 expressed in E. coli; 2020 Methods specify pET28/Rosetta(DE3) pLysS nickel purification. The older His6/anaerobic-purification detail is database-attributed; exact tag orientation and native-host occupancy are not established.; Evidence PMID:31950558: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography. (//passage[41]); Evidence MetaCyc:MONOMER-21152: Native commentary attributes an E. coli-expressed His6 construct and anaerobic purification to the older PMID 29133429 work; that paper was not completely acquired here. (/ptools-xml/Protein[@frameid='MONOMER-21152']/comment); Mutant reaction-block evidence and purified heterologous-protein evidence are distinct, both assigned to 2020. The qualifier restricts the recombinant assay support; separate native-host evidence supports whole-route physiology. The current reviewed protein is assigned to strain ATCC 11170; recombinant expression in E. coli does not change its biological origin.; Evidence: MetaCyc:ENZRXN-29276, MetaCyc:ENZRXN-29276, MetaCyc:ENZRXN-29276, MetaCyc:ENZRXN-29276, MetaCyc:ENZRXN-29276, PMID:31950558, PMID:31950558, UniProtKB:Q2RXI1, UniProtKB:Q2RXI1, UniProtKB:Q2RXI1catalyzes UniProtKB:Q2RXI1 — has_cofactor → CHEBI:48828; subject molecular state: Recombinant R. rubrum Ald2 apoenzyme after EDTA treatment and dialysis, separately reconstituted with 0.1 mM Co2+ for one hour. This is one alternative assay preparation; bound metal in the native host and simultaneous Co/Ni occupancy are not established.; Evidence PMID:31950558: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography. (//passage[41]); Evidence PMID:31950558: Apoenzymes were prepared by 24-hour EDTA dialysis followed by 24-hour Chelex-treated buffer dialysis; individual metals were added at 0.1 mM for one hour before activity measurement. (//passage[54]); Co2+ is an alternative high-activity reconstitution condition for R. rubrum Ald2, not a simultaneous requirement or identified cellular occupancy.; Evidence: PMID:31950558, PMID:31950558, MetaCyc:MONOMER-21152has cofactor UniProtKB:Q2RXI1 — has_cofactor → CHEBI:49786; subject molecular state: Recombinant R. rubrum Ald2 apoenzyme after EDTA treatment and dialysis, separately reconstituted with 0.1 mM Ni2+ for one hour. This is one alternative assay preparation; bound metal in the native host and simultaneous Co/Ni occupancy are not established.; Evidence PMID:31950558: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography. (//passage[41]); Evidence PMID:31950558: Apoenzymes were prepared by 24-hour EDTA dialysis followed by 24-hour Chelex-treated buffer dialysis; individual metals were added at 0.1 mM for one hour before activity measurement. (//passage[54]); Ni2+ is an alternative high-activity reconstitution condition for R. rubrum Ald2, not a simultaneous requirement or identified cellular occupancy.; Evidence: PMID:31950558, PMID:31950558, MetaCyc:MONOMER-21152has cofactor 5'-deoxyadenosine; CHEBI:17319; Declared type: small_molecule small molecule 5'-deoxyadenosine hydrogenphosphate; CHEBI:43474; Declared type: small_molecule small molecule hydrogenphosphate 5-deoxy-α-D-ribose 1-phosphate(2−); CHEBI:58749; Declared type: small_molecule small molecule 5-deoxy-α-D-ribose 1-phosphate(2−) adenine; CHEBI:16708; Declared type: small_molecule small molecule adenine 5-deoxy-D-ribulose 1-phosphate(2−); CHEBI:144504; Declared type: small_molecule small molecule 5-deoxy-D-ribulose 1-phosphate(2−) glycerone phosphate(2−); CHEBI:57642; Declared type: small_molecule small molecule glycerone phosphate(2−) acetaldehyde; CHEBI:15343; Declared type: small_molecule small molecule acetaldehyde cobalt(2+); CHEBI:48828; Declared type: cofactor cofactor cobalt(2+) nickel(2+); CHEBI:49786; Declared type: cofactor cofactor nickel(2+) S-methyl-5'-thioadenosine phosphorylase; MetaCyc:CPLX-8605; Declared type: complex complex S-methyl-5'-thioadenosine phosphorylase S-methyl-5'-thioadenosine phosphorylase dimer; MetaCyc:CPLX-8604; Declared type: complex complex S-methyl-5'-thioadenosine phosphorylase dimer S-methyl-5'-thioadenosine phosphorylase monomer; MetaCyc:MONOMER-17874; Declared type: protein protein S-methyl-5'-thioadenosine phosphorylase monomer Methylthioribose-1-phosphate isomerase; UniProtKB:Q2RXI0; Declared type: protein protein Methylthioribose-1-phosphate isomerase 5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase; UniProtKB:Q2RXI1; Declared type: protein protein 5-methylthioribulose-1- phosphate/5-deoxyribulose-1- phosphate aldolase 5'-deoxyadenosine phosphorolysis; MetaCyc:RXN-14304; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity 5'-deoxyadenosine phosphorolysis 5-deoxyribose 1-phosphate isomerization; MetaCyc:RXN-21315; Declared type: molecular_activity; Source reaction direction: reversible molecular activity 5-deoxyribose 1-phosphate isomerization 5-deoxyribulose 1-phosphate aldol cleavage; MetaCyc:RXN-21316; Declared type: molecular_activity; Source reaction direction: reversible molecular activity 5-deoxyribulose 1-phosphate aldol cleavage 5'-deoxyadenosine degradation I; MetaCyc:PWY-8130; Declared type: pathway pathway 5'-deoxyadenosine degradation I S-methyl-5'-thioadenosine phosphorylase; MetaCyc:CPLX-8605; Declared type: complex; experimental construct: pET28-expressed R. rubrum recombinant protein purified from E. coli Rosetta(DE3) pLysS by nickel chromatography; exact affinity-tag identity/orientation for MtnP is not established by accessible Methods. Native assembly identity is preserved separately.; Evidence PMID:31950558: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography. (//passage[41]) experimental construct S-methyl-5'-thioadenosine phosphorylase [experimental construct: pET28-expressed R. rubrum recombinant protein purified from E. coli Rosetta(DE3) pLysS by nickel…] Methylthioribose-1-phosphate isomerase; UniProtKB:Q2RXI0; Declared type: protein; experimental construct: Recombinant R. rubrum MtnA expressed in E. coli; native commentary attributes a His10 construct, while the 2020 Methods give pET28/Rosetta(DE3) pLysS nickel purification. Exact tag orientation is unresolved; native 2020 evidence is partially purified.; Evidence PMID:31950558: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography. (//passage[41]); Evidence MetaCyc:MONOMER-17870: Native commentary attributes a His10 construct expressed in E. coli; the complete activity frame separately preserves partially purified heterologous evidence for 2020. (/ptools-xml/Protein[@frameid='MONOMER-17870']/comment) experimental construct Methylthioribose-1-phosphate isomerase [experimental construct: Recombinant R. rubrum MtnA expressed in E. coli; native commentary attributes a His10 construct,…] 5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase; UniProtKB:Q2RXI1; Declared type: protein; experimental construct: Recombinant R. rubrum Ald2 expressed in E. coli; 2020 Methods specify pET28/Rosetta(DE3) pLysS nickel purification. The older His6/anaerobic-purification detail is database-attributed; exact tag orientation and native-host occupancy are not established.; Evidence PMID:31950558: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography. (//passage[41]); Evidence MetaCyc:MONOMER-21152: Native commentary attributes an E. coli-expressed His6 construct and anaerobic purification to the older PMID 29133429 work; that paper was not completely acquired here. (/ptools-xml/Protein[@frameid='MONOMER-21152']/comment) experimental construct 5-methylthioribulose-1- phosphate/5-deoxyribulose-1- phosphate aldolase [experimental construct: Recombinant R. rubrum Ald2 expressed in E. coli; 2020 Methods specify pET28/Rosetta(DE3) pLysS…] 5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase; UniProtKB:Q2RXI1; Declared type: protein; molecular state: Recombinant R. rubrum Ald2 apoenzyme after EDTA treatment and dialysis, separately reconstituted with 0.1 mM Co2+ for one hour. This is one alternative assay preparation; bound metal in the native host and simultaneous Co/Ni occupancy are not established.; Evidence PMID:31950558: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography. (//passage[41]); Evidence PMID:31950558: Apoenzymes were prepared by 24-hour EDTA dialysis followed by 24-hour Chelex-treated buffer dialysis; individual metals were added at 0.1 mM for one hour before activity measurement. (//passage[54]) molecular state 5-methylthioribulose-1- phosphate/5-deoxyribulose-1- phosphate aldolase [molecular state: Recombinant R. rubrum Ald2 apoenzyme after EDTA treatment and dialysis, separately reconstituted…] 5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase; UniProtKB:Q2RXI1; Declared type: protein; molecular state: Recombinant R. rubrum Ald2 apoenzyme after EDTA treatment and dialysis, separately reconstituted with 0.1 mM Ni2+ for one hour. This is one alternative assay preparation; bound metal in the native host and simultaneous Co/Ni occupancy are not established.; Evidence PMID:31950558: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography. (//passage[41]); Evidence PMID:31950558: Apoenzymes were prepared by 24-hour EDTA dialysis followed by 24-hour Chelex-treated buffer dialysis; individual metals were added at 0.1 mM for one hour before activity measurement. (//passage[54]) molecular state 5-methylthioribulose-1- phosphate/5-deoxyribulose-1- phosphate aldolase [molecular state: Recombinant R. rubrum Ald2 apoenzyme after EDTA treatment and dialysis, separately reconstituted…]

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Rhodospirillum rubrum ATCC 11170
NCBITaxon:269796		taxon
Rhodospirillum rubrum
NCBITaxon:1085		taxon
5'-deoxyadenosine
CHEBI:17319		small molecule
hydrogenphosphate
CHEBI:43474		small molecule
5-deoxy-α-D-ribose 1-phosphate(2−)
CHEBI:58749		small molecule
adenine
CHEBI:16708		small molecule
5-deoxy-D-ribulose 1-phosphate(2−)
CHEBI:144504		small molecule
glycerone phosphate(2−)
CHEBI:57642		small molecule
acetaldehyde
CHEBI:15343		small molecule
cobalt(2+)
CHEBI:48828		cofactor
nickel(2+)
CHEBI:49786		cofactor
S-methyl-5'-thioadenosine phosphorylase
MetaCyc:CPLX-8605		complex
S-methyl-5'-thioadenosine phosphorylase dimer
MetaCyc:CPLX-8604		complex
S-methyl-5'-thioadenosine phosphorylase monomer
MetaCyc:MONOMER-17874		protein
Methylthioribose-1-phosphate isomerase
UniProtKB:Q2RXI0		protein
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase
UniProtKB:Q2RXI1		protein
5'-deoxyadenosine phosphorolysis
MetaCyc:RXN-14304		molecular activityleft to right
5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315		molecular activityreversible
5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316		molecular activityreversible

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
5'-deoxyadenosine phosphorolysis
MetaCyc:RXN-14304		part_of

This native reaction is explicitly listed in the exact three-event pathway. Whole-route physiological scope is the tested ATCC 11170 strain; this edge does not describe the heterologous expression host.

MetaCyc:PWY-8130
  • MetaCyc:PWY-8130

    Source assertion: MetaCyc:RXN-14304 is explicitly present in the native reaction-list.

    Source location/ptools-xml/Pathway[@frameid='PWY-8130']/reaction-list/Reaction
  • MetaCyc:RXN-14304

    Source assertion: The native reaction backlinks include PWY-8130.

    Source location/ptools-xml/Reaction[@frameid='RXN-14304']/in-pathway/Pathway
  • PMID:31950558

    Source assertion: Wild-type and deletion strains of R. rubrum ATCC 11170 were grown aerobically or anaerobically, with plasmid complementation of the pathway-gene deletions.

    Source location//passage[43]
  • PMID:31950558

    Source assertion: Anaerobic labeled-5′-deoxyadenosine feeding showed blocks at pathway entry in ΔmtnP, 5-deoxyribose 1-phosphate in ΔmtnA, and 5-deoxyribulose 1-phosphate in Δald2.

    Source location//passage[14]
  • PMID:31950558

    Source assertion: The three mutants accumulated 5′-deoxyadenosine and MTA extracellularly; complementation restored wild-type abundance. The twofold comparison is 5′-deoxyadenosine versus MTA.

    Source location//passage[12]
  • NCBITaxon:269796

    Source assertion: NCBI identifies taxon 269796 as Rhodospirillum rubrum ATCC 11170, at strain rank under species 1085.

    Source location/TaxaSet/Taxon/ScientificName
5'-deoxyadenosine
CHEBI:17319		consumes

One stoichiometric occurrence on the native written left side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.

5'-deoxyadenosine phosphorolysis
MetaCyc:RXN-14304
  • MetaCyc:RXN-14304

    Source assertion: MetaCyc:CH33ADO occurs on the left side; no coefficient override is supplied, so the written stoichiometric occurrence is one.

    Source location/ptools-xml/Reaction[@frameid='RXN-14304']/left[1]
  • MetaCyc:CH33ADO

    Source assertion: Native complete InChI: InChI=1S/C10H13N5O3/c1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15/h2-4,6-7,10,16-17H,1H3,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1

    Source location/ptools-xml/Compound[@frameid='CH33ADO']/inchi
  • CHEBI:17319

    Source assertion: Current released ChEBI complete InChI: InChI=1S/C10H13N5O3/c1-4-6(16)7(17)10(18-4)15-3-14-5-8(11)12-2-13-9(5)15/h2-4,6-7,10,16-17H,1H3,(H2,11,12,13)/t4-,6-,7-,10-/m1/s1

    Source location$.default_structure.standard_inchi
  • RHEA:24869

    Source assertion: Rhea family 24869 independently represents the same chemical transformation; complete side/participant/compound traversal confirms CHEBI:17319 on the corresponding left side with coefficient 1.

    Source location/rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/24869'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/24869_L'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Participant_24869_compound_2028'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Compound_2028']
hydrogenphosphate
CHEBI:43474		consumes

One stoichiometric occurrence on the native written left side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.

5'-deoxyadenosine phosphorolysis
MetaCyc:RXN-14304
  • MetaCyc:RXN-14304

    Source assertion: MetaCyc:Pi occurs on the left side; no coefficient override is supplied, so the written stoichiometric occurrence is one.

    Source location/ptools-xml/Reaction[@frameid='RXN-14304']/left[2]
  • MetaCyc:Pi

    Source assertion: Native complete InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-2

    Source location/ptools-xml/Compound[@frameid='Pi']/inchi
  • CHEBI:43474

    Source assertion: Current released ChEBI complete InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-2

    Source location$.default_structure.standard_inchi
  • RHEA:24869

    Source assertion: Rhea family 24869 independently represents the same chemical transformation; complete side/participant/compound traversal confirms CHEBI:43474 on the corresponding left side with coefficient 1.

    Source location/rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/24869'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/24869_L'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Participant_24869_compound_5518'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Compound_5518']
5'-deoxyadenosine phosphorolysis
MetaCyc:RXN-14304		produces

One stoichiometric occurrence on the native written right side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.

5-deoxy-α-D-ribose 1-phosphate(2−)
CHEBI:58749
  • MetaCyc:RXN-14304

    Source assertion: MetaCyc:CPD-15199 occurs on the right side; no coefficient override is supplied, so the written stoichiometric occurrence is one.

    Source location/ptools-xml/Reaction[@frameid='RXN-14304']/right[1]
  • MetaCyc:CPD-15199

    Source assertion: Native complete InChI: InChI=1S/C5H11O7P/c1-2-3(6)4(7)5(11-2)12-13(8,9)10/h2-7H,1H3,(H2,8,9,10)/p-2/t2-,3-,4-,5-/m1/s1

    Source location/ptools-xml/Compound[@frameid='CPD-15199']/inchi
  • CHEBI:58749

    Source assertion: Current released ChEBI complete InChI: InChI=1S/C5H11O7P/c1-2-3(6)4(7)5(11-2)12-13(8,9)10/h2-7H,1H3,(H2,8,9,10)/p-2/t2-,3-,4-,5-/m1/s1

    Source location$.default_structure.standard_inchi
  • RHEA:24869

    Source assertion: Rhea family 24869 independently represents the same chemical transformation; complete side/participant/compound traversal confirms CHEBI:58749 on the corresponding right side with coefficient 1.

    Source location/rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/24869'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/24869_R'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Participant_24869_compound_5347'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Compound_5347']
5'-deoxyadenosine phosphorolysis
MetaCyc:RXN-14304		produces

One stoichiometric occurrence on the native written right side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.

adenine
CHEBI:16708
  • MetaCyc:RXN-14304

    Source assertion: MetaCyc:ADENINE occurs on the right side; no coefficient override is supplied, so the written stoichiometric occurrence is one.

    Source location/ptools-xml/Reaction[@frameid='RXN-14304']/right[2]
  • MetaCyc:ADENINE

    Source assertion: Native complete InChI: InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)

    Source location/ptools-xml/Compound[@frameid='ADENINE']/inchi
  • CHEBI:16708

    Source assertion: Current released ChEBI complete InChI: InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)

    Source location$.default_structure.standard_inchi
  • RHEA:24869

    Source assertion: Rhea family 24869 independently represents the same chemical transformation; complete side/participant/compound traversal confirms CHEBI:16708 on the corresponding right side with coefficient 1.

    Source location/rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/24869'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/24869_R'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Participant_24869_compound_4174'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Compound_4174']
5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315		part_of

This native reaction is explicitly listed in the exact three-event pathway. Whole-route physiological scope is the tested ATCC 11170 strain; this edge does not describe the heterologous expression host.

MetaCyc:PWY-8130
  • MetaCyc:PWY-8130

    Source assertion: MetaCyc:RXN-21315 is explicitly present in the native reaction-list.

    Source location/ptools-xml/Pathway[@frameid='PWY-8130']/reaction-list/Reaction
  • MetaCyc:RXN-21315

    Source assertion: The native reaction backlinks include PWY-8130.

    Source location/ptools-xml/Reaction[@frameid='RXN-21315']/in-pathway/Pathway
  • PMID:31950558

    Source assertion: Wild-type and deletion strains of R. rubrum ATCC 11170 were grown aerobically or anaerobically, with plasmid complementation of the pathway-gene deletions.

    Source location//passage[43]
  • PMID:31950558

    Source assertion: Anaerobic labeled-5′-deoxyadenosine feeding showed blocks at pathway entry in ΔmtnP, 5-deoxyribose 1-phosphate in ΔmtnA, and 5-deoxyribulose 1-phosphate in Δald2.

    Source location//passage[14]
  • PMID:31950558

    Source assertion: The three mutants accumulated 5′-deoxyadenosine and MTA extracellularly; complementation restored wild-type abundance. The twofold comparison is 5′-deoxyadenosine versus MTA.

    Source location//passage[12]
  • NCBITaxon:269796

    Source assertion: NCBI identifies taxon 269796 as Rhodospirillum rubrum ATCC 11170, at strain rank under species 1085.

    Source location/TaxaSet/Taxon/ScientificName
5-deoxy-α-D-ribose 1-phosphate(2−)
CHEBI:58749		consumes

One stoichiometric occurrence on the native written left side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.

5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315
  • MetaCyc:RXN-21315

    Source assertion: MetaCyc:CPD-15199 occurs on the left side; no coefficient override is supplied, so the written stoichiometric occurrence is one.

    Source location/ptools-xml/Reaction[@frameid='RXN-21315']/left[1]
  • MetaCyc:CPD-15199

    Source assertion: Native complete InChI: InChI=1S/C5H11O7P/c1-2-3(6)4(7)5(11-2)12-13(8,9)10/h2-7H,1H3,(H2,8,9,10)/p-2/t2-,3-,4-,5-/m1/s1

    Source location/ptools-xml/Compound[@frameid='CPD-15199']/inchi
  • CHEBI:58749

    Source assertion: Current released ChEBI complete InChI: InChI=1S/C5H11O7P/c1-2-3(6)4(7)5(11-2)12-13(8,9)10/h2-7H,1H3,(H2,8,9,10)/p-2/t2-,3-,4-,5-/m1/s1

    Source location$.default_structure.standard_inchi
  • RHEA:61296

    Source assertion: Rhea family 61296 independently represents the same chemical transformation; complete side/participant/compound traversal confirms CHEBI:58749 on the corresponding left side with coefficient 1.

    Source location/rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/61296'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/61296_L'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Participant_61296_compound_5347'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Compound_5347']
5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315		produces

One stoichiometric occurrence on the native written right side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.

5-deoxy-D-ribulose 1-phosphate(2−)
CHEBI:144504
  • MetaCyc:RXN-21315

    Source assertion: MetaCyc:CPD-23219 occurs on the right side; no coefficient override is supplied, so the written stoichiometric occurrence is one.

    Source location/ptools-xml/Reaction[@frameid='RXN-21315']/right[1]
  • MetaCyc:CPD-23219

    Source assertion: Native complete InChI: InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h3,5-6,8H,2H2,1H3,(H2,9,10,11)/p-2/t3-,5-/m1/s1

    Source location/ptools-xml/Compound[@frameid='CPD-23219']/inchi
  • CHEBI:144504

    Source assertion: Current released ChEBI complete InChI: InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h3,5-6,8H,2H2,1H3,(H2,9,10,11)/p-2/t3-,5-/m1/s1

    Source location$.default_structure.standard_inchi
  • RHEA:61296

    Source assertion: Rhea family 61296 independently represents the same chemical transformation; complete side/participant/compound traversal confirms CHEBI:144504 on the corresponding right side with coefficient 1.

    Source location/rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/61296'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/61296_R'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Participant_61296_compound_15777'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Compound_15777']
5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316		part_of

This native reaction is explicitly listed in the exact three-event pathway. Whole-route physiological scope is the tested ATCC 11170 strain; this edge does not describe the heterologous expression host.

MetaCyc:PWY-8130
  • MetaCyc:PWY-8130

    Source assertion: MetaCyc:RXN-21316 is explicitly present in the native reaction-list.

    Source location/ptools-xml/Pathway[@frameid='PWY-8130']/reaction-list/Reaction
  • MetaCyc:RXN-21316

    Source assertion: The native reaction backlinks include PWY-8130.

    Source location/ptools-xml/Reaction[@frameid='RXN-21316']/in-pathway/Pathway
  • PMID:31950558

    Source assertion: Wild-type and deletion strains of R. rubrum ATCC 11170 were grown aerobically or anaerobically, with plasmid complementation of the pathway-gene deletions.

    Source location//passage[43]
  • PMID:31950558

    Source assertion: Anaerobic labeled-5′-deoxyadenosine feeding showed blocks at pathway entry in ΔmtnP, 5-deoxyribose 1-phosphate in ΔmtnA, and 5-deoxyribulose 1-phosphate in Δald2.

    Source location//passage[14]
  • PMID:31950558

    Source assertion: The three mutants accumulated 5′-deoxyadenosine and MTA extracellularly; complementation restored wild-type abundance. The twofold comparison is 5′-deoxyadenosine versus MTA.

    Source location//passage[12]
  • NCBITaxon:269796

    Source assertion: NCBI identifies taxon 269796 as Rhodospirillum rubrum ATCC 11170, at strain rank under species 1085.

    Source location/TaxaSet/Taxon/ScientificName
5-deoxy-D-ribulose 1-phosphate(2−)
CHEBI:144504		consumes

One stoichiometric occurrence on the native written left side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.

5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316
  • MetaCyc:RXN-21316

    Source assertion: MetaCyc:CPD-23219 occurs on the left side; no coefficient override is supplied, so the written stoichiometric occurrence is one.

    Source location/ptools-xml/Reaction[@frameid='RXN-21316']/left[1]
  • MetaCyc:CPD-23219

    Source assertion: Native complete InChI: InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h3,5-6,8H,2H2,1H3,(H2,9,10,11)/p-2/t3-,5-/m1/s1

    Source location/ptools-xml/Compound[@frameid='CPD-23219']/inchi
  • CHEBI:144504

    Source assertion: Current released ChEBI complete InChI: InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h3,5-6,8H,2H2,1H3,(H2,9,10,11)/p-2/t3-,5-/m1/s1

    Source location$.default_structure.standard_inchi
  • RHEA:61300

    Source assertion: Rhea family 61300 independently represents the same chemical transformation; complete side/participant/compound traversal confirms CHEBI:144504 on the corresponding left side with coefficient 1.

    Source location/rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/61300'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/61300_L'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Participant_61300_compound_15777'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Compound_15777']
5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316		produces

One stoichiometric occurrence on the native written right side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.

glycerone phosphate(2−)
CHEBI:57642
  • MetaCyc:RXN-21316

    Source assertion: MetaCyc:DIHYDROXY-ACETONE-PHOSPHATE occurs on the right side; no coefficient override is supplied, so the written stoichiometric occurrence is one.

    Source location/ptools-xml/Reaction[@frameid='RXN-21316']/right[1]
  • MetaCyc:DIHYDROXY-ACETONE-PHOSPHATE

    Source assertion: Native complete InChI: InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h4H,1-2H2,(H2,6,7,8)/p-2

    Source location/ptools-xml/Compound[@frameid='DIHYDROXY-ACETONE-PHOSPHATE']/inchi
  • CHEBI:57642

    Source assertion: Current released ChEBI complete InChI: InChI=1S/C3H7O6P/c4-1-3(5)2-9-10(6,7)8/h4H,1-2H2,(H2,6,7,8)/p-2

    Source location$.default_structure.standard_inchi
  • RHEA:61300

    Source assertion: Rhea family 61300 independently represents the same chemical transformation; complete side/participant/compound traversal confirms CHEBI:57642 on the corresponding right side with coefficient 1.

    Source location/rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/61300'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/61300_R'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Participant_61300_compound_4255'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Compound_4255']
5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316		produces

One stoichiometric occurrence on the native written right side. For a reversible reaction this preserves its source equation orientation without asserting irreversibility.

acetaldehyde
CHEBI:15343
  • MetaCyc:RXN-21316

    Source assertion: MetaCyc:ACETALD occurs on the right side; no coefficient override is supplied, so the written stoichiometric occurrence is one.

    Source location/ptools-xml/Reaction[@frameid='RXN-21316']/right[2]
  • MetaCyc:ACETALD

    Source assertion: Native complete InChI: InChI=1S/C2H4O/c1-2-3/h2H,1H3

    Source location/ptools-xml/Compound[@frameid='ACETALD']/inchi
  • CHEBI:15343

    Source assertion: Current released ChEBI complete InChI: InChI=1S/C2H4O/c1-2-3/h2H,1H3

    Source location$.default_structure.standard_inchi
  • RHEA:61300

    Source assertion: Rhea family 61300 independently represents the same chemical transformation; complete side/participant/compound traversal confirms CHEBI:15343 on the corresponding right side with coefficient 1.

    Source location/rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/61300'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/61300_R'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Participant_61300_compound_3952'] | /rdf:RDF/rdf:Description[@rdf:about='http://rdf.rhea-db.org/Compound_3952']
5'-deoxyadenosine phosphorolysis
MetaCyc:RXN-14304		provides_input_for

The shared intermediate is 5-deoxy-α-D-ribose 1-phosphate. This records chemical continuity and native ordering, not physical channeling.

5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315
  • MetaCyc:PWY-8130

    Source assertion: RXN-14304 is the predecessor of RXN-21315 in the pathway ordering.

    Source location/ptools-xml/Pathway[@frameid='PWY-8130']/reaction-ordering[2]
  • MetaCyc:PWY-8130

    Source assertion: Left-to-right pathway layouts transfer 5-deoxy-α-D-ribose 1-phosphate between RXN-14304 and RXN-21315.

    Source location/ptools-xml/Pathway[@frameid='PWY-8130']/reaction-layout
5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315		provides_input_for

The shared intermediate is 5-deoxy-D-ribulose 1-phosphate. This records chemical continuity and native ordering, not physical channeling.

5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316
  • MetaCyc:PWY-8130

    Source assertion: RXN-21315 is the predecessor of RXN-21316 in the pathway ordering.

    Source location/ptools-xml/Pathway[@frameid='PWY-8130']/reaction-ordering[1]
  • MetaCyc:PWY-8130

    Source assertion: Left-to-right pathway layouts transfer 5-deoxy-D-ribulose 1-phosphate between RXN-21315 and RXN-21316.

    Source location/ptools-xml/Pathway[@frameid='PWY-8130']/reaction-layout
S-methyl-5'-thioadenosine phosphorylase dimer
MetaCyc:CPLX-8604		part_of

The native component coefficient is 2. This preserves the native topology; CPLX-8604 retains its conflicting dimer label. Physiological stoichiometry has not been directly measured by the sources inspected here. Native assembly species assignment; the physiological strain scope is recorded separately.

S-methyl-5'-thioadenosine phosphorylase
MetaCyc:CPLX-8605
  • MetaCyc:CPLX-8605

    Source assertion: CPLX-8605 has 2 copies of CPLX-8604 in its explicit component slot.

    Source location/ptools-xml/Protein[@frameid='CPLX-8605']/component
  • MetaCyc:CPLX-8604

    Source assertion: CPLX-8604 explicitly records reciprocal membership in CPLX-8605.

    Source location/ptools-xml/Protein[@frameid='CPLX-8604']/component-of
  • UniProtKB:Q2RXH9

    Source assertion: The SUBUNIT comment states homohexamer, dimer of a homotrimer, supported by ECO:0000255 from HAMAP MF_01963; this is inference, not a direct assembly measurement.

    Source location$.comments[5]
  • MetaCyc:CPLX-8605

    Source assertion: The native protein complex is assigned to Rhodospirillum rubrum, with NCBI taxon cross-reference 1085.

    Source location/ptools-xml/Protein[@frameid='CPLX-8605']/species
  • NCBITaxon:1085

    Source assertion: NCBI taxon 1085 is the species Rhodospirillum rubrum.

    Source location/TaxaSet/Taxon/ScientificName
S-methyl-5'-thioadenosine phosphorylase monomer
MetaCyc:MONOMER-17874		part_of

The native component coefficient is 3. This preserves the native topology; CPLX-8604 retains its conflicting dimer label. Physiological stoichiometry has not been directly measured by the sources inspected here. The current reviewed protein is assigned to strain ATCC 11170; recombinant expression in E. coli does not change its biological origin.

S-methyl-5'-thioadenosine phosphorylase dimer
MetaCyc:CPLX-8604
  • MetaCyc:CPLX-8604

    Source assertion: CPLX-8604 has 3 copies of MONOMER-17874 in its explicit component slot.

    Source location/ptools-xml/Protein[@frameid='CPLX-8604']/component
  • MetaCyc:MONOMER-17874

    Source assertion: MONOMER-17874 explicitly records reciprocal membership in CPLX-8604.

    Source location/ptools-xml/Protein[@frameid='MONOMER-17874']/component-of
  • UniProtKB:Q2RXH9

    Source assertion: The SUBUNIT comment states homohexamer, dimer of a homotrimer, supported by ECO:0000255 from HAMAP MF_01963; this is inference, not a direct assembly measurement.

    Source location$.comments[5]
  • UniProtKB:Q2RXH9

    Source assertion: The reviewed entry assigns this protein to Rhodospirillum rubrum strain ATCC 11170 / S1, NCBI taxon 269796.

    Source location$.organism
  • UniProtKB:Q2RXH9

    Source assertion: The entry gives the matching mtnP, mtnA or ald2 gene and Rru_A0361, Rru_A0360 or Rru_A0359 locus, respectively.

    Source location$.genes
S-methyl-5'-thioadenosine phosphorylase
MetaCyc:CPLX-8605

experimental construct: pET28-expressed R. rubrum recombinant protein purified from E. coli Rosetta(DE3) pLysS by nickel chromatography; exact affinity-tag identity/orientation for MtnP is not established by accessible Methods. Native assembly identity is preserved separately.

Qualification evidence
  • PMID:31950558

    Source assertion: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography.

    Source location//passage[41]
catalyzes

Purified heterologous evidence is assigned to both 2012 and 2020; the 2020 table marks these kinetic values as literature measurements. The qualifier restricts the recombinant assay support; separate native-host evidence supports whole-route physiology.

5'-deoxyadenosine phosphorolysis
MetaCyc:RXN-14304
  • MetaCyc:ENZRXN-29275

    Source assertion: ENZRXN-29275 explicitly assigns this enzyme to RXN-14304.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29275']/enzyme
  • MetaCyc:ENZRXN-29275

    Source assertion: ENZRXN-29275 explicitly points to RXN-14304.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29275']/reaction
  • MetaCyc:ENZRXN-29275

    Source assertion: Native annotation: Purified heterologous evidence is assigned to both 2012 and 2020; the 2020 table marks these kinetic values as literature measurements.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29275']/evidence
  • MetaCyc:ENZRXN-29275

    Source assertion: Km is 40 micromolar for CH33ADO; the native kinetic slot cites PMID 31950558.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29275']/km
  • MetaCyc:ENZRXN-29275

    Source assertion: kcat is 6.7 s−1 for CH33ADO; the native kinetic slot cites PMID 31950558.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29275']/kcat
  • PMID:31950558

    Source assertion: Table 1 gives Km 40 micromolar and kcat 6.7 s−1 for R. rubrum MtnP activity with 5′-deoxyadenosine. Values are assay-specific.

    Source location//passage[119]
  • PMID:31950558

    Source assertion: Figure 3D describes sequential purified R. rubrum proteins converting 5′-deoxyadenosine, with acetaldehyde verified by gas chromatography and coupled alcohol-dehydrogenase testing.

    Source location//passage[116]
  • UniProtKB:Q2RXH9

    Source assertion: The reviewed catalytic-activity comment assigns the corresponding 5′-deoxyadenosine-route reaction with primary experimental evidence.

    Source location$.comments[2]
  • PMID:31950558

    Source assertion: The Table 1 hash-marked kinetic entries are values originally reported elsewhere.

    Source location//passage[121]
  • UniProtKB:Q2RXH9

    Source assertion: The reviewed kinetic annotation attributes the 5′-deoxyadenosine-route Km and kcat values to PMID 23042035; this preserves the earlier citation separately from native 2020 slots.

    Source location$.comments[3]
Methylthioribose-1-phosphate isomerase
UniProtKB:Q2RXI0

experimental construct: Recombinant R. rubrum MtnA expressed in E. coli; native commentary attributes a His10 construct, while the 2020 Methods give pET28/Rosetta(DE3) pLysS nickel purification. Exact tag orientation is unresolved; native 2020 evidence is partially purified.

Qualification evidence
  • PMID:31950558

    Source assertion: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography.

    Source location//passage[41]
  • MetaCyc:MONOMER-17870

    Source assertion: Native commentary attributes a His10 construct expressed in E. coli; the complete activity frame separately preserves partially purified heterologous evidence for 2020.

    Source location/ptools-xml/Protein[@frameid='MONOMER-17870']/comment
catalyzes

Earlier purified heterologous and mutant evidence is distinct from the partially purified heterologous tier assigned to 2020. The qualifier restricts the recombinant assay support; separate native-host evidence supports whole-route physiology. The current reviewed protein is assigned to strain ATCC 11170; recombinant expression in E. coli does not change its biological origin.

5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315
  • MetaCyc:ENZRXN-29274

    Source assertion: ENZRXN-29274 explicitly assigns this enzyme to RXN-21315.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29274']/enzyme
  • MetaCyc:ENZRXN-29274

    Source assertion: ENZRXN-29274 explicitly points to RXN-21315.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29274']/reaction
  • MetaCyc:ENZRXN-29274

    Source assertion: Native annotation: Earlier purified heterologous and mutant evidence is distinct from the partially purified heterologous tier assigned to 2020.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29274']/evidence
  • MetaCyc:ENZRXN-29274

    Source assertion: Km is 171 micromolar for CPD-15199; the native kinetic slot cites PMID 31950558.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29274']/km
  • MetaCyc:ENZRXN-29274

    Source assertion: kcat is 0.18 s−1 for CPD-15199; the native kinetic slot cites PMID 31950558.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29274']/kcat
  • PMID:31950558

    Source assertion: Table 1 gives Km 171 micromolar and kcat 0.18 s−1 for R. rubrum MtnA activity with 5-deoxyribose 1-phosphate. Values are assay-specific.

    Source location//passage[119]
  • PMID:31950558

    Source assertion: Figure 3D describes sequential purified R. rubrum proteins converting 5′-deoxyadenosine, with acetaldehyde verified by gas chromatography and coupled alcohol-dehydrogenase testing.

    Source location//passage[116]
  • UniProtKB:Q2RXI0

    Source assertion: The reviewed catalytic-activity comment assigns the corresponding 5′-deoxyadenosine-route reaction with primary experimental evidence.

    Source location$.comments[2]
  • PMID:31950558

    Source assertion: The Table 1 hash-marked kinetic entries are values originally reported elsewhere.

    Source location//passage[121]
  • UniProtKB:Q2RXI0

    Source assertion: The reviewed kinetic annotation attributes the 5′-deoxyadenosine-route Km and kcat values to PMID 23042035; this preserves the earlier citation separately from native 2020 slots.

    Source location$.comments[3]
  • UniProtKB:Q2RXI0

    Source assertion: The reviewed entry assigns this protein to Rhodospirillum rubrum strain ATCC 11170 / S1, NCBI taxon 269796.

    Source location$.organism
  • UniProtKB:Q2RXI0

    Source assertion: The entry gives the matching mtnP, mtnA or ald2 gene and Rru_A0361, Rru_A0360 or Rru_A0359 locus, respectively.

    Source location$.genes
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase
UniProtKB:Q2RXI1

experimental construct: Recombinant R. rubrum Ald2 expressed in E. coli; 2020 Methods specify pET28/Rosetta(DE3) pLysS nickel purification. The older His6/anaerobic-purification detail is database-attributed; exact tag orientation and native-host occupancy are not established.

Qualification evidence
  • PMID:31950558

    Source assertion: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography.

    Source location//passage[41]
  • MetaCyc:MONOMER-21152

    Source assertion: Native commentary attributes an E. coli-expressed His6 construct and anaerobic purification to the older PMID 29133429 work; that paper was not completely acquired here.

    Source location/ptools-xml/Protein[@frameid='MONOMER-21152']/comment
catalyzes

Mutant reaction-block evidence and purified heterologous-protein evidence are distinct, both assigned to 2020. The qualifier restricts the recombinant assay support; separate native-host evidence supports whole-route physiology. The current reviewed protein is assigned to strain ATCC 11170; recombinant expression in E. coli does not change its biological origin.

5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316
  • MetaCyc:ENZRXN-29276

    Source assertion: ENZRXN-29276 explicitly assigns this enzyme to RXN-21316.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29276']/enzyme
  • MetaCyc:ENZRXN-29276

    Source assertion: ENZRXN-29276 explicitly points to RXN-21316.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29276']/reaction
  • MetaCyc:ENZRXN-29276

    Source assertion: Native annotation: Mutant reaction-block evidence and purified heterologous-protein evidence are distinct, both assigned to 2020.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29276']/evidence
  • MetaCyc:ENZRXN-29276

    Source assertion: Km is 229 micromolar for CPD-23219; the native kinetic slot cites PMID 31950558.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29276']/km
  • MetaCyc:ENZRXN-29276

    Source assertion: kcat is 1.94 s−1 for CPD-23219; the native kinetic slot cites PMID 31950558.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29276']/kcat
  • PMID:31950558

    Source assertion: Table 1 gives Km 229 micromolar and kcat 1.94 s−1 for R. rubrum Ald2 activity with 5-deoxyribulose 1-phosphate. Values are assay-specific.

    Source location//passage[119]
  • PMID:31950558

    Source assertion: Figure 3D describes sequential purified R. rubrum proteins converting 5′-deoxyadenosine, with acetaldehyde verified by gas chromatography and coupled alcohol-dehydrogenase testing.

    Source location//passage[116]
  • UniProtKB:Q2RXI1

    Source assertion: The reviewed catalytic-activity comment assigns the corresponding 5′-deoxyadenosine-route reaction with primary experimental evidence.

    Source location$.comments[2]
  • UniProtKB:Q2RXI1

    Source assertion: The reviewed entry assigns this protein to Rhodospirillum rubrum strain ATCC 11170 / S1, NCBI taxon 269796.

    Source location$.organism
  • UniProtKB:Q2RXI1

    Source assertion: The entry gives the matching mtnP, mtnA or ald2 gene and Rru_A0361, Rru_A0360 or Rru_A0359 locus, respectively.

    Source location$.genes
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase
UniProtKB:Q2RXI1

molecular state: Recombinant R. rubrum Ald2 apoenzyme after EDTA treatment and dialysis, separately reconstituted with 0.1 mM Co2+ for one hour. This is one alternative assay preparation; bound metal in the native host and simultaneous Co/Ni occupancy are not established.

Qualification evidence
  • PMID:31950558

    Source assertion: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography.

    Source location//passage[41]
  • PMID:31950558

    Source assertion: Apoenzymes were prepared by 24-hour EDTA dialysis followed by 24-hour Chelex-treated buffer dialysis; individual metals were added at 0.1 mM for one hour before activity measurement.

    Source location//passage[54]
has_cofactor

Co2+ is an alternative high-activity reconstitution condition for R. rubrum Ald2, not a simultaneous requirement or identified cellular occupancy.

cobalt(2+)
CHEBI:48828
  • PMID:31950558

    Source assertion: R. rubrum Ald2 had the highest activity with Co2+ and Ni2+ among the tested individual metal reconstitution conditions.

    Source location//passage[17]
  • PMID:31950558

    Source assertion: Figure 3E distinguishes purified recombinant preparations from ED apoenzyme reconstituted with 0.1 mM of the indicated metal.

    Source location//passage[116]
  • MetaCyc:MONOMER-21152

    Source assertion: The native Ald2 commentary states that a divalent metal cation is required and the highest activity was achieved with Ni2+ and Co2+.

    Source location/ptools-xml/Protein[@frameid='MONOMER-21152']/comment
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase
UniProtKB:Q2RXI1

molecular state: Recombinant R. rubrum Ald2 apoenzyme after EDTA treatment and dialysis, separately reconstituted with 0.1 mM Ni2+ for one hour. This is one alternative assay preparation; bound metal in the native host and simultaneous Co/Ni occupancy are not established.

Qualification evidence
  • PMID:31950558

    Source assertion: R. rubrum MtnP, MtnA and Ald2 genes were expressed from pET28 in E. coli Rosetta(DE3) pLysS; recombinant proteins were purified by nickel chromatography.

    Source location//passage[41]
  • PMID:31950558

    Source assertion: Apoenzymes were prepared by 24-hour EDTA dialysis followed by 24-hour Chelex-treated buffer dialysis; individual metals were added at 0.1 mM for one hour before activity measurement.

    Source location//passage[54]
has_cofactor

Ni2+ is an alternative high-activity reconstitution condition for R. rubrum Ald2, not a simultaneous requirement or identified cellular occupancy.

nickel(2+)
CHEBI:49786
  • PMID:31950558

    Source assertion: R. rubrum Ald2 had the highest activity with Co2+ and Ni2+ among the tested individual metal reconstitution conditions.

    Source location//passage[17]
  • PMID:31950558

    Source assertion: Figure 3E distinguishes purified recombinant preparations from ED apoenzyme reconstituted with 0.1 mM of the indicated metal.

    Source location//passage[116]
  • MetaCyc:MONOMER-21152

    Source assertion: The native Ald2 commentary states that a divalent metal cation is required and the highest activity was achieved with Ni2+ and Co2+.

    Source location/ptools-xml/Protein[@frameid='MONOMER-21152']/comment

References

Curation history