5'-deoxyadenosine degradation II

MetaCyc:PWY-8131

This exact MetaCyc route converts 5'-deoxyadenosine to adenine, dihydroxyacetone phosphate (DHAP) and acetaldehyde in four events: nucleosidase hydrolysis releases 5-deoxyribose and adenine; ATP-dependent phosphorylation forms 5-deoxyribose 1-phosphate; isomerization forms 5-deoxyribulose 1-phosphate; and aldol cleavage gives DHAP and acetaldehyde. Water, ATP(4-), ADP(3-) and the proton are explicit stoichiometric participants. All 14 native side occurrences and three consecutive intermediate transfers are represented. Metabolite continuity does not imply physical substrate channeling. The whole-route physiological evidence is for Escherichia coli ATCC 25922. The 2020 study followed labeled 5'-deoxyadenosine through these intermediates and used pfs, mtnK, mtnA and ald2 deletions to distinguish the steps. Ald2 deletion retained a small residual activity, consistent with a promiscuous fuculose-phosphate aldolase, but this did not restore growth on 5-deoxyribose. Growth with 5-deoxyribose as sole carbon source required each DHAP-shunt-specific gene. The K12 BW25113 comparator did not grow on this substrate. The taxon list also records component evidence: MG1655 nucleosidase, the Bacillus HD73/HD73-20 three-enzyme module, and the two shared Rhodospirillum rubrum ATCC 11170 steps. It does not assert the complete four-event route in every listed taxon. Both final native reaction frames are reversible, although the pathway layout and physiological activity annotations use the degradative left-to-right direction. Bacillus DrdA also has explicit reverse aldol-condensation evidence. These are preserved as reversible native nodes with their written sides, rather than replaced by irreversible forward Rhea nodes. Rhea release 142 independently supports all four reaction families and the same 14 chemical sides. The ATP, ADP and sugar phosphates retain their specific charge states. The cyclic, anomer-unspecified native 5-deoxyribose structure matches CHEBI:149540 by complete InChI; its native CHEBI:62012 and PubChem:45489773 links instead denote an open-chain structure and are not used as exact mappings. The alpha assignment for the kinase product and the 3R,4R aldol product assignment have biochemical inference support in the 2018 paper, rather than direct complete stereochemical determination in each organism. Current NCBIProtein accessions represent the four ATCC 25922 enzymes: WP_000689844.1 (MtnN/Pfs), WP_000132325.1 (MtnK), WP_001022015.1 (MtnA) and WP_000439686.1 (Ald2). Each complete sequence exactly matches its archived UniProt accession, the corresponding UniParc sequence and a single translated CDS on ATCC 25922 chromosome NZ_CP032085.1. Their current loci are D1792_RS20095, D1792_RS18645, D1792_RS18650 and D1792_RS18655, respectively; native MetaCyc DR76 locus names belong to a different assembly annotation. The historical UniProt records are deleted and are not active identifier owners. RefSeq product labels are preserved, including the generic L-fuculose-phosphate aldolase label for WP_000439686.1; functional Ald2 assignment comes from the explicit identity bridge and experimental evidence, not that generic label alone. The ATCC enzymes were expressed from pET28 constructs in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Exact tag orientation is not asserted because the 2020 supplementary primers were inaccessible. Native activity annotations distinguish purified heterologous protein, mutant reaction blocks and the separate unpurified native-host tier for Ald2; the last tier alone does not identify a purified enzyme. The 2020 Results call Ald2 natively purified and report activity and violet color like Co2+-reconstituted enzyme; the Methods describe EcAld2 expression in Rosetta(DE3) pLysS. This is treated as an as-purified recombinant preparation, not evidence of purification from the native ATCC host. Native kinetic slots give Km/kcat pairs of 4.7 micromolar/57 s−1 for MtnN, 25/16.1 for MtnK, 222/2.02 for MtnA and 598/22 for Ald2, with their substrates and source citations retained on the activity edges. These are assay-specific parameters, not universal cellular fluxes. The R. rubrum proteins contribute the shared isomerase and aldolase activities only; its complete 5'-deoxyadenosine route begins with MtnP phosphorylase, an alternative entry reaction outside this record. Native MtnA commentary describes a His10 construct, and Ald2 commentary a His6 construct with anaerobic purification. The MtnA activity frame assigns partially purified heterologous evidence to the 2020 study, alongside distinct earlier purified-protein and mutant evidence. Native Km/kcat pairs are 171 micromolar/0.18 s−1 for MtnA and 229/1.94 for Ald2. Co2+ and Ni2+ confer the highest Ald2 activity among tested reconstitution conditions. Alternative metals are separate assay states, not simultaneous required components. The 2018 Bacillus thuringiensis experiments used HD73-20 (BGSC 4D22), with current protein identities assigned to strain HD73. DrdK and DrdI carried N-terminal His6 tags and DrdA a C-terminal His6 tag in activity assays; a separate tag-free DrdA preparation was used for crystallography and metal-loading analyses. Together the three enzymes converted 5-deoxyribose plus ATP to DHAP. Size exclusion supported DrdK and DrdI dimers and a DrdA oligomer possibly tetrameric; the crystal lattice supplied a proposed tetramer. Functional protein edges therefore do not invent exact physiological complex identifiers. DrdK Km/kcat values were 178 micromolar/15.4 s−1 for 5-deoxyribose and 216/17.1 for ATP. DrdI had a 22 ± 7 mM Km and 3.5 ± 0.7 s−1 kcat; DrdA had 36 ± 3 micromolar and 6.3 ± 0.2 s−1. Values in the primary table refer to one subunit. Bacillus DrdA preferred Mn2+ in demetallation/reconstitution assays; Co2+ and Mg2+ supported lower activity under the stated alternative conditions. Zn2+ did not activate the enzyme even though zinc predominated in an unsupplemented heterologous tag-free preparation. The tag-free mineral-supplemented ICP/EPR results and structures support manganese binding without equating bound zinc with an active cofactor. ATCC Ald2 instead preferred Co2+, and the authors did not establish the bound cobalt oxidation state in the as-purified preparation. Metal conclusions remain protein- and preparation-specific. The 2018 DrdK ATPase estimate used glycerol-containing buffers; the 2020 work removed glycerol and measured 0.04 s−1 intrinsic ATPase for E. coli and B. subtilis kinases, explicitly questioning the earlier Bacillus thuringiensis estimate. An extra ATPase pathway event is not inferred. The native MG1655 nucleosidase is a homodimer containing two EG11090/P0AF12 chains. The complex catalyzes the hydrolysis event; its individual subunit is represented by membership, not isolated-chain catalysis. The native activity frame reports a 4.6 micromolar Km for 5'-deoxyadenosine and distinct experimental and purified-protein evidence codes linked to older papers. Those older papers were not fully acquired in this work, so these are database-attributed statements. K12 nucleosidase activity does not establish the downstream DHAP shunt. Later ATCC 25922 experiments support carbon acquisition as a physiological benefit. In the 2024 aerobic glucose growth-inhibition assays with added MTA or 5-deoxyadenosine, deletion of mtnK, mtnA and ald2 did not significantly change sensitivity; Pfs deletion increased sensitivity. Added 5-deoxyribose at up to 4 mM did not significantly inhibit the tested strains, and shunt deletion did not change that response. Separately, deleting the shunt abolished growth on 5-deoxyribose as sole carbon source, and complementation restored it. The chemistry can operate anaerobically, but growth on 5-deoxyribose required suitable electron-acceptor conditions: oxygen or TMAO supported the tested growth, while nitrate and fermentation did not. Engineered K12 expressing the shunt is distinct from native K12. MTA metabolism, sulfur salvage, extracellular oxidation and the 2'-deoxyribonucleoside route to glyceraldehyde 3-phosphate are adjacent mechanisms outside this exact four-event record. The 2025 work places mtnK, mtnA, ald2 and a putative permease in an operon and supports MtnR/YjhU repression and CRP-dependent activation under carbon catabolite control. The permease substrate and the direct MtnR ligand are unresolved. CRP binding to a promoter fragment was tested with a His-tagged protein and cAMP; a predicted fine binding site is not equated with nucleotide-resolved occupancy. This optional regulation remains contextual narrative without unverified graph endpoints. The source's inconsistent secondary TSS offsets and other caption/aggregate-count discrepancies are retained in the review ledger; exact disputed numbers are not propagated. The complete four primary main texts were read, together with available material 2018, 2024 and 2025 supplements and figures. The 2020 supporting PDF/spreadsheet and original figure images could not be obtained through the tested official routes; no claim depends solely on those inaccessible materials. One retained 2024 EMF image was not rendered, and no EMF-only assertion is made. This route is distinct from the maintained 2'-deoxyribonucleoside route to glyceraldehyde 3-phosphate. Broader PWY-8130, PWY-8132 and PathBank PW002085/SMP0002097 leads remain unassessed for adoption; this addition does not establish source exhaustion.

Pathway type
metabolic
Organism scope

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Pathway network

46 nodes · 38 asserted directed edges

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Pathway network: 5'-deoxyadenosine degradation II 46 nodes · 38 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. CHEBI:17319 — consumes → MetaCyc:RXN0-6550; Native written left side, coefficient 1. Native physiological direction and pathway layout are left-to-right.; Evidence: MetaCyc:RXN0-6550consumes CHEBI:15377 — consumes → MetaCyc:RXN0-6550; Native written left side, coefficient 1. Native physiological direction and pathway layout are left-to-right.; Evidence: MetaCyc:RXN0-6550consumes MetaCyc:RXN0-6550 — produces → CHEBI:149540; Native written right side, coefficient 1. Native physiological direction and pathway layout are left-to-right. Cyclic CPD0-2167 is resolved by its exact InChI to CHEBI:149540; its CHEBI:62012 and PubChem:45489773 links denote an open-chain structure and are not adopted.; Evidence: MetaCyc:RXN0-6550produces MetaCyc:RXN0-6550 — produces → CHEBI:16708; Native written right side, coefficient 1. Native physiological direction and pathway layout are left-to-right.; Evidence: MetaCyc:RXN0-6550produces MetaCyc:RXN0-6550 — part_of → MetaCyc:PWY-8131; Event 1 of the exact native four-reaction route; taxon scope is separately qualified in the description.; Evidence: MetaCyc:PWY-8131part of CHEBI:30616 — consumes → MetaCyc:RXN-21317; Native written left side, coefficient 1. Native physiological direction and pathway layout are left-to-right.; Evidence: MetaCyc:RXN-21317consumes CHEBI:149540 — consumes → MetaCyc:RXN-21317; Native written left side, coefficient 1. Native physiological direction and pathway layout are left-to-right. Cyclic CPD0-2167 is resolved by its exact InChI to CHEBI:149540; its CHEBI:62012 and PubChem:45489773 links denote an open-chain structure and are not adopted.; Evidence: MetaCyc:RXN-21317consumes MetaCyc:RXN-21317 — produces → CHEBI:456216; Native written right side, coefficient 1. Native physiological direction and pathway layout are left-to-right.; Evidence: MetaCyc:RXN-21317produces MetaCyc:RXN-21317 — produces → CHEBI:58749; Native written right side, coefficient 1. Native physiological direction and pathway layout are left-to-right.; Evidence: MetaCyc:RXN-21317produces MetaCyc:RXN-21317 — produces → CHEBI:15378; Native written right side, coefficient 1. Native physiological direction and pathway layout are left-to-right.; Evidence: MetaCyc:RXN-21317produces MetaCyc:RXN-21317 — part_of → MetaCyc:PWY-8131; Event 2 of the exact native four-reaction route; taxon scope is separately qualified in the description.; Evidence: MetaCyc:PWY-8131part of CHEBI:58749 — consumes → MetaCyc:RXN-21315; Native written left side, coefficient 1. The native reaction is reversible; the pathway uses the written left-to-right degradative orientation.; Evidence: MetaCyc:RXN-21315consumes MetaCyc:RXN-21315 — produces → CHEBI:144504; Native written right side, coefficient 1. The native reaction is reversible; the pathway uses the written left-to-right degradative orientation.; Evidence: MetaCyc:RXN-21315produces MetaCyc:RXN-21315 — part_of → MetaCyc:PWY-8131; Event 3 of the exact native four-reaction route; taxon scope is separately qualified in the description.; Evidence: MetaCyc:PWY-8131part of CHEBI:144504 — consumes → MetaCyc:RXN-21316; Native written left side, coefficient 1. The native reaction is reversible; the pathway uses the written left-to-right degradative orientation.; Evidence: MetaCyc:RXN-21316consumes MetaCyc:RXN-21316 — produces → CHEBI:57642; Native written right side, coefficient 1. The native reaction is reversible; the pathway uses the written left-to-right degradative orientation.; Evidence: MetaCyc:RXN-21316produces MetaCyc:RXN-21316 — produces → CHEBI:15343; Native written right side, coefficient 1. The native reaction is reversible; the pathway uses the written left-to-right degradative orientation.; Evidence: MetaCyc:RXN-21316produces MetaCyc:RXN-21316 — part_of → MetaCyc:PWY-8131; Event 4 of the exact native four-reaction route; taxon scope is separately qualified in the description.; Evidence: MetaCyc:PWY-8131part of MetaCyc:RXN0-6550 — provides_input_for → MetaCyc:RXN-21317; The preceding event supplies CHEBI:149540 to the next event in the degradative route. This records metabolite continuity, without asserting substrate channeling or a physical enzyme complex.; Evidence: MetaCyc:PWY-8131, PMID:31950558provides input for MetaCyc:RXN-21317 — provides_input_for → MetaCyc:RXN-21315; The preceding event supplies CHEBI:58749 to the next event in the degradative route. This records metabolite continuity, without asserting substrate channeling or a physical enzyme complex.; Evidence: MetaCyc:PWY-8131, PMID:31950558provides input for MetaCyc:RXN-21315 — provides_input_for → MetaCyc:RXN-21316; The preceding event supplies CHEBI:144504 to the next event in the degradative route. This records metabolite continuity, without asserting substrate channeling or a physical enzyme complex.; Evidence: MetaCyc:PWY-8131, PMID:31950558provides input for MetaCyc:CPLX0-1541 — catalyzes → MetaCyc:RXN0-6550; MG1655 nucleosidase homodimer supports this reaction. Native two-chain complex assignment is retained. Its older cited primary papers were not fully obtained; their activity and Km assertions are explicitly database-attributed. This evidence does not establish a complete K12 DHAP shunt. ; Evidence: MetaCyc:ENZRXN0-7418, MetaCyc:ENZRXN0-7418, MetaCyc:ENZRXN0-7418, MetaCyc:ENZRXN0-7418, MetaCyc:ENZRXN0-7418catalyzes NCBIProtein:WP_000689844.1 — enables → MetaCyc:RXN0-6550; subject experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.; Evidence PMID:31950558: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3. ((//passage)[41]); ATCC 25922 MtnN/Pfs supports this reaction. The current RefSeq sequence exactly matches historical UniProt C3TPS2 version 128, UPI0000036BC8, and the translated D1792_RS20095 CDS on ATCC 25922 chromosome NZ_CP032085.1 (complement(4193872..4194570); 232 residues). The multispecies RefSeq label alone is not strain evidence. Native DR76 locus names and this D1792 assembly are kept distinct. ; Evidence: MetaCyc:ENZRXN-29282, MetaCyc:ENZRXN-29282, MetaCyc:ENZRXN-29282, MetaCyc:ENZRXN-29282, MetaCyc:MONOMER-21156, NCBIProtein:WP_000689844.1, PMID:31950558enables NCBIProtein:WP_000132325.1 — enables → MetaCyc:RXN-21317; subject experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.; Evidence PMID:31950558: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3. ((//passage)[41]); ATCC 25922 MtnK supports this reaction. The current RefSeq sequence exactly matches historical UniProt A0A066SUF2 version 82, UPI00019AF94B, and the translated D1792_RS18645 CDS on ATCC 25922 chromosome NZ_CP032085.1 (3887722..3888981; 419 residues). The multispecies RefSeq label alone is not strain evidence. Native DR76 locus names and this D1792 assembly are kept distinct. ; Evidence: MetaCyc:ENZRXN-29281, MetaCyc:ENZRXN-29281, MetaCyc:ENZRXN-29281, MetaCyc:ENZRXN-29281, MetaCyc:ENZRXN-29281, MetaCyc:MONOMER-21155, NCBIProtein:WP_000132325.1, PMID:31950558enables NCBIProtein:WP_001022015.1 — enables → MetaCyc:RXN-21315; subject experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.; Evidence PMID:31950558: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3. ((//passage)[41]); ATCC 25922 MtnA supports this reaction. The current RefSeq sequence exactly matches historical UniProt J7QBE0 version 94, UPI00019AF94C, and the translated D1792_RS18650 CDS on ATCC 25922 chromosome NZ_CP032085.1 (3888991..3890106; 371 residues). The multispecies RefSeq label alone is not strain evidence. Native DR76 locus names and this D1792 assembly are kept distinct. ; Evidence: MetaCyc:ENZRXN-29280, MetaCyc:ENZRXN-29280, MetaCyc:ENZRXN-29280, MetaCyc:ENZRXN-29280, MetaCyc:ENZRXN-29280, MetaCyc:MONOMER-21154, NCBIProtein:WP_001022015.1, PMID:31950558enables NCBIProtein:WP_000439686.1 — enables → MetaCyc:RXN-21316; subject experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.; Evidence PMID:31950558: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3. ((//passage)[41]); ATCC 25922 Ald2 supports this reaction. The current RefSeq sequence exactly matches historical UniProt J7RCN0 version 94, UPI00019AF94D, and the translated D1792_RS18655 CDS on ATCC 25922 chromosome NZ_CP032085.1 (3890137..3890778; 213 residues). The multispecies RefSeq label alone is not strain evidence. Native DR76 locus names and this D1792 assembly are kept distinct. The issuer product label remains L-fuculose-phosphate aldolase; the accepted exact sequence bridge plus experimental evidence identifies this Ald2 activity. ; Evidence: MetaCyc:ENZRXN-29279, MetaCyc:ENZRXN-29279, MetaCyc:ENZRXN-29279, MetaCyc:ENZRXN-29279, MetaCyc:ENZRXN-29279, MetaCyc:MONOMER-21153, NCBIProtein:WP_000439686.1, PMID:31950558enables UniProtKB:Q2RXI0 — enables → MetaCyc:RXN-21315; subject experimental construct: Native protein commentary describes a His10-tagged MtnA construct expressed in E. coli. The activity frame separately assigns partially purified heterologous protein evidence to the 2020 citation.; Evidence MetaCyc:MONOMER-17870: The complete protein comment describes cloning mtnA as a His10 construct, expression in E. coli and in vitro assay, citing the 2012 and 2020 studies. (/ptools-xml/Protein[@frameid="MONOMER-17870"]/comment); R. rubrum ATCC 11170 MtnA supports this reaction. Only the shared isomerization event is assigned here; the R. rubrum whole route begins with MtnP phosphorylase. Native 2020 activity evidence is PART-PURIFIED-PROTEIN-HH, distinct from its earlier purified and mutant tiers. ; Evidence: MetaCyc:ENZRXN-29274, MetaCyc:ENZRXN-29274, MetaCyc:ENZRXN-29274, MetaCyc:ENZRXN-29274, MetaCyc:ENZRXN-29274, MetaCyc:ENZRXN-29274, PMID:31950558enables UniProtKB:Q2RXI1 — enables → MetaCyc:RXN-21316; subject experimental construct: Recombinant Ald2 was expressed in E. coli and purified; native commentary describes a His6 construct and anaerobic purification. The 2020 preparation follows the previously reported expression plasmid.; Evidence MetaCyc:MONOMER-21152: The native comment describes His6-tagged Ald2 expressed in E. coli and purified anaerobically, then separately describes subsequent recombinant 5-deoxyribulose 1-phosphate activity. (/ptools-xml/Protein[@frameid="MONOMER-21152"]/comment); Evidence PMID:31950558: R. rubrum Ald2 used the previously reported pET28 expression plasmid; proteins were expressed in Rosetta(DE3) pLysS and purified by nickel chromatography. ((//passage)[41]); R. rubrum ATCC 11170 Ald2 supports this reaction. Only the shared aldol-cleavage event is assigned here; Co2+ and Ni2+ give the highest reconstituted activity. The R. rubrum whole route has phosphorylase entry. ; Evidence: MetaCyc:ENZRXN-29276, MetaCyc:ENZRXN-29276, MetaCyc:ENZRXN-29276, MetaCyc:ENZRXN-29276, MetaCyc:ENZRXN-29276, PMID:31950558enables UniProtKB:P0DTQ2 — enables → MetaCyc:RXN-21317; subject experimental construct: N-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified by Ni affinity chromatography. Tag-free DrdA used for structural and metal-loading studies is a separate preparation.; Evidence PMID:30082730: Genes were amplified from HD73-20 (BGSC 4D22) genomic DNA; cloning generated N-terminal His6-tagged DrdK and DrdI. ((//body//p)[35]); Evidence PMID:30082730: The Bacillus constructs were expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified using nickel affinity chromatography. ((//body//p)[36]); B. thuringiensis HD73-20 DrdK supports this reaction. The current UniProt identity is strain HD73, whereas the assayed gene source and deletion host were HD73-20 (BGSC 4D22). The evidence establishes the downstream three-enzyme module, not all four events in Bacillus. ; Evidence: MetaCyc:ENZRXN-29537, MetaCyc:ENZRXN-29537, MetaCyc:ENZRXN-29537, MetaCyc:ENZRXN-29537, MetaCyc:ENZRXN-29537, MetaCyc:ENZRXN-29537, PMID:30082730enables UniProtKB:P0DTQ1 — enables → MetaCyc:RXN-21315; subject experimental construct: N-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified by Ni affinity chromatography. Tag-free DrdA used for structural and metal-loading studies is a separate preparation.; Evidence PMID:30082730: Genes were amplified from HD73-20 (BGSC 4D22) genomic DNA; cloning generated N-terminal His6-tagged DrdK and DrdI. ((//body//p)[35]); Evidence PMID:30082730: The Bacillus constructs were expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified using nickel affinity chromatography. ((//body//p)[36]); B. thuringiensis HD73-20 DrdI supports this reaction. The current UniProt identity is strain HD73, whereas the assayed gene source and deletion host were HD73-20 (BGSC 4D22). The evidence establishes the downstream three-enzyme module, not all four events in Bacillus. Primary Table 1 gives Km 22 ± 7 mM and kcat 3.5 ± 0.7 s−1; the native activity frame has no kinetic slots. ; Evidence: MetaCyc:ENZRXN-29539, MetaCyc:ENZRXN-29539, MetaCyc:ENZRXN-29539, PMID:30082730enables UniProtKB:P0DTQ0 — enables → MetaCyc:RXN-21316; subject experimental construct: C-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified by Ni affinity chromatography. Tag-free DrdA used for structural and metal-loading studies is a separate preparation.; Evidence PMID:30082730: Genes were amplified from HD73-20 (BGSC 4D22) genomic DNA; cloning generated C-terminal His6-tagged DrdA. ((//body//p)[35]); Evidence PMID:30082730: The Bacillus constructs were expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified using nickel affinity chromatography. ((//body//p)[36]); B. thuringiensis HD73-20 DrdA supports this reaction. The current UniProt identity is strain HD73, whereas the assayed gene source and deletion host were HD73-20 (BGSC 4D22). The evidence establishes the downstream three-enzyme module, not all four events in Bacillus. Primary Table 1 gives Km 36 ± 3 micromolar and kcat 6.3 ± 0.2 s−1; the native activity frame has no kinetic slots. SEC describes an oligomer possibly tetrameric, while the crystal lattice supplies a proposed tetramer; no exact physiological complex node is invented. ; Evidence: MetaCyc:ENZRXN-29540, MetaCyc:ENZRXN-29540, PMID:30082730enables UniProtKB:P0AF12 — part_of → MetaCyc:CPLX0-1541; The native MG1655 complex contains two EG11090-MONOMER chains, linked to current P0AF12. This is a reference homodimer composition, not a claim about the ATCC tagged preparation.; Evidence: MetaCyc:CPLX0-1541, MetaCyc:EG11090-MONOMERpart of NCBIProtein:WP_000439686.1 — has_cofactor → CHEBI:48828; subject molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this condition does not specify universal cellular metal stoichiometry or occupancy.; Evidence PMID:31950558: Metal-dependent activity was tested with reconstituted Ald2 apoenzyme; the source distinguishes the reconstituted preparation from other enzyme preparations. ((//passage)[26]); ATCC 25922 Ald2: Co2+ restored maximal apoenzyme activity and matched the activity/color of the as-purified enzyme. The reported expression preparation was recombinant; its bound cobalt oxidation state was not established.; Evidence: PMID:31950558has cofactor UniProtKB:Q2RXI1 — has_cofactor → CHEBI:48828; subject molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this condition does not specify universal cellular metal stoichiometry or occupancy.; Evidence PMID:31950558: Metal-dependent activity was tested with reconstituted Ald2 apoenzyme; the source distinguishes the reconstituted preparation from other enzyme preparations. ((//passage)[17]); R. rubrum Ald2: Co2+ is one of the two highest-activity apoenzyme reconstitution conditions; this does not establish a universal physiological metal occupancy.; Evidence: PMID:31950558has cofactor UniProtKB:Q2RXI1 — has_cofactor → CHEBI:49786; subject molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this condition does not specify universal cellular metal stoichiometry or occupancy.; Evidence PMID:31950558: Metal-dependent activity was tested with reconstituted Ald2 apoenzyme; the source distinguishes the reconstituted preparation from other enzyme preparations. ((//passage)[17]); R. rubrum Ald2: Ni2+ is an alternative high-activity apoenzyme reconstitution condition, not a simultaneous requirement with Co2+.; Evidence: PMID:31950558has cofactor UniProtKB:P0DTQ0 — has_cofactor → CHEBI:29035; subject molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or 2 mM MgCl2. Each metal is an alternative condition; tag-free metal-loading experiments are separate.; Evidence PMID:30082730: DrdA was isolated by Ni affinity chromatography, demetallated by EDTA dialysis, and assayed with 0.1 mM metal chlorides or 2 mM MgCl2; preparations before dialysis and without added metal were controls. ((//body//p)[10]); Evidence PMID:30082730: The activity-assay DrdA construct has a C-terminal His6 tag. ((//body//p)[35]); HD73-20 DrdA: Mn2+ gave the highest activity after demetallation; apparent Kmetal was 0.95 ± 0.31 micromolar. Separate tag-free ICP/EPR and crystal preparations support Mn binding.; Evidence: PMID:30082730, PMID:30082730, PMID:30082730, PMID:30082730has cofactor UniProtKB:P0DTQ0 — has_cofactor → CHEBI:48828; subject molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or 2 mM MgCl2. Each metal is an alternative condition; tag-free metal-loading experiments are separate.; Evidence PMID:30082730: DrdA was isolated by Ni affinity chromatography, demetallated by EDTA dialysis, and assayed with 0.1 mM metal chlorides or 2 mM MgCl2; preparations before dialysis and without added metal were controls. ((//body//p)[10]); Evidence PMID:30082730: The activity-assay DrdA construct has a C-terminal His6 tag. ((//body//p)[35]); HD73-20 DrdA: Co2+ supported activity in the alternative 0.1 mM reconstitution condition, below the activity with Mn2+.; Evidence: PMID:30082730has cofactor UniProtKB:P0DTQ0 — has_cofactor → CHEBI:18420; subject molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or 2 mM MgCl2. Each metal is an alternative condition; tag-free metal-loading experiments are separate.; Evidence PMID:30082730: DrdA was isolated by Ni affinity chromatography, demetallated by EDTA dialysis, and assayed with 0.1 mM metal chlorides or 2 mM MgCl2; preparations before dialysis and without added metal were controls. ((//body//p)[10]); Evidence PMID:30082730: The activity-assay DrdA construct has a C-terminal His6 tag. ((//body//p)[35]); HD73-20 DrdA: Mg2+ supported lower activity in the alternative 2 mM condition. Different assay concentrations do not support an unqualified affinity ranking.; Evidence: PMID:30082730has cofactor acetaldehyde; CHEBI:15343; Declared type: small_molecule small molecule acetaldehyde adenine; CHEBI:16708; Declared type: small_molecule small molecule adenine ADP(3−); CHEBI:456216; Declared type: small_molecule small molecule ADP(3−) ATP(4−); CHEBI:30616; Declared type: small_molecule small molecule ATP(4−) 5'-deoxyadenosine; CHEBI:17319; Declared type: small_molecule small molecule 5'-deoxyadenosine 5-deoxy-α-D-ribose 1-phosphate(2−); CHEBI:58749; Declared type: small_molecule small molecule 5-deoxy-α-D-ribose 1-phosphate(2−) 5-deoxy-D-ribulose 1-phosphate(2−); CHEBI:144504; Declared type: small_molecule small molecule 5-deoxy-D-ribulose 1-phosphate(2−) 5-deoxy-D-ribofuranose; CHEBI:149540; Declared type: small_molecule small molecule 5-deoxy-D-ribofuranose glycerone phosphate(2−); CHEBI:57642; Declared type: small_molecule small molecule glycerone phosphate(2−) hydron; CHEBI:15378; Declared type: small_molecule small molecule hydron water; CHEBI:15377; Declared type: small_molecule small molecule water cobalt(2+); CHEBI:48828; Declared type: cofactor cofactor cobalt(2+) manganese(2+); CHEBI:29035; Declared type: cofactor cofactor manganese(2+) nickel(2+); CHEBI:49786; Declared type: cofactor cofactor nickel(2+) magnesium(2+); CHEBI:18420; Declared type: cofactor cofactor magnesium(2+) 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; UniProtKB:P0AF12; Declared type: protein protein 5'-methylthioadenosine/S- adenosylhomocysteine nucleosidase 5-deoxyribose kinase; UniProtKB:P0DTQ2; Declared type: protein protein 5-deoxyribose kinase 5-deoxyribose 1-phosphate isomerase; UniProtKB:P0DTQ1; Declared type: protein protein 5-deoxyribose 1-phosphate isomerase 5-deoxy-D-ribulose 1-phosphate aldolase; UniProtKB:P0DTQ0; Declared type: protein protein 5-deoxy-D-ribulose 1-phosphate aldolase 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 S-methyl-5-thioribose kinase; NCBIProtein:WP_000132325.1; Declared type: protein protein S-methyl-5-thioribose kinase S-methyl-5-thioribose-1-phosphate isomerase; NCBIProtein:WP_001022015.1; Declared type: protein protein S-methyl-5-thioribose-1- phosphate isomerase L-fuculose-phosphate aldolase; NCBIProtein:WP_000439686.1; Declared type: protein protein L-fuculose-phosphate aldolase 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; NCBIProtein:WP_000689844.1; Declared type: protein protein 5'-methylthioadenosine/S- adenosylhomocysteine nucleosidase 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; MetaCyc:CPLX0-1541; Declared type: complex complex 5'-methylthioadenosine/S- adenosylhomocysteine nucleosidase 5'-deoxyadenosine hydrolysis; MetaCyc:RXN0-6550; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity 5'-deoxyadenosine hydrolysis 5-deoxyribose phosphorylation; MetaCyc:RXN-21317; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity 5-deoxyribose phosphorylation 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 II; MetaCyc:PWY-8131; Declared type: pathway pathway 5'-deoxyadenosine degradation II 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase; NCBIProtein:WP_000689844.1; Declared type: protein; experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.; Evidence PMID:31950558: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3. ((//passage)[41]) experimental construct 5'-methylthioadenosine/S- adenosylhomocysteine nucleosidase [experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by…] S-methyl-5-thioribose kinase; NCBIProtein:WP_000132325.1; Declared type: protein; experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.; Evidence PMID:31950558: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3. ((//passage)[41]) experimental construct S-methyl-5-thioribose kinase [experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by…] S-methyl-5-thioribose-1-phosphate isomerase; NCBIProtein:WP_001022015.1; Declared type: protein; experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.; Evidence PMID:31950558: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3. ((//passage)[41]) experimental construct S-methyl-5-thioribose-1- phosphate isomerase [experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by…] L-fuculose-phosphate aldolase; NCBIProtein:WP_000439686.1; Declared type: protein; experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.; Evidence PMID:31950558: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3. ((//passage)[41]) experimental construct L-fuculose-phosphate aldolase [experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by…] Methylthioribose-1-phosphate isomerase; UniProtKB:Q2RXI0; Declared type: protein; experimental construct: Native protein commentary describes a His10-tagged MtnA construct expressed in E. coli. The activity frame separately assigns partially purified heterologous protein evidence to the 2020 citation.; Evidence MetaCyc:MONOMER-17870: The complete protein comment describes cloning mtnA as a His10 construct, expression in E. coli and in vitro assay, citing the 2012 and 2020 studies. (/ptools-xml/Protein[@frameid="MONOMER-17870"]/comment) experimental construct Methylthioribose-1-phosphate isomerase [experimental construct: Native protein commentary describes a His10-tagged MtnA construct expressed in E. coli. The…] 5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase; UniProtKB:Q2RXI1; Declared type: protein; experimental construct: Recombinant Ald2 was expressed in E. coli and purified; native commentary describes a His6 construct and anaerobic purification. The 2020 preparation follows the previously reported expression plasmid.; Evidence MetaCyc:MONOMER-21152: The native comment describes His6-tagged Ald2 expressed in E. coli and purified anaerobically, then separately describes subsequent recombinant 5-deoxyribulose 1-phosphate activity. (/ptools-xml/Protein[@frameid="MONOMER-21152"]/comment); Evidence PMID:31950558: R. rubrum Ald2 used the previously reported pET28 expression plasmid; proteins were expressed in Rosetta(DE3) pLysS and purified by nickel chromatography. ((//passage)[41]) experimental construct 5-methylthioribulose-1- phosphate/5-deoxyribulose-1- phosphate aldolase [experimental construct: Recombinant Ald2 was expressed in E. coli and purified; native commentary describes a His6…] 5-deoxyribose kinase; UniProtKB:P0DTQ2; Declared type: protein; experimental construct: N-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified by Ni affinity chromatography. Tag-free DrdA used for structural and metal-loading studies is a separate preparation.; Evidence PMID:30082730: Genes were amplified from HD73-20 (BGSC 4D22) genomic DNA; cloning generated N-terminal His6-tagged DrdK and DrdI. ((//body//p)[35]); Evidence PMID:30082730: The Bacillus constructs were expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified using nickel affinity chromatography. ((//body//p)[36]) experimental construct 5-deoxyribose kinase [experimental construct: N-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus…] 5-deoxyribose 1-phosphate isomerase; UniProtKB:P0DTQ1; Declared type: protein; experimental construct: N-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified by Ni affinity chromatography. Tag-free DrdA used for structural and metal-loading studies is a separate preparation.; Evidence PMID:30082730: Genes were amplified from HD73-20 (BGSC 4D22) genomic DNA; cloning generated N-terminal His6-tagged DrdK and DrdI. ((//body//p)[35]); Evidence PMID:30082730: The Bacillus constructs were expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified using nickel affinity chromatography. ((//body//p)[36]) experimental construct 5-deoxyribose 1-phosphate isomerase [experimental construct: N-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus…] 5-deoxy-D-ribulose 1-phosphate aldolase; UniProtKB:P0DTQ0; Declared type: protein; experimental construct: C-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified by Ni affinity chromatography. Tag-free DrdA used for structural and metal-loading studies is a separate preparation.; Evidence PMID:30082730: Genes were amplified from HD73-20 (BGSC 4D22) genomic DNA; cloning generated C-terminal His6-tagged DrdA. ((//body//p)[35]); Evidence PMID:30082730: The Bacillus constructs were expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified using nickel affinity chromatography. ((//body//p)[36]) experimental construct 5-deoxy-D-ribulose 1-phosphate aldolase [experimental construct: C-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus…] L-fuculose-phosphate aldolase; NCBIProtein:WP_000439686.1; Declared type: protein; molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this condition does not specify universal cellular metal stoichiometry or occupancy.; Evidence PMID:31950558: Metal-dependent activity was tested with reconstituted Ald2 apoenzyme; the source distinguishes the reconstituted preparation from other enzyme preparations. ((//passage)[26]) molecular state L-fuculose-phosphate aldolase [molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this…] 5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase; UniProtKB:Q2RXI1; Declared type: protein; molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this condition does not specify universal cellular metal stoichiometry or occupancy.; Evidence PMID:31950558: Metal-dependent activity was tested with reconstituted Ald2 apoenzyme; the source distinguishes the reconstituted preparation from other enzyme preparations. ((//passage)[17]) molecular state 5-methylthioribulose-1- phosphate/5-deoxyribulose-1- phosphate aldolase [molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this…] 5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase; UniProtKB:Q2RXI1; Declared type: protein; molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this condition does not specify universal cellular metal stoichiometry or occupancy.; Evidence PMID:31950558: Metal-dependent activity was tested with reconstituted Ald2 apoenzyme; the source distinguishes the reconstituted preparation from other enzyme preparations. ((//passage)[17]) molecular state 5-methylthioribulose-1- phosphate/5-deoxyribulose-1- phosphate aldolase [molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this…] 5-deoxy-D-ribulose 1-phosphate aldolase; UniProtKB:P0DTQ0; Declared type: protein; molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or 2 mM MgCl2. Each metal is an alternative condition; tag-free metal-loading experiments are separate.; Evidence PMID:30082730: DrdA was isolated by Ni affinity chromatography, demetallated by EDTA dialysis, and assayed with 0.1 mM metal chlorides or 2 mM MgCl2; preparations before dialysis and without added metal were controls. ((//body//p)[10]); Evidence PMID:30082730: The activity-assay DrdA construct has a C-terminal His6 tag. ((//body//p)[35]) molecular state 5-deoxy-D-ribulose 1-phosphate aldolase [molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or…] 5-deoxy-D-ribulose 1-phosphate aldolase; UniProtKB:P0DTQ0; Declared type: protein; molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or 2 mM MgCl2. Each metal is an alternative condition; tag-free metal-loading experiments are separate.; Evidence PMID:30082730: DrdA was isolated by Ni affinity chromatography, demetallated by EDTA dialysis, and assayed with 0.1 mM metal chlorides or 2 mM MgCl2; preparations before dialysis and without added metal were controls. ((//body//p)[10]); Evidence PMID:30082730: The activity-assay DrdA construct has a C-terminal His6 tag. ((//body//p)[35]) molecular state 5-deoxy-D-ribulose 1-phosphate aldolase [molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or…] 5-deoxy-D-ribulose 1-phosphate aldolase; UniProtKB:P0DTQ0; Declared type: protein; molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or 2 mM MgCl2. Each metal is an alternative condition; tag-free metal-loading experiments are separate.; Evidence PMID:30082730: DrdA was isolated by Ni affinity chromatography, demetallated by EDTA dialysis, and assayed with 0.1 mM metal chlorides or 2 mM MgCl2; preparations before dialysis and without added metal were controls. ((//body//p)[10]); Evidence PMID:30082730: The activity-assay DrdA construct has a C-terminal His6 tag. ((//body//p)[35]) molecular state 5-deoxy-D-ribulose 1-phosphate aldolase [molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or…]

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Escherichia coli ATCC 25922
NCBITaxon:1322345		taxon
Bacillus thuringiensis serovar kurstaki str. HD73
NCBITaxon:1279365		taxon
Rhodospirillum rubrum ATCC 11170
NCBITaxon:269796		taxon
Escherichia coli str. K-12 substr. MG1655
NCBITaxon:511145		taxon
acetaldehyde
CHEBI:15343		small molecule
adenine
CHEBI:16708		small molecule
ADP(3−)
CHEBI:456216		small molecule
ATP(4−)
CHEBI:30616		small molecule
5'-deoxyadenosine
CHEBI:17319		small molecule
5-deoxy-α-D-ribose 1-phosphate(2−)
CHEBI:58749		small molecule
5-deoxy-D-ribulose 1-phosphate(2−)
CHEBI:144504		small molecule
5-deoxy-D-ribofuranose
CHEBI:149540		small molecule
glycerone phosphate(2−)
CHEBI:57642		small molecule
hydron
CHEBI:15378		small molecule
water
CHEBI:15377		small molecule
cobalt(2+)
CHEBI:48828		cofactor
manganese(2+)
CHEBI:29035		cofactor
nickel(2+)
CHEBI:49786		cofactor
magnesium(2+)
CHEBI:18420		cofactor
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
UniProtKB:P0AF12		protein
5-deoxyribose kinase
UniProtKB:P0DTQ2		protein
5-deoxyribose 1-phosphate isomerase
UniProtKB:P0DTQ1		protein
5-deoxy-D-ribulose 1-phosphate aldolase
UniProtKB:P0DTQ0		protein
Methylthioribose-1-phosphate isomerase
UniProtKB:Q2RXI0		protein
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase
UniProtKB:Q2RXI1		protein
S-methyl-5-thioribose kinase
NCBIProtein:WP_000132325.1		protein
S-methyl-5-thioribose-1-phosphate isomerase
NCBIProtein:WP_001022015.1		protein
L-fuculose-phosphate aldolase
NCBIProtein:WP_000439686.1		protein
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
NCBIProtein:WP_000689844.1		protein
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
MetaCyc:CPLX0-1541		complex
5'-deoxyadenosine hydrolysis
MetaCyc:RXN0-6550		molecular activityleft to right
5-deoxyribose phosphorylation
MetaCyc:RXN-21317		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
CHEBI:17319		consumes

Native written left side, coefficient 1. Native physiological direction and pathway layout are left-to-right.

5'-deoxyadenosine hydrolysis
MetaCyc:RXN0-6550
  • MetaCyc:RXN0-6550

    Source assertion: RXN0-6550 lists CH33ADO on its left side with coefficient 1; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Reaction[@frameid="RXN0-6550"]/left[1]
water
CHEBI:15377		consumes

Native written left side, coefficient 1. Native physiological direction and pathway layout are left-to-right.

5'-deoxyadenosine hydrolysis
MetaCyc:RXN0-6550
  • MetaCyc:RXN0-6550

    Source assertion: RXN0-6550 lists WATER on its left side with coefficient 1; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Reaction[@frameid="RXN0-6550"]/left[2]
5'-deoxyadenosine hydrolysis
MetaCyc:RXN0-6550		produces

Native written right side, coefficient 1. Native physiological direction and pathway layout are left-to-right. Cyclic CPD0-2167 is resolved by its exact InChI to CHEBI:149540; its CHEBI:62012 and PubChem:45489773 links denote an open-chain structure and are not adopted.

5-deoxy-D-ribofuranose
CHEBI:149540
  • MetaCyc:RXN0-6550

    Source assertion: RXN0-6550 lists CPD0-2167 on its right side with coefficient 1; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Reaction[@frameid="RXN0-6550"]/right[1]
5'-deoxyadenosine hydrolysis
MetaCyc:RXN0-6550		produces

Native written right side, coefficient 1. Native physiological direction and pathway layout are left-to-right.

adenine
CHEBI:16708
  • MetaCyc:RXN0-6550

    Source assertion: RXN0-6550 lists ADENINE on its right side with coefficient 1; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Reaction[@frameid="RXN0-6550"]/right[2]
5'-deoxyadenosine hydrolysis
MetaCyc:RXN0-6550		part_of

Event 1 of the exact native four-reaction route; taxon scope is separately qualified in the description.

MetaCyc:PWY-8131
  • MetaCyc:PWY-8131

    Source assertion: The complete reaction-list contains RXN0-6550; its pathway reaction-layout direction is L2R.

    Source location/ptools-xml/Pathway[@frameid="PWY-8131"]/reaction-list/Reaction[@frameid="RXN0-6550"]
ATP(4−)
CHEBI:30616		consumes

Native written left side, coefficient 1. Native physiological direction and pathway layout are left-to-right.

5-deoxyribose phosphorylation
MetaCyc:RXN-21317
  • MetaCyc:RXN-21317

    Source assertion: RXN-21317 lists ATP on its left side with coefficient 1; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Reaction[@frameid="RXN-21317"]/left[1]
5-deoxy-D-ribofuranose
CHEBI:149540		consumes

Native written left side, coefficient 1. Native physiological direction and pathway layout are left-to-right. Cyclic CPD0-2167 is resolved by its exact InChI to CHEBI:149540; its CHEBI:62012 and PubChem:45489773 links denote an open-chain structure and are not adopted.

5-deoxyribose phosphorylation
MetaCyc:RXN-21317
  • MetaCyc:RXN-21317

    Source assertion: RXN-21317 lists CPD0-2167 on its left side with coefficient 1; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Reaction[@frameid="RXN-21317"]/left[2]
5-deoxyribose phosphorylation
MetaCyc:RXN-21317		produces

Native written right side, coefficient 1. Native physiological direction and pathway layout are left-to-right.

ADP(3−)
CHEBI:456216
  • MetaCyc:RXN-21317

    Source assertion: RXN-21317 lists ADP on its right side with coefficient 1; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Reaction[@frameid="RXN-21317"]/right[1]
5-deoxyribose phosphorylation
MetaCyc:RXN-21317		produces

Native written right side, coefficient 1. Native physiological direction and pathway layout are left-to-right.

5-deoxy-α-D-ribose 1-phosphate(2−)
CHEBI:58749
  • MetaCyc:RXN-21317

    Source assertion: RXN-21317 lists CPD-15199 on its right side with coefficient 1; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Reaction[@frameid="RXN-21317"]/right[2]
5-deoxyribose phosphorylation
MetaCyc:RXN-21317		produces

Native written right side, coefficient 1. Native physiological direction and pathway layout are left-to-right.

hydron
CHEBI:15378
  • MetaCyc:RXN-21317

    Source assertion: RXN-21317 lists PROTON on its right side with coefficient 1; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Reaction[@frameid="RXN-21317"]/right[3]
5-deoxyribose phosphorylation
MetaCyc:RXN-21317		part_of

Event 2 of the exact native four-reaction route; taxon scope is separately qualified in the description.

MetaCyc:PWY-8131
  • MetaCyc:PWY-8131

    Source assertion: The complete reaction-list contains RXN-21317; its pathway reaction-layout direction is L2R.

    Source location/ptools-xml/Pathway[@frameid="PWY-8131"]/reaction-list/Reaction[@frameid="RXN-21317"]
5-deoxy-α-D-ribose 1-phosphate(2−)
CHEBI:58749		consumes

Native written left side, coefficient 1. The native reaction is reversible; the pathway uses the written left-to-right degradative orientation.

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

    Source assertion: RXN-21315 lists CPD-15199 on its left side with coefficient 1; reaction-direction is REVERSIBLE.

    Source location/ptools-xml/Reaction[@frameid="RXN-21315"]/left[1]
5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315		produces

Native written right side, coefficient 1. The native reaction is reversible; the pathway uses the written left-to-right degradative orientation.

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

    Source assertion: RXN-21315 lists CPD-23219 on its right side with coefficient 1; reaction-direction is REVERSIBLE.

    Source location/ptools-xml/Reaction[@frameid="RXN-21315"]/right[1]
5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315		part_of

Event 3 of the exact native four-reaction route; taxon scope is separately qualified in the description.

MetaCyc:PWY-8131
  • MetaCyc:PWY-8131

    Source assertion: The complete reaction-list contains RXN-21315; its pathway reaction-layout direction is L2R.

    Source location/ptools-xml/Pathway[@frameid="PWY-8131"]/reaction-list/Reaction[@frameid="RXN-21315"]
5-deoxy-D-ribulose 1-phosphate(2−)
CHEBI:144504		consumes

Native written left side, coefficient 1. The native reaction is reversible; the pathway uses the written left-to-right degradative orientation.

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

    Source assertion: RXN-21316 lists CPD-23219 on its left side with coefficient 1; reaction-direction is REVERSIBLE.

    Source location/ptools-xml/Reaction[@frameid="RXN-21316"]/left[1]
5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316		produces

Native written right side, coefficient 1. The native reaction is reversible; the pathway uses the written left-to-right degradative orientation.

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

    Source assertion: RXN-21316 lists DIHYDROXY-ACETONE-PHOSPHATE on its right side with coefficient 1; reaction-direction is REVERSIBLE.

    Source location/ptools-xml/Reaction[@frameid="RXN-21316"]/right[1]
5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316		produces

Native written right side, coefficient 1. The native reaction is reversible; the pathway uses the written left-to-right degradative orientation.

acetaldehyde
CHEBI:15343
  • MetaCyc:RXN-21316

    Source assertion: RXN-21316 lists ACETALD on its right side with coefficient 1; reaction-direction is REVERSIBLE.

    Source location/ptools-xml/Reaction[@frameid="RXN-21316"]/right[2]
5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316		part_of

Event 4 of the exact native four-reaction route; taxon scope is separately qualified in the description.

MetaCyc:PWY-8131
  • MetaCyc:PWY-8131

    Source assertion: The complete reaction-list contains RXN-21316; its pathway reaction-layout direction is L2R.

    Source location/ptools-xml/Pathway[@frameid="PWY-8131"]/reaction-list/Reaction[@frameid="RXN-21316"]
5'-deoxyadenosine hydrolysis
MetaCyc:RXN0-6550		provides_input_for

The preceding event supplies CHEBI:149540 to the next event in the degradative route. This records metabolite continuity, without asserting substrate channeling or a physical enzyme complex.

5-deoxyribose phosphorylation
MetaCyc:RXN-21317
  • MetaCyc:PWY-8131

    Source assertion: The reaction-ordering places RXN0-6550 immediately before RXN-21317; their pathway layouts connect through CPD0-2167.

    Source location/ptools-xml/Pathway[@frameid="PWY-8131"]/reaction-ordering[1]
  • PMID:31950558

    Source assertion: ATCC 25922 sequentially metabolized 5-deoxyadenosine through 5-deoxyribose, 5-deoxyribose 1-phosphate and 5-deoxyribulose 1-phosphate to DHAP and acetaldehyde; gene deletions blocked the corresponding steps.

    Source location(//passage)[21]
5-deoxyribose phosphorylation
MetaCyc:RXN-21317		provides_input_for

The preceding event supplies CHEBI:58749 to the next event in the degradative route. This records metabolite continuity, without asserting substrate channeling or a physical enzyme complex.

5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315
  • MetaCyc:PWY-8131

    Source assertion: The reaction-ordering places RXN-21317 immediately before RXN-21315; their pathway layouts connect through CPD-15199.

    Source location/ptools-xml/Pathway[@frameid="PWY-8131"]/reaction-ordering[2]
  • PMID:31950558

    Source assertion: ATCC 25922 sequentially metabolized 5-deoxyadenosine through 5-deoxyribose, 5-deoxyribose 1-phosphate and 5-deoxyribulose 1-phosphate to DHAP and acetaldehyde; gene deletions blocked the corresponding steps.

    Source location(//passage)[21]
5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315		provides_input_for

The preceding event supplies CHEBI:144504 to the next event in the degradative route. This records metabolite continuity, without asserting substrate channeling or a physical enzyme complex.

5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316
  • MetaCyc:PWY-8131

    Source assertion: The reaction-ordering places RXN-21315 immediately before RXN-21316; their pathway layouts connect through CPD-23219.

    Source location/ptools-xml/Pathway[@frameid="PWY-8131"]/reaction-ordering[3]
  • PMID:31950558

    Source assertion: ATCC 25922 sequentially metabolized 5-deoxyadenosine through 5-deoxyribose, 5-deoxyribose 1-phosphate and 5-deoxyribulose 1-phosphate to DHAP and acetaldehyde; gene deletions blocked the corresponding steps.

    Source location(//passage)[21]
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
MetaCyc:CPLX0-1541		catalyzes

MG1655 nucleosidase homodimer supports this reaction. Native two-chain complex assignment is retained. Its older cited primary papers were not fully obtained; their activity and Km assertions are explicitly database-attributed. This evidence does not establish a complete K12 DHAP shunt.

5'-deoxyadenosine hydrolysis
MetaCyc:RXN0-6550
  • MetaCyc:ENZRXN0-7418

    Source assertion: The enzyme field names CPLX0-1541 for reaction MetaCyc:RXN0-6550; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN0-7418"]
  • MetaCyc:ENZRXN0-7418

    Source assertion: Native evidence tier EV-EXP is linked to PUB-15911379. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN0-7418"]/evidence[1]
  • MetaCyc:ENZRXN0-7418

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN is linked to PUB-20961145. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN0-7418"]/evidence[2]
  • MetaCyc:ENZRXN0-7418

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN is linked to PUB-19328201. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN0-7418"]/evidence[3]
  • MetaCyc:ENZRXN0-7418

    Source assertion: The native km slot reports 4.6 μM for CH33ADO, citing PUB-20961145. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN0-7418"]/km[1]
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
NCBIProtein:WP_000689844.1

experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.

Qualification evidence
  • PMID:31950558

    Source assertion: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3.

    Source location(//passage)[41]
enables

ATCC 25922 MtnN/Pfs supports this reaction. The current RefSeq sequence exactly matches historical UniProt C3TPS2 version 128, UPI0000036BC8, and the translated D1792_RS20095 CDS on ATCC 25922 chromosome NZ_CP032085.1 (complement(4193872..4194570); 232 residues). The multispecies RefSeq label alone is not strain evidence. Native DR76 locus names and this D1792 assembly are kept distinct.

5'-deoxyadenosine hydrolysis
MetaCyc:RXN0-6550
  • MetaCyc:ENZRXN-29282

    Source assertion: The enzyme field names MONOMER-21156 for reaction MetaCyc:RXN0-6550; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29282"]
  • MetaCyc:ENZRXN-29282

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN-HH is linked to PUB-31950558. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29282"]/evidence[1]
  • MetaCyc:ENZRXN-29282

    Source assertion: The native km slot reports 4.7 μM for CH33ADO, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29282"]/km[1]
  • MetaCyc:ENZRXN-29282

    Source assertion: The native kcat slot reports 57.0 sec-1 for CH33ADO, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29282"]/kcat[1]
  • MetaCyc:MONOMER-21156

    Source assertion: The native protein frame identifies the ATCC 25922 enzyme and links historical UniProt accession C3TPS2; current graph identity is established separately by the retained exact sequence/chromosome bridge.

    Source location/ptools-xml/Protein[@frameid="MONOMER-21156"]
  • NCBIProtein:WP_000689844.1

    Source assertion: Current RefSeq WP_000689844.1 supplies the 232-residue sequence and its issuer product name. Complete sequence identity to the archived native accession and ATCC chromosome CDS is documented in the accompanying identity ledger.

    Source location/GBSet/GBSeq/GBSeq_sequence
  • PMID:31950558

    Source assertion: The main study experimentally supports this scoped enzyme activity in the DHAP shunt; the corresponding preparation, organism and substrate context are retained in the edge description.

    Source location(//passage)[24]
S-methyl-5-thioribose kinase
NCBIProtein:WP_000132325.1

experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.

Qualification evidence
  • PMID:31950558

    Source assertion: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3.

    Source location(//passage)[41]
enables

ATCC 25922 MtnK supports this reaction. The current RefSeq sequence exactly matches historical UniProt A0A066SUF2 version 82, UPI00019AF94B, and the translated D1792_RS18645 CDS on ATCC 25922 chromosome NZ_CP032085.1 (3887722..3888981; 419 residues). The multispecies RefSeq label alone is not strain evidence. Native DR76 locus names and this D1792 assembly are kept distinct.

5-deoxyribose phosphorylation
MetaCyc:RXN-21317
  • MetaCyc:ENZRXN-29281

    Source assertion: The enzyme field names MONOMER-21155 for reaction MetaCyc:RXN-21317; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29281"]
  • MetaCyc:ENZRXN-29281

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN-HH is linked to PUB-31950558. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29281"]/evidence[1]
  • MetaCyc:ENZRXN-29281

    Source assertion: Native evidence tier EV-EXP-IMP-REACTION-BLOCKED is linked to PUB-31950558. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29281"]/evidence[2]
  • MetaCyc:ENZRXN-29281

    Source assertion: The native km slot reports 25.0 μM for CPD0-2167, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29281"]/km[1]
  • MetaCyc:ENZRXN-29281

    Source assertion: The native kcat slot reports 16.1 sec-1 for CPD0-2167, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29281"]/kcat[1]
  • MetaCyc:MONOMER-21155

    Source assertion: The native protein frame identifies the ATCC 25922 enzyme and links historical UniProt accession A0A066SUF2; current graph identity is established separately by the retained exact sequence/chromosome bridge.

    Source location/ptools-xml/Protein[@frameid="MONOMER-21155"]
  • NCBIProtein:WP_000132325.1

    Source assertion: Current RefSeq WP_000132325.1 supplies the 419-residue sequence and its issuer product name. Complete sequence identity to the archived native accession and ATCC chromosome CDS is documented in the accompanying identity ledger.

    Source location/GBSet/GBSeq/GBSeq_sequence
  • PMID:31950558

    Source assertion: The main study experimentally supports this scoped enzyme activity in the DHAP shunt; the corresponding preparation, organism and substrate context are retained in the edge description.

    Source location(//passage)[25]
S-methyl-5-thioribose-1-phosphate isomerase
NCBIProtein:WP_001022015.1

experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.

Qualification evidence
  • PMID:31950558

    Source assertion: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3.

    Source location(//passage)[41]
enables

ATCC 25922 MtnA supports this reaction. The current RefSeq sequence exactly matches historical UniProt J7QBE0 version 94, UPI00019AF94C, and the translated D1792_RS18650 CDS on ATCC 25922 chromosome NZ_CP032085.1 (3888991..3890106; 371 residues). The multispecies RefSeq label alone is not strain evidence. Native DR76 locus names and this D1792 assembly are kept distinct.

5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315
  • MetaCyc:ENZRXN-29280

    Source assertion: The enzyme field names MONOMER-21154 for reaction MetaCyc:RXN-21315; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29280"]
  • MetaCyc:ENZRXN-29280

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN-HH is linked to PUB-31950558. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29280"]/evidence[1]
  • MetaCyc:ENZRXN-29280

    Source assertion: Native evidence tier EV-EXP-IMP-REACTION-BLOCKED is linked to PUB-31950558. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29280"]/evidence[2]
  • MetaCyc:ENZRXN-29280

    Source assertion: The native km slot reports 222.0 μM for CPD-15199, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29280"]/km[1]
  • MetaCyc:ENZRXN-29280

    Source assertion: The native kcat slot reports 2.02 sec-1 for CPD-15199, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29280"]/kcat[1]
  • MetaCyc:MONOMER-21154

    Source assertion: The native protein frame identifies the ATCC 25922 enzyme and links historical UniProt accession J7QBE0; current graph identity is established separately by the retained exact sequence/chromosome bridge.

    Source location/ptools-xml/Protein[@frameid="MONOMER-21154"]
  • NCBIProtein:WP_001022015.1

    Source assertion: Current RefSeq WP_001022015.1 supplies the 371-residue sequence and its issuer product name. Complete sequence identity to the archived native accession and ATCC chromosome CDS is documented in the accompanying identity ledger.

    Source location/GBSet/GBSeq/GBSeq_sequence
  • PMID:31950558

    Source assertion: The main study experimentally supports this scoped enzyme activity in the DHAP shunt; the corresponding preparation, organism and substrate context are retained in the edge description.

    Source location(//passage)[25]
L-fuculose-phosphate aldolase
NCBIProtein:WP_000439686.1

experimental construct: ATCC 25922 gene cloned into pET28; protein expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Main Methods establish this preparation; inaccessible supplementary primers do not establish tag orientation here.

Qualification evidence
  • PMID:31950558

    Source assertion: ATCC 25922 mtnN, mtnK, mtnA and ald2 were cloned into pET28, expressed in Rosetta(DE3) pLysS and purified by nickel chromatography; primers are assigned to supplementary Table S3.

    Source location(//passage)[41]
enables

ATCC 25922 Ald2 supports this reaction. The current RefSeq sequence exactly matches historical UniProt J7RCN0 version 94, UPI00019AF94D, and the translated D1792_RS18655 CDS on ATCC 25922 chromosome NZ_CP032085.1 (3890137..3890778; 213 residues). The multispecies RefSeq label alone is not strain evidence. Native DR76 locus names and this D1792 assembly are kept distinct. The issuer product label remains L-fuculose-phosphate aldolase; the accepted exact sequence bridge plus experimental evidence identifies this Ald2 activity.

5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316
  • MetaCyc:ENZRXN-29279

    Source assertion: The enzyme field names MONOMER-21153 for reaction MetaCyc:RXN-21316; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29279"]
  • MetaCyc:ENZRXN-29279

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN-HH is linked to PUB-31950558. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29279"]/evidence[1]
  • MetaCyc:ENZRXN-29279

    Source assertion: Native evidence tier EV-EXP-IDA-UNPURIFIED-PROTEIN-NH is linked to PUB-31950558. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29279"]/evidence[2]
  • MetaCyc:ENZRXN-29279

    Source assertion: The native km slot reports 598.0 μM for CPD-23219, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29279"]/km[1]
  • MetaCyc:ENZRXN-29279

    Source assertion: The native kcat slot reports 22.0 sec-1 for CPD-23219, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29279"]/kcat[1]
  • MetaCyc:MONOMER-21153

    Source assertion: The native protein frame identifies the ATCC 25922 enzyme and links historical UniProt accession J7RCN0; current graph identity is established separately by the retained exact sequence/chromosome bridge.

    Source location/ptools-xml/Protein[@frameid="MONOMER-21153"]
  • NCBIProtein:WP_000439686.1

    Source assertion: Current RefSeq WP_000439686.1 supplies the 213-residue sequence and its issuer product name. Complete sequence identity to the archived native accession and ATCC chromosome CDS is documented in the accompanying identity ledger.

    Source location/GBSet/GBSeq/GBSeq_sequence
  • PMID:31950558

    Source assertion: The main study experimentally supports this scoped enzyme activity in the DHAP shunt; the corresponding preparation, organism and substrate context are retained in the edge description.

    Source location(//passage)[26]
Methylthioribose-1-phosphate isomerase
UniProtKB:Q2RXI0

experimental construct: Native protein commentary describes a His10-tagged MtnA construct expressed in E. coli. The activity frame separately assigns partially purified heterologous protein evidence to the 2020 citation.

Qualification evidence
  • MetaCyc:MONOMER-17870

    Source assertion: The complete protein comment describes cloning mtnA as a His10 construct, expression in E. coli and in vitro assay, citing the 2012 and 2020 studies.

    Source location/ptools-xml/Protein[@frameid="MONOMER-17870"]/comment
enables

R. rubrum ATCC 11170 MtnA supports this reaction. Only the shared isomerization event is assigned here; the R. rubrum whole route begins with MtnP phosphorylase. Native 2020 activity evidence is PART-PURIFIED-PROTEIN-HH, distinct from its earlier purified and mutant tiers.

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

    Source assertion: The enzyme field names MONOMER-17870 for reaction MetaCyc:RXN-21315; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

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

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN-HH is linked to PUB-23042035. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29274"]/evidence[1]
  • MetaCyc:ENZRXN-29274

    Source assertion: Native evidence tier EV-EXP-IMP-REACTION-BLOCKED is linked to PUB-23042035. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29274"]/evidence[2]
  • MetaCyc:ENZRXN-29274

    Source assertion: Native evidence tier EV-EXP-IDA-PART-PURIFIED-PROTEIN-HH is linked to PUB-31950558. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29274"]/evidence[3]
  • MetaCyc:ENZRXN-29274

    Source assertion: The native km slot reports 171.0 μM for CPD-15199, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29274"]/km[1]
  • MetaCyc:ENZRXN-29274

    Source assertion: The native kcat slot reports 0.18 sec-1 for CPD-15199, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29274"]/kcat[1]
  • PMID:31950558

    Source assertion: The main study experimentally supports this scoped enzyme activity in the DHAP shunt; the corresponding preparation, organism and substrate context are retained in the edge description.

    Source location(//passage)[17]
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase
UniProtKB:Q2RXI1

experimental construct: Recombinant Ald2 was expressed in E. coli and purified; native commentary describes a His6 construct and anaerobic purification. The 2020 preparation follows the previously reported expression plasmid.

Qualification evidence
  • MetaCyc:MONOMER-21152

    Source assertion: The native comment describes His6-tagged Ald2 expressed in E. coli and purified anaerobically, then separately describes subsequent recombinant 5-deoxyribulose 1-phosphate activity.

    Source location/ptools-xml/Protein[@frameid="MONOMER-21152"]/comment
  • PMID:31950558

    Source assertion: R. rubrum Ald2 used the previously reported pET28 expression plasmid; proteins were expressed in Rosetta(DE3) pLysS and purified by nickel chromatography.

    Source location(//passage)[41]
enables

R. rubrum ATCC 11170 Ald2 supports this reaction. Only the shared aldol-cleavage event is assigned here; Co2+ and Ni2+ give the highest reconstituted activity. The R. rubrum whole route has phosphorylase entry.

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

    Source assertion: The enzyme field names MONOMER-21152 for reaction MetaCyc:RXN-21316; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

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

    Source assertion: Native evidence tier EV-EXP-IMP-REACTION-BLOCKED is linked to PUB-31950558. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29276"]/evidence[1]
  • MetaCyc:ENZRXN-29276

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN-HH is linked to PUB-31950558. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29276"]/evidence[2]
  • MetaCyc:ENZRXN-29276

    Source assertion: The native km slot reports 229.0 μM for CPD-23219, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29276"]/km[1]
  • MetaCyc:ENZRXN-29276

    Source assertion: The native kcat slot reports 1.94 sec-1 for CPD-23219, citing PUB-31950558. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29276"]/kcat[1]
  • PMID:31950558

    Source assertion: The main study experimentally supports this scoped enzyme activity in the DHAP shunt; the corresponding preparation, organism and substrate context are retained in the edge description.

    Source location(//passage)[17]
5-deoxyribose kinase
UniProtKB:P0DTQ2

experimental construct: N-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified by Ni affinity chromatography. Tag-free DrdA used for structural and metal-loading studies is a separate preparation.

Qualification evidence
  • PMID:30082730

    Source assertion: Genes were amplified from HD73-20 (BGSC 4D22) genomic DNA; cloning generated N-terminal His6-tagged DrdK and DrdI.

    Source location(//body//p)[35]
  • PMID:30082730

    Source assertion: The Bacillus constructs were expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified using nickel affinity chromatography.

    Source location(//body//p)[36]
enables

B. thuringiensis HD73-20 DrdK supports this reaction. The current UniProt identity is strain HD73, whereas the assayed gene source and deletion host were HD73-20 (BGSC 4D22). The evidence establishes the downstream three-enzyme module, not all four events in Bacillus.

5-deoxyribose phosphorylation
MetaCyc:RXN-21317
  • MetaCyc:ENZRXN-29537

    Source assertion: The enzyme field names MONOMER-21301 for reaction MetaCyc:RXN-21317; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29537"]
  • MetaCyc:ENZRXN-29537

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN-HH is linked to PUB-30082730. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29537"]/evidence[1]
  • MetaCyc:ENZRXN-29537

    Source assertion: The native km slot reports 216.0 μM for ATP, citing PUB-30082730. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29537"]/km[1]
  • MetaCyc:ENZRXN-29537

    Source assertion: The native km slot reports 178.0 μM for CPD0-2167, citing PUB-30082730. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29537"]/km[2]
  • MetaCyc:ENZRXN-29537

    Source assertion: The native kcat slot reports 17.1 sec-1 for ATP, citing PUB-30082730. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29537"]/kcat[1]
  • MetaCyc:ENZRXN-29537

    Source assertion: The native kcat slot reports 15.4 sec-1 for CPD0-2167, citing PUB-30082730. This value retains its source-specific assay context.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29537"]/kcat[2]
  • PMID:30082730

    Source assertion: Together DrdK, DrdI and DrdA with ATP converted 5-deoxyribose to DHAP; phosphorylation precedes isomerization and aldol cleavage.

    Source location(//body//p)[9]
5-deoxyribose 1-phosphate isomerase
UniProtKB:P0DTQ1

experimental construct: N-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified by Ni affinity chromatography. Tag-free DrdA used for structural and metal-loading studies is a separate preparation.

Qualification evidence
  • PMID:30082730

    Source assertion: Genes were amplified from HD73-20 (BGSC 4D22) genomic DNA; cloning generated N-terminal His6-tagged DrdK and DrdI.

    Source location(//body//p)[35]
  • PMID:30082730

    Source assertion: The Bacillus constructs were expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified using nickel affinity chromatography.

    Source location(//body//p)[36]
enables

B. thuringiensis HD73-20 DrdI supports this reaction. The current UniProt identity is strain HD73, whereas the assayed gene source and deletion host were HD73-20 (BGSC 4D22). The evidence establishes the downstream three-enzyme module, not all four events in Bacillus. Primary Table 1 gives Km 22 ± 7 mM and kcat 3.5 ± 0.7 s−1; the native activity frame has no kinetic slots.

5-deoxyribose 1-phosphate isomerization
MetaCyc:RXN-21315
  • MetaCyc:ENZRXN-29539

    Source assertion: The enzyme field names MONOMER-21302 for reaction MetaCyc:RXN-21315; reaction-direction is PHYSIOL-LEFT-TO-RIGHT.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29539"]
  • MetaCyc:ENZRXN-29539

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN-HH is linked to PUB-30082730. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29539"]/evidence[1]
  • MetaCyc:ENZRXN-29539

    Source assertion: Native evidence tier EV-EXP-IMP-REACTION-BLOCKED is linked to PUB-30082730. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29539"]/evidence[2]
  • PMID:30082730

    Source assertion: Together DrdK, DrdI and DrdA with ATP converted 5-deoxyribose to DHAP; phosphorylation precedes isomerization and aldol cleavage.

    Source location(//body//p)[9]
5-deoxy-D-ribulose 1-phosphate aldolase
UniProtKB:P0DTQ0

experimental construct: C-terminal His6-tagged protein encoded by HD73-20 genomic DNA, expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified by Ni affinity chromatography. Tag-free DrdA used for structural and metal-loading studies is a separate preparation.

Qualification evidence
  • PMID:30082730

    Source assertion: Genes were amplified from HD73-20 (BGSC 4D22) genomic DNA; cloning generated C-terminal His6-tagged DrdA.

    Source location(//body//p)[35]
  • PMID:30082730

    Source assertion: The Bacillus constructs were expressed in E. coli BL21 CodonPlus (DE3)-RIPL and purified using nickel affinity chromatography.

    Source location(//body//p)[36]
enables

B. thuringiensis HD73-20 DrdA supports this reaction. The current UniProt identity is strain HD73, whereas the assayed gene source and deletion host were HD73-20 (BGSC 4D22). The evidence establishes the downstream three-enzyme module, not all four events in Bacillus. Primary Table 1 gives Km 36 ± 3 micromolar and kcat 6.3 ± 0.2 s−1; the native activity frame has no kinetic slots. SEC describes an oligomer possibly tetrameric, while the crystal lattice supplies a proposed tetramer; no exact physiological complex node is invented.

5-deoxyribulose 1-phosphate aldol cleavage
MetaCyc:RXN-21316
  • MetaCyc:ENZRXN-29540

    Source assertion: The enzyme field names MONOMER-21303 for reaction MetaCyc:RXN-21316; reaction-direction is REVERSIBLE.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29540"]
  • MetaCyc:ENZRXN-29540

    Source assertion: Native evidence tier EV-EXP-IDA-PURIFIED-PROTEIN-HH is linked to PUB-30082730. This is the database attribution, not a claim to have independently read each cited paper.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-29540"]/evidence[1]
  • PMID:30082730

    Source assertion: Together DrdK, DrdI and DrdA with ATP converted 5-deoxyribose to DHAP; phosphorylation precedes isomerization and aldol cleavage.

    Source location(//body//p)[9]
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
UniProtKB:P0AF12		part_of

The native MG1655 complex contains two EG11090-MONOMER chains, linked to current P0AF12. This is a reference homodimer composition, not a claim about the ATCC tagged preparation.

5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
MetaCyc:CPLX0-1541
  • MetaCyc:CPLX0-1541

    Source assertion: The component slot lists EG11090-MONOMER with coefficient 2.

    Source location/ptools-xml/Protein[@frameid="CPLX0-1541"]/component
  • MetaCyc:EG11090-MONOMER

    Source assertion: The native monomer frame links UniProt accession P0AF12.

    Source location/ptools-xml/Protein[@frameid="EG11090-MONOMER"]/dblink[dblink-db="UNIPROT"]
L-fuculose-phosphate aldolase
NCBIProtein:WP_000439686.1

molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this condition does not specify universal cellular metal stoichiometry or occupancy.

Qualification evidence
  • PMID:31950558

    Source assertion: Metal-dependent activity was tested with reconstituted Ald2 apoenzyme; the source distinguishes the reconstituted preparation from other enzyme preparations.

    Source location(//passage)[26]
has_cofactor

ATCC 25922 Ald2: Co2+ restored maximal apoenzyme activity and matched the activity/color of the as-purified enzyme. The reported expression preparation was recombinant; its bound cobalt oxidation state was not established.

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

    Source assertion: ATCC 25922 Ald2: Co2+ restored maximal apoenzyme activity and matched the activity/color of the as-purified enzyme. The reported expression preparation was recombinant; its bound cobalt oxidation state was not established.

    Source location(//passage)[26]
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase
UniProtKB:Q2RXI1

molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this condition does not specify universal cellular metal stoichiometry or occupancy.

Qualification evidence
  • PMID:31950558

    Source assertion: Metal-dependent activity was tested with reconstituted Ald2 apoenzyme; the source distinguishes the reconstituted preparation from other enzyme preparations.

    Source location(//passage)[17]
has_cofactor

R. rubrum Ald2: Co2+ is one of the two highest-activity apoenzyme reconstitution conditions; this does not establish a universal physiological metal occupancy.

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

    Source assertion: R. rubrum Ald2: Co2+ is one of the two highest-activity apoenzyme reconstitution conditions; this does not establish a universal physiological metal occupancy.

    Source location(//passage)[17]
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase
UniProtKB:Q2RXI1

molecular state: Recombinant Ald2 apoenzyme reconstituted with the indicated alternative metal. Activity under this condition does not specify universal cellular metal stoichiometry or occupancy.

Qualification evidence
  • PMID:31950558

    Source assertion: Metal-dependent activity was tested with reconstituted Ald2 apoenzyme; the source distinguishes the reconstituted preparation from other enzyme preparations.

    Source location(//passage)[17]
has_cofactor

R. rubrum Ald2: Ni2+ is an alternative high-activity apoenzyme reconstitution condition, not a simultaneous requirement with Co2+.

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

    Source assertion: R. rubrum Ald2: Ni2+ is an alternative high-activity apoenzyme reconstitution condition, not a simultaneous requirement with Co2+.

    Source location(//passage)[17]
5-deoxy-D-ribulose 1-phosphate aldolase
UniProtKB:P0DTQ0

molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or 2 mM MgCl2. Each metal is an alternative condition; tag-free metal-loading experiments are separate.

Qualification evidence
  • PMID:30082730

    Source assertion: DrdA was isolated by Ni affinity chromatography, demetallated by EDTA dialysis, and assayed with 0.1 mM metal chlorides or 2 mM MgCl2; preparations before dialysis and without added metal were controls.

    Source location(//body//p)[10]
  • PMID:30082730

    Source assertion: The activity-assay DrdA construct has a C-terminal His6 tag.

    Source location(//body//p)[35]
has_cofactor

HD73-20 DrdA: Mn2+ gave the highest activity after demetallation; apparent Kmetal was 0.95 ± 0.31 micromolar. Separate tag-free ICP/EPR and crystal preparations support Mn binding.

manganese(2+)
CHEBI:29035
  • PMID:30082730

    Source assertion: Demetallated DrdA had its highest activity with Mn2+; the apparent Kmetal was 0.95 ± 0.31 micromolar.

    Source location(//body//p)[14]
  • PMID:30082730

    Source assertion: A separate tag-free DrdA preparation was used for ICP and EPR metal analysis; mineral supplementation increased manganese incorporation, and EPR supported protein-bound Mn2+.

    Source location(//body//p)[15]
  • PMID:30082730

    Source assertion: The DrdA crystal structure shows an active-site manganese ion; the crystal lattice supplies a proposed tetrameric assembly.

    Source location(//body//p)[20]
  • PMID:30082730

    Source assertion: For crystallization, a separate tag-free DrdA construct was expressed in E. coli BL21(DE3) with mineral supplementation and purified by ammonium sulfate precipitation, anion exchange and size exclusion chromatography.

    Source location(//body//p)[46]
5-deoxy-D-ribulose 1-phosphate aldolase
UniProtKB:P0DTQ0

molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or 2 mM MgCl2. Each metal is an alternative condition; tag-free metal-loading experiments are separate.

Qualification evidence
  • PMID:30082730

    Source assertion: DrdA was isolated by Ni affinity chromatography, demetallated by EDTA dialysis, and assayed with 0.1 mM metal chlorides or 2 mM MgCl2; preparations before dialysis and without added metal were controls.

    Source location(//body//p)[10]
  • PMID:30082730

    Source assertion: The activity-assay DrdA construct has a C-terminal His6 tag.

    Source location(//body//p)[35]
has_cofactor

HD73-20 DrdA: Co2+ supported activity in the alternative 0.1 mM reconstitution condition, below the activity with Mn2+.

cobalt(2+)
CHEBI:48828
  • PMID:30082730

    Source assertion: HD73-20 DrdA: Co2+ supported activity in the alternative 0.1 mM reconstitution condition, below the activity with Mn2+.

    Source location(//body//p)[14]
5-deoxy-D-ribulose 1-phosphate aldolase
UniProtKB:P0DTQ0

molecular state: C-terminal His6-tagged DrdA was demetallated with EDTA, then assayed with 0.1 mM metal chloride or 2 mM MgCl2. Each metal is an alternative condition; tag-free metal-loading experiments are separate.

Qualification evidence
  • PMID:30082730

    Source assertion: DrdA was isolated by Ni affinity chromatography, demetallated by EDTA dialysis, and assayed with 0.1 mM metal chlorides or 2 mM MgCl2; preparations before dialysis and without added metal were controls.

    Source location(//body//p)[10]
  • PMID:30082730

    Source assertion: The activity-assay DrdA construct has a C-terminal His6 tag.

    Source location(//body//p)[35]
has_cofactor

HD73-20 DrdA: Mg2+ supported lower activity in the alternative 2 mM condition. Different assay concentrations do not support an unqualified affinity ranking.

magnesium(2+)
CHEBI:18420
  • PMID:30082730

    Source assertion: HD73-20 DrdA: Mg2+ supported lower activity in the alternative 2 mM condition. Different assay concentrations do not support an unqualified affinity ranking.

    Source location(//body//p)[14]

References

Curation history