S-methyl-5-thio-α-D-ribose 1-phosphate degradation III

MetaCyc:PWY-8132

This exact five-event MetaCyc pathway, also called the DHAP–ethylene shunt, starts with S-methyl-5-thio-α-D-ribose 1-phosphate (MTR1P). MtnA makes the corresponding ribulose phosphate; Ald2 cleaves it to dihydroxyacetone phosphate (DHAP) and (methylsulfanyl)acetaldehyde. Reduction gives 2-methylthioethanol (MT-EtOH), which methylthio-alkane reductase (Mar) converts to ethylene and methanethiol. O-acetylhomoserine sulfhydrylase captures methanethiol as methionine. Upstream MTA phosphorolysis supplies MTR1P but lies outside these five events. The graph preserves all 22 native reaction-side occurrences, four intermediate transfers and the complete nested Mar assembly; continuity does not assert physical substrate channeling. Native physiology was studied in Rhodospirillum rubrum ATCC 11170/S1 and Rhodopseudomonas palustris CGA010, a derivative of CGA009. Anaerobic isotope-feeding, gene deletions and complementation establish the MtnP/MtnA/Ald2 module, formation of MT-EtOH and approximately equimolar ethylene production from consumed MT-EtOH. Several upstream deletion backgrounds retain low ethylene or residual growth, so their phenotypes are not generalized to abolition of every sulfur-salvage route. The R. rubrum strain identifier anchors the selected protein chains; the species entries preserve experimentally supported scope without asserting that every strain carries this pathway. The first event is native REVERSIBLE despite a degradative left-to-right pathway layout. RXN-21319 is written as alcohol plus NAD giving aldehyde, NADH and a proton, but its native RIGHT-TO-LEFT direction and pathway layout select aldehyde reduction. Its graph consumption/production arrows follow that selected reduction while the reaction direction retains the source equation axis. The other three reactions are PHYSIOL-LEFT-TO-RIGHT. The NAD/NADH pair is the formal putative native equation, not an identification of the cellular aldehyde reductase or its physiological cofactor. In the 2017 coupled assay, recombinant Ald2 produced the aldehyde and DHAP, and added yeast alcohol dehydrogenase plus NADH converted the aldehyde to MT-EtOH. The native aldehyde was not detected during feeding, consistent with rapid reduction, but this does not identify the bacterial enzyme. The 2018 aerobic DHAP–methanethiol pathway shares the early module in R. palustris; its terminal chemistry and oxygen context are distinct from the anaerobic ethylene route. Historical 2017/2018 descriptions left the sulfur endpoint unresolved. The 2020 native-host radiotracer study instead detected Mar-dependent methanethiol and methionine from MT-EtOH, superseding that historical uncertainty. The Mar equation retains one MT-EtOH, two reduced ferredoxin equivalents and two protons yielding one ethylene, one methanethiol, one water and two oxidized ferredoxin equivalents. These ferredoxins are generic protein redox classes, not small-molecule structures or identified R. rubrum proteins. MetaCyc proposes ferredoxin or flavodoxin by analogy; its commentary calls the missing partner an electron acceptor, although the represented reduction requires an electron donor. The 2020 supporting thermodynamics explicitly state that the actual donor is unknown and use H2 only as a reference. Current UniProt uses a generic AH2/A donor pair. Those representations are not asserted to be exact reaction equivalents. The 2020 work separated the marBHDK locus (Rru_A0793–Rru_A0796) from nitrogen fixation. Disruption of marH or the full cluster prevented growth with MT-EtOH as sole sulfur source and eliminated induced ethylene above basal levels; complementation restored the phenotype. Deletion of the separate nflDK pair did not prevent this route. MarBH combined with the alternate NflDK supported only weak alternative activity in the tested complementation setting, so NflDK is not silently substituted for the native MarDK catalyst. MarB is a proposed cofactor-maturation protein, not a fourth structural chain in the represented Mar assembly. R. rubrum MtnA is Q2RXI0/Rru_A0360, Ald2 is Q2RXI1/Rru_A0359 and Oah is Q2RWB7/Rru_A0774. The first two current UniProt entries are reviewed; Oah remains an unreviewed submission whose chain identity is corroborated by native gene/product links and whose methanethiol-specific activity was experimentally described in 2012. MarD, MarK and MarH are current Q2RW97/Rru_A0794, Q2RW98/Rru_A0793 and Q2RW96/Rru_A0795. Their native MONOMER-21380/21381/21382 identifiers are retained as assembly members with exact chain cross-mappings, rather than adding duplicate biological chains. Native CPLX-9562 contains one CPLX-9561 reductase component and one CPLX-9560 catalytic component. CPLX-9561 contains two MarH chains; CPLX-9560 contains two MarK and two MarD chains, with reciprocal memberships. The 2025 purified components were a MarH2 dimer and a Mar(DK)2 tetramer by mass photometry. Their ATP-analogue-trapped association contained particles with one or two MarH2 dimers. Focused refinement produced the reported MarDK2H2 structural fragment after the second MarD could not be resolved. These are distinct assembly contexts: the fragment and trapped octamer are not replacements for the complete native nested topology or proof of one fixed physiological docking stoichiometry. The 2025 structural and activity experiments used R. rubrum marBHDK expressed in engineered Rhodobacter capsulatus MM0422, derived from MM0246 (ΔnifD::SpR ΔanfHDGK::gmR ΔdraTG ΔmodABC ΔgtaI) carrying pMM0181. MarH had an N-terminal His6 tag and MarD a C-terminal Strep-tag II; these distinguish the tested preparation from the unmodified native chains. R. capsulatus is the heterologous production host and is not added as a native DHAP–ethylene pathway taxon. The purified components were assayed at a catalytic:reductase molar ratio of 1:5 owing to MarH precipitation, not because the native assembly has five reductase dimers. Purified Mar reduced MT-EtOH at 2.3 nmol ethylene per mg Mar(DK)2 per minute in the 2025 conditions. Activity required both components, ATP and sodium dithionite; assays used 15 mM substrate, 3.5 mM ATP, 5 mM dithionite, an ATP-regeneration system and 30 °C. These conditions establish an ATP-dependent reconstituted activity, not ATP turnover stoichiometry or use of dithionite in the cell. Dimethyl sulfide and ethyl methyl sulfide gave methane and ethane in parallel substrate assays, but are outside this five-event graph. H2 formation and acetylene reduction were additional in vitro activities; no nitrogen-fixation activity above background was detected under the tested 15N2 conditions. The 2025 MarH2 structure contains one interfacial [4Fe–4S] cluster and two bound MgADP–AlF3 moieties. A P-cluster bridges MarD/MarK and an [Fe8S9C] active-site cluster sits in MarD, providing a structural electron-transfer route. The central carbide was modeled from geometry and maturation context because the map did not resolve that atom independently; EPR supplied additional support for its assignment. Homocitrate, Mo and V were not detected in these preparations. The generic ChEBI [4Fe–4S] cofactor reference identifies the cluster type, not a claim that its neutral database depiction fixes the experimental redox state. Full P-cluster and [Fe8S9C] context is preserved in prose because no independently checked exact cofactor identifiers for those states are introduced. Proposed substrate-access channels, an S2B binding site and candidate proton-transfer residues in the 2025 paper are structural interpretations, not measured elementary reaction steps. Its evolutionary analysis supports a proposed common ancestor with complex metalloclusters, but does not demonstrate the ancestral substrate or physiological activity. The record therefore separates measured C–S cleavage and component electron transfer from those mechanistic and evolutionary hypotheses. Ald2 assays used a recombinant His6 preparation expressed in E. coli and purified anaerobically; the 2017 SI and native commentary support that construct. The 2020 Methods specify pET28 expression in E. coli Rosetta(DE3) pLysS and nickel purification. MtnA and Oah His10 details are native database attributions to the older 2012 work because its detailed SI was not accessible here; exact tag orientations are not established. These construct scopes do not convert recombinant assays into native-host protein purification. The MTR1P-specific MtnA values are Km 134 micromolar and kcat 0.1 s−1. The native slots and current UniProt attribute them to 2012, while 2020 Table 1 repeats them as literature values. For R. rubrum Ald2 with MTRu1P, the reported pair is Km 288 micromolar and kcat 0.94 s−1. The accessible Table 1 catalytic-efficiency entry is inconsistent with that pair and is not propagated or silently corrected. Native ENZRXN-29277 also places 3.1950558e7 in specific-activity and Vmax fields without slot-level citations; the digits reproduce PMID31950558. Those two apparent transcription artifacts are retained as source defects and rejected as biochemical measurements. R. rubrum Ald2 required a divalent metal in the reconstitution experiments, with Co2+ and Ni2+ giving the highest activities among the tested conditions. Each graph cofactor edge is an alternative recombinant apoenzyme preparation after EDTA treatment and dialysis, followed by one hour with 0.1 mM of the selected metal. It does not assert simultaneous Co/Ni occupancy or identify the native cellular metal. The current UniProt one-cobalt-per-subunit statement carries a by-similarity qualification. Magnesium in the older coupled assay likewise does not establish an exclusive physiological metal for MtnA or Ald2. For Oah with O-acetylhomoserine, the native kcat 3.5 s−1, experimental molecular mass 46 kDa and pI 5.91 are database-attributed to the 2012 study; its accessible main text confirms methanethiol-specific Rru_A0774 activity but does not expose the detailed SI measurements. Current Q2RWB7 annotates pyridoxal phosphate by automated inference, so the cofactor edge preserves that evidence tier instead of claiming an R. rubrum cofactor-occupancy measurement. Native Oah commentary attributes a 320-fold induction to a different 1988 citation. The 2012 main text reports a 30–320-fold range for the fourteen-gene thiol cluster; an Oah-specific exact fold is not inferred from that range. All nine native activity frames are retained, including contexts outside this route's demonstrated organisms. E. coli ATCC 25922 MtnA and Ald2 have MTR1P/MTRu1P pairs of 50 micromolar/0.49 s−1 and 275 micromolar/22 s−1, respectively, but the 2020 primary work found no conversion beyond MT-EtOH and no growth using these methylthio compounds as sole sulfur sources. Its native Ald2 activity includes native-host purification wording alongside heterologous evidence, whereas the accessible Methods describe recombinant expression. These shared-module data do not establish a complete E. coli Mar pathway. Arabidopsis MTI1 complementation and Klebsiella isomerase activity are catalog contexts, not added route taxa. Thermus thermophilus HB8 Oah activity is another separate catalog context: pH optimum 7.8, temperature optimum 70 °C, O-acetylhomoserine Km 6800 micromolar, PLP and methionine inhibition are attributed to its 2001 study. They are not transferred to R. rubrum. Native and current identity evidence also resolve the older MtnA/MtnP locus-name transposition in one 2012 passage and the native MtnA commentary's mistaken ribulose-phosphate arrest statement; the primary mutant block is at the upstream ribose phosphate. The 2017 SI double-rlp1/rlp2 strain row also mislists the ald2 locus RPA4655 where the single-rlp1 row and cloning context support RPA2169; it is not treated as an ald2 deletion. Mar expression is induced during sulfur limitation and depends on the LysR-family regulator SalR/Rru_A0785 in the tested R. rubrum background. Loss of SalR prevented the induced sulfur-assimilation and hydrocarbon-production phenotype; transcriptomics and genetic dependence do not themselves show direct SalR binding at a promoter. Sulfate inhibition differed by substrate in the 2020 figure (approximately 110 micromolar for MT-EtOH and 140 micromolar for DMS). This is separate from nitrogenase regulation by nitrogen availability. The complete upstream route is not assigned to additional species merely from mar homology or VOSC-growth assays. Fourteen defined chemical participants have exact native-to-current ChEBI InChI agreement, including full stereochemical and protonation layers. Reduced and oxidized ferredoxins instead have issued generic class identities with no defined formula. Their two-equivalent formal redox bookkeeping is retained without claiming a particular ferredoxin, experimental donor, or fully specified protein atom balance. Native Rhea cross-references 19990/10049 and current UniProt 81439/81440 remain source context; attempted direct retrievals were blocked, so no exact Rhea reaction mapping is asserted from those links alone. Numerical native Gibbs energies, where present, are computational annotations, not fresh thermodynamic measurements. The complete 2017, 2018 and 2025 scientific main-text/method/table/caption projections were read against retained originals. The 2017 SI scientific methods, figures and strain/assay tables through PDF page 18, all ten pages of the 2025 SI, and the 2020 Science scientific main text plus its retained supporting text and figures were read; selected original figure images were also inspected. The prior complete 2012 and 2020 Molecular Microbiology main-text readings were inherited with fresh checks of relevant passages. Their inaccessible SI/figure bodies, the 2020 Science external spreadsheets/databases, raw 2025 structural and spectroscopy datasets, and unread 2017 SI gene-inventory tail are not claimed as newly examined. These limits do not turn a missing gene identity, source conflict or proposed donor into a demonstrated fact. Broader pathway-source discovery and public-release licensing remain separate work.

Pathway type

metabolic

Organism scope

Read the source YAML

Pathway network

42 nodes · 44 asserted directed edges

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

Find a node

Reaction / activity
Chemical / cofactor
Protein / complex
Pathway
Solid arrow: mechanistic relation
Dashed arrow: membership, location or cofactor relation

Show at full size (scroll to explore)

Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Rhodospirillum rubrum ATCC 11170 `NCBITaxon:269796`	taxon
Rhodospirillum rubrum `NCBITaxon:1085`	taxon
Rhodopseudomonas palustris `NCBITaxon:1076`	taxon
acetate `CHEBI:30089`	small molecule
S-methyl-5-thio-D-ribulose 1-phosphate(2−) `CHEBI:58548`	small molecule
(methylsulfanyl)acetaldehyde `CHEBI:141184`	small molecule
S-methyl-5-thio-α-D-ribose 1-phosphate(2−) `CHEBI:58533`	small molecule
O-acetyl-L-homoserine zwitterion `CHEBI:57716`	small molecule
methanethiol `CHEBI:16007`	small molecule
2-methylthioethanol `CHEBI:63861`	small molecule
glycerone phosphate(2−) `CHEBI:57642`	small molecule
ethene `CHEBI:18153`	small molecule
L-methionine zwitterion `CHEBI:57844`	small molecule
NAD(1−) `CHEBI:57540`	small molecule
NADH(2−) `CHEBI:57945`	small molecule
oxidized ferredoxin `CHEBI:17908`	protein
hydron `CHEBI:15378`	small molecule
reduced ferredoxin `CHEBI:17513`	protein
water `CHEBI:15377`	small molecule
cobalt(2+) `CHEBI:48828`	cofactor
nickel(2+) `CHEBI:49786`	cofactor
tetra-μ3-sulfido-tetrairon `CHEBI:49883`	cofactor
pyridoxal 5'-phosphate(2−) `CHEBI:597326`	cofactor
methylthio-alkane reductase `MetaCyc:CPLX-9562`	complex
methylthio-alkane reductase reductase component dimer `MetaCyc:CPLX-9561`	complex
methylthio-alkane reductase catalytic component `MetaCyc:CPLX-9560`	complex
methylthio-alkane reductase catalytic subunit α `MetaCyc:MONOMER-21380`	protein
methylthio-alkane reductase catalytic subunit β `MetaCyc:MONOMER-21381`	protein
methylthio-alkane reductase reductase component `MetaCyc:MONOMER-21382`	protein
Methylthioribose-1-phosphate isomerase `UniProtKB:Q2RXI0`	protein
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase `UniProtKB:Q2RXI1`	protein
O-acetylhomoserine/O-acetylserine sulfhydrylase `UniProtKB:Q2RWB7`	protein
MTR1P isomerization `MetaCyc:5.3.1.23-RXN`	molecular activity	reversible
MTRu1P aldol cleavage `MetaCyc:RXN-21318`	molecular activity	left to right
Putative methylthioacetaldehyde reduction `MetaCyc:RXN-21319`	molecular activity	right to left
MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	molecular activity	left to right
Methanethiol incorporation into methionine `MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN`	molecular activity	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
MTR1P isomerization `MetaCyc:5.3.1.23-RXN`	part_of This exact reaction belongs to the five-event native pathway.	`MetaCyc:PWY-8132`	MetaCyc:PWY-8132 Source assertion: MetaCyc:5.3.1.23-RXN occurs in the exact native reaction-list. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-list` MetaCyc:5.3.1.23-RXN Source assertion: The reaction has a reciprocal PWY8132 membership. Source location `/ptools-xml/Reaction[@frameid='5.3.1.23-RXN']/in-pathway` PMID:29133429 Source assertion: Native R. rubrum andR. palustris isotope feeding supports the pathway module. Source location `/article/body/sec[1]/sec[3]/p[2]` PMID:32855335 Source assertion: Strains are R. rubrum ATCC11170/S1 andR. palustris CGA010. Source location `PDF page 23` NCBITaxon:269796 Source assertion: NCBI strain269796 is R. rubrum ATCC11170. Source location `/TaxaSet/Taxon/ScientificName` NCBITaxon:1076 Source assertion: NCBI species1076 is R. palustris. Source location `/TaxaSet/Taxon/ScientificName` MetaCyc:PWY-8132 Source assertion: Native pathway species are R. rubrum andR. palustris, without asserting all strains. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/species`
S-methyl-5-thio-α-D-ribose 1-phosphate(2−) `CHEBI:58533`	consumes Native written left occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated.	MTR1P isomerization `MetaCyc:5.3.1.23-RXN`	MetaCyc:5.3.1.23-RXN Source assertion: MetaCyc:CPD-444 is the native written left participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='5.3.1.23-RXN']/left[1]` MetaCyc:CPD-444 Source assertion: The complete native InChI agrees exactly with CHEBI:58533, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='CPD-444']/inchi` CHEBI:58533 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
MTR1P isomerization `MetaCyc:5.3.1.23-RXN`	produces Native written right occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated.	S-methyl-5-thio-D-ribulose 1-phosphate(2−) `CHEBI:58548`	MetaCyc:5.3.1.23-RXN Source assertion: MetaCyc:CPD-1063 is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='5.3.1.23-RXN']/right[1]` MetaCyc:CPD-1063 Source assertion: The complete native InChI agrees exactly with CHEBI:58548, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='CPD-1063']/inchi` CHEBI:58548 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
MTRu1P aldol cleavage `MetaCyc:RXN-21318`	part_of This exact reaction belongs to the five-event native pathway.	`MetaCyc:PWY-8132`	MetaCyc:PWY-8132 Source assertion: MetaCyc:RXN-21318 occurs in the exact native reaction-list. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-list` MetaCyc:RXN-21318 Source assertion: The reaction has a reciprocal PWY8132 membership. Source location `/ptools-xml/Reaction[@frameid='RXN-21318']/in-pathway`
S-methyl-5-thio-D-ribulose 1-phosphate(2−) `CHEBI:58548`	consumes Native written left occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated.	MTRu1P aldol cleavage `MetaCyc:RXN-21318`	MetaCyc:RXN-21318 Source assertion: MetaCyc:CPD-1063 is the native written left participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21318']/left[1]` MetaCyc:CPD-1063 Source assertion: The complete native InChI agrees exactly with CHEBI:58548, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='CPD-1063']/inchi` CHEBI:58548 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
MTRu1P aldol cleavage `MetaCyc:RXN-21318`	produces Native written right occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated.	glycerone phosphate(2−) `CHEBI:57642`	MetaCyc:RXN-21318 Source assertion: MetaCyc:DIHYDROXY-ACETONE-PHOSPHATE is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21318']/right[1]` MetaCyc:DIHYDROXY-ACETONE-PHOSPHATE Source assertion: The complete native InChI agrees exactly with CHEBI:57642, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='DIHYDROXY-ACETONE-PHOSPHATE']/inchi` CHEBI:57642 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
MTRu1P aldol cleavage `MetaCyc:RXN-21318`	produces Native written right occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated.	(methylsulfanyl)acetaldehyde `CHEBI:141184`	MetaCyc:RXN-21318 Source assertion: MetaCyc:CPD-23221 is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21318']/right[2]` MetaCyc:CPD-23221 Source assertion: The complete native InChI agrees exactly with CHEBI:141184, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='CPD-23221']/inchi` CHEBI:141184 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
Putative methylthioacetaldehyde reduction `MetaCyc:RXN-21319`	part_of This exact reaction belongs to the five-event native pathway.	`MetaCyc:PWY-8132`	MetaCyc:PWY-8132 Source assertion: MetaCyc:RXN-21319 occurs in the exact native reaction-list. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-list` MetaCyc:RXN-21319 Source assertion: The reaction has a reciprocal PWY8132 membership. Source location `/ptools-xml/Reaction[@frameid='RXN-21319']/in-pathway`
Putative methylthioacetaldehyde reduction `MetaCyc:RXN-21319`	produces Native written left occurrence, coefficient 1. Graph arrows follow the selected right-to-left reduction; formal NAD/NADH use does not identify the cellular enzyme/cofactor.	2-methylthioethanol `CHEBI:63861`	MetaCyc:RXN-21319 Source assertion: MetaCyc:CPD-7677 is the native written left participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21319']/left[1]` MetaCyc:CPD-7677 Source assertion: The complete native InChI agrees exactly with CHEBI:63861, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='CPD-7677']/inchi` CHEBI:63861 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
Putative methylthioacetaldehyde reduction `MetaCyc:RXN-21319`	produces Native written left occurrence, coefficient 1. Graph arrows follow the selected right-to-left reduction; formal NAD/NADH use does not identify the cellular enzyme/cofactor.	NAD(1−) `CHEBI:57540`	MetaCyc:RXN-21319 Source assertion: MetaCyc:NAD is the native written left participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21319']/left[2]` MetaCyc:NAD Source assertion: The complete native InChI agrees exactly with CHEBI:57540, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='NAD']/inchi` CHEBI:57540 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
(methylsulfanyl)acetaldehyde `CHEBI:141184`	consumes Native written right occurrence, coefficient 1. Graph arrows follow the selected right-to-left reduction; formal NAD/NADH use does not identify the cellular enzyme/cofactor.	Putative methylthioacetaldehyde reduction `MetaCyc:RXN-21319`	MetaCyc:RXN-21319 Source assertion: MetaCyc:CPD-23221 is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21319']/right[1]` MetaCyc:CPD-23221 Source assertion: The complete native InChI agrees exactly with CHEBI:141184, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='CPD-23221']/inchi` CHEBI:141184 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
NADH(2−) `CHEBI:57945`	consumes Native written right occurrence, coefficient 1. Graph arrows follow the selected right-to-left reduction; formal NAD/NADH use does not identify the cellular enzyme/cofactor.	Putative methylthioacetaldehyde reduction `MetaCyc:RXN-21319`	MetaCyc:RXN-21319 Source assertion: MetaCyc:NADH is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21319']/right[2]` MetaCyc:NADH Source assertion: The complete native InChI agrees exactly with CHEBI:57945, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='NADH']/inchi` CHEBI:57945 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
hydron `CHEBI:15378`	consumes Native written right occurrence, coefficient 1. Graph arrows follow the selected right-to-left reduction; formal NAD/NADH use does not identify the cellular enzyme/cofactor.	Putative methylthioacetaldehyde reduction `MetaCyc:RXN-21319`	MetaCyc:RXN-21319 Source assertion: MetaCyc:PROTON is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21319']/right[3]` MetaCyc:PROTON Source assertion: The complete native InChI agrees exactly with CHEBI:15378, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='PROTON']/inchi` CHEBI:15378 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	part_of This exact reaction belongs to the five-event native pathway.	`MetaCyc:PWY-8132`	MetaCyc:PWY-8132 Source assertion: MetaCyc:RXN-21320 occurs in the exact native reaction-list. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-list` MetaCyc:RXN-21320 Source assertion: The reaction has a reciprocal PWY8132 membership. Source location `/ptools-xml/Reaction[@frameid='RXN-21320']/in-pathway`
2-methylthioethanol `CHEBI:63861`	consumes Native written left occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated. Ferredoxin/proton stoichiometry is the source formal proposal, not a measured physiological donor assignment.	MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	MetaCyc:RXN-21320 Source assertion: MetaCyc:CPD-7677 is the native written left participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21320']/left[1]` MetaCyc:CPD-7677 Source assertion: The complete native InChI agrees exactly with CHEBI:63861, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='CPD-7677']/inchi` CHEBI:63861 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
reduced ferredoxin `CHEBI:17513`	consumes Native written left occurrence, coefficient 2. Arrows follow the degradative pathway layout; native reversibility is retained where stated. Ferredoxin/proton stoichiometry is the source formal proposal, not a measured physiological donor assignment.	MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	MetaCyc:RXN-21320 Source assertion: MetaCyc:Reduced-ferredoxins is the native written left participant, coefficient 2; the explicit coefficient is retained. Source location `/ptools-xml/Reaction[@frameid='RXN-21320']/left[2]` MetaCyc:Reduced-ferredoxins Source assertion: The native entity is an issued generic ferredoxin Protein class, not a defined small molecule. Source location `/ptools-xml/Protein[@frameid='Reduced-ferredoxins']/parent` CHEBI:17513 Source assertion: The current issuing name is reduced ferredoxin; no molecular formula or particular physiological protein is asserted. Source location `$.name`
hydron `CHEBI:15378`	consumes Native written left occurrence, coefficient 2. Arrows follow the degradative pathway layout; native reversibility is retained where stated. Ferredoxin/proton stoichiometry is the source formal proposal, not a measured physiological donor assignment.	MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	MetaCyc:RXN-21320 Source assertion: MetaCyc:PROTON is the native written left participant, coefficient 2; the explicit coefficient is retained. Source location `/ptools-xml/Reaction[@frameid='RXN-21320']/left[3]` MetaCyc:PROTON Source assertion: The complete native InChI agrees exactly with CHEBI:15378, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='PROTON']/inchi` CHEBI:15378 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	produces Native written right occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated. Ferredoxin/proton stoichiometry is the source formal proposal, not a measured physiological donor assignment.	ethene `CHEBI:18153`	MetaCyc:RXN-21320 Source assertion: MetaCyc:ETHYLENE-CMPD is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21320']/right[1]` MetaCyc:ETHYLENE-CMPD Source assertion: The complete native InChI agrees exactly with CHEBI:18153, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='ETHYLENE-CMPD']/inchi` CHEBI:18153 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	produces Native written right occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated. Ferredoxin/proton stoichiometry is the source formal proposal, not a measured physiological donor assignment.	methanethiol `CHEBI:16007`	MetaCyc:RXN-21320 Source assertion: MetaCyc:CPD-7671 is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21320']/right[2]` MetaCyc:CPD-7671 Source assertion: The complete native InChI agrees exactly with CHEBI:16007, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='CPD-7671']/inchi` CHEBI:16007 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	produces Native written right occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated. Ferredoxin/proton stoichiometry is the source formal proposal, not a measured physiological donor assignment.	water `CHEBI:15377`	MetaCyc:RXN-21320 Source assertion: MetaCyc:WATER is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='RXN-21320']/right[3]` MetaCyc:WATER Source assertion: The complete native InChI agrees exactly with CHEBI:15377, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='WATER']/inchi` CHEBI:15377 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	produces Native written right occurrence, coefficient 2. Arrows follow the degradative pathway layout; native reversibility is retained where stated. Ferredoxin/proton stoichiometry is the source formal proposal, not a measured physiological donor assignment.	oxidized ferredoxin `CHEBI:17908`	MetaCyc:RXN-21320 Source assertion: MetaCyc:Oxidized-ferredoxins is the native written right participant, coefficient 2; the explicit coefficient is retained. Source location `/ptools-xml/Reaction[@frameid='RXN-21320']/right[4]` MetaCyc:Oxidized-ferredoxins Source assertion: The native entity is an issued generic ferredoxin Protein class, not a defined small molecule. Source location `/ptools-xml/Protein[@frameid='Oxidized-ferredoxins']/parent` CHEBI:17908 Source assertion: The current issuing name is oxidized ferredoxin; no molecular formula or particular physiological protein is asserted. Source location `$.name`
Methanethiol incorporation into methionine `MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN`	part_of This exact reaction belongs to the five-event native pathway.	`MetaCyc:PWY-8132`	MetaCyc:PWY-8132 Source assertion: MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN occurs in the exact native reaction-list. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-list` MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN Source assertion: The reaction has a reciprocal PWY8132 membership. Source location `/ptools-xml/Reaction[@frameid='O-ACETYLHOMOSERINE-THIOL-LYASE-RXN']/in-pathway`
O-acetyl-L-homoserine zwitterion `CHEBI:57716`	consumes Native written left occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated.	Methanethiol incorporation into methionine `MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN`	MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN Source assertion: MetaCyc:CPD-667 is the native written left participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='O-ACETYLHOMOSERINE-THIOL-LYASE-RXN']/left[1]` MetaCyc:CPD-667 Source assertion: The complete native InChI agrees exactly with CHEBI:57716, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='CPD-667']/inchi` CHEBI:57716 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
methanethiol `CHEBI:16007`	consumes Native written left occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated.	Methanethiol incorporation into methionine `MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN`	MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN Source assertion: MetaCyc:CPD-7671 is the native written left participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='O-ACETYLHOMOSERINE-THIOL-LYASE-RXN']/left[2]` MetaCyc:CPD-7671 Source assertion: The complete native InChI agrees exactly with CHEBI:16007, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='CPD-7671']/inchi` CHEBI:16007 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
Methanethiol incorporation into methionine `MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN`	produces Native written right occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated.	L-methionine zwitterion `CHEBI:57844`	MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN Source assertion: MetaCyc:MET is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='O-ACETYLHOMOSERINE-THIOL-LYASE-RXN']/right[1]` MetaCyc:MET Source assertion: The complete native InChI agrees exactly with CHEBI:57844, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='MET']/inchi` CHEBI:57844 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
Methanethiol incorporation into methionine `MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN`	produces Native written right occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated.	acetate `CHEBI:30089`	MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN Source assertion: MetaCyc:ACET is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='O-ACETYLHOMOSERINE-THIOL-LYASE-RXN']/right[2]` MetaCyc:ACET Source assertion: The complete native InChI agrees exactly with CHEBI:30089, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='ACET']/inchi` CHEBI:30089 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
Methanethiol incorporation into methionine `MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN`	produces Native written right occurrence, coefficient 1. Arrows follow the degradative pathway layout; native reversibility is retained where stated.	hydron `CHEBI:15378`	MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN Source assertion: MetaCyc:PROTON is the native written right participant, coefficient 1; one is implicit without a coefficient override. Source location `/ptools-xml/Reaction[@frameid='O-ACETYLHOMOSERINE-THIOL-LYASE-RXN']/right[3]` MetaCyc:PROTON Source assertion: The complete native InChI agrees exactly with CHEBI:15378, including charge/stereochemical layers. Source location `/ptools-xml/Compound[@frameid='PROTON']/inchi` CHEBI:15378 Source assertion: Complete current ChEBI structure independently confirms the selected chemical identity. Source location `$.default_structure.standard_inchi`
MTR1P isomerization `MetaCyc:5.3.1.23-RXN`	provides_input_for Transfer of MTRu1P preserves pathway ordering and material continuity without a claim of physical channeling.	MTRu1P aldol cleavage `MetaCyc:RXN-21318`	MetaCyc:PWY-8132 Source assertion: 5.3.1.23-RXN precedes RXN-21318 in the exact native ordering. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-ordering[Reaction/@frameid='RXN-21318']` MetaCyc:PWY-8132 Source assertion: The layouts select the connected metabolic sequence; RXN21319 uses R2L. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-layout`
MTRu1P aldol cleavage `MetaCyc:RXN-21318`	provides_input_for Transfer of methylthioacetaldehyde preserves pathway ordering and material continuity without a claim of physical channeling.	Putative methylthioacetaldehyde reduction `MetaCyc:RXN-21319`	MetaCyc:PWY-8132 Source assertion: RXN-21318 precedes RXN-21319 in the exact native ordering. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-ordering[Reaction/@frameid='RXN-21319']` MetaCyc:PWY-8132 Source assertion: The layouts select the connected metabolic sequence; RXN21319 uses R2L. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-layout`
Putative methylthioacetaldehyde reduction `MetaCyc:RXN-21319`	provides_input_for Transfer of MT-EtOH preserves pathway ordering and material continuity without a claim of physical channeling.	MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	MetaCyc:PWY-8132 Source assertion: RXN-21319 precedes RXN-21320 in the exact native ordering. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-ordering[Reaction/@frameid='RXN-21320']` MetaCyc:PWY-8132 Source assertion: The layouts select the connected metabolic sequence; RXN21319 uses R2L. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-layout`
MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	provides_input_for Transfer of methanethiol preserves pathway ordering and material continuity without a claim of physical channeling.	Methanethiol incorporation into methionine `MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN`	MetaCyc:PWY-8132 Source assertion: RXN-21320 precedes O-ACETYLHOMOSERINE-THIOL-LYASE-RXN in the exact native ordering. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-ordering[Reaction/@frameid='O-ACETYLHOMOSERINE-THIOL-LYASE-RXN']` MetaCyc:PWY-8132 Source assertion: The layouts select the connected metabolic sequence; RXN21319 uses R2L. Source location `/ptools-xml/Pathway[@frameid='PWY-8132']/reaction-layout`
methylthio-alkane reductase reductase component dimer `MetaCyc:CPLX-9561`	part_of Native component coefficient 1. Complete nested topology is retained; ATP-analogue-trapped docking states and the refined structural fragment are distinct contexts.	methylthio-alkane reductase `MetaCyc:CPLX-9562`	MetaCyc:CPLX-9562 Source assertion: CPLX-9562 explicitly contains 1 copies of CPLX-9561. Source location `/ptools-xml/Protein[@frameid='CPLX-9562']/component[Protein/@frameid='CPLX-9561']` MetaCyc:CPLX-9561 Source assertion: CPLX-9561 has reciprocal membership in CPLX-9562. Source location `/ptools-xml/Protein[@frameid='CPLX-9561']/component-of` PMID:41140912 Source assertion: Separate purified MarH2 and Mar(DK)2 components are supported by mass photometry. Source location `/article/body/sec[2]/sec[1]/p[1]` PMID:41140912 Source assertion: Trapped one/two-dimer association and refined MarDK2H2 are distinct structural contexts. Source location `/article/body/sec[2]/sec[1]/p[4]`
methylthio-alkane reductase catalytic component `MetaCyc:CPLX-9560`	part_of Native component coefficient 1. Complete nested topology is retained; ATP-analogue-trapped docking states and the refined structural fragment are distinct contexts.	methylthio-alkane reductase `MetaCyc:CPLX-9562`	MetaCyc:CPLX-9562 Source assertion: CPLX-9562 explicitly contains 1 copies of CPLX-9560. Source location `/ptools-xml/Protein[@frameid='CPLX-9562']/component[Protein/@frameid='CPLX-9560']` MetaCyc:CPLX-9560 Source assertion: CPLX-9560 has reciprocal membership in CPLX-9562. Source location `/ptools-xml/Protein[@frameid='CPLX-9560']/component-of` PMID:41140912 Source assertion: Separate purified MarH2 and Mar(DK)2 components are supported by mass photometry. Source location `/article/body/sec[2]/sec[1]/p[1]` PMID:41140912 Source assertion: Trapped one/two-dimer association and refined MarDK2H2 are distinct structural contexts. Source location `/article/body/sec[2]/sec[1]/p[4]`
methylthio-alkane reductase reductase component `MetaCyc:MONOMER-21382`	part_of Native component coefficient 2. Complete nested topology is retained; ATP-analogue-trapped docking states and the refined structural fragment are distinct contexts.	methylthio-alkane reductase reductase component dimer `MetaCyc:CPLX-9561`	MetaCyc:CPLX-9561 Source assertion: CPLX-9561 explicitly contains 2 copies of MONOMER-21382. Source location `/ptools-xml/Protein[@frameid='CPLX-9561']/component[Protein/@frameid='MONOMER-21382']` MetaCyc:MONOMER-21382 Source assertion: MONOMER-21382 has reciprocal membership in CPLX-9561. Source location `/ptools-xml/Protein[@frameid='MONOMER-21382']/component-of` PMID:41140912 Source assertion: Separate purified MarH2 and Mar(DK)2 components are supported by mass photometry. Source location `/article/body/sec[2]/sec[1]/p[1]` PMID:41140912 Source assertion: Trapped one/two-dimer association and refined MarDK2H2 are distinct structural contexts. Source location `/article/body/sec[2]/sec[1]/p[4]`
methylthio-alkane reductase catalytic subunit β `MetaCyc:MONOMER-21381`	part_of Native component coefficient 2. Complete nested topology is retained; ATP-analogue-trapped docking states and the refined structural fragment are distinct contexts.	methylthio-alkane reductase catalytic component `MetaCyc:CPLX-9560`	MetaCyc:CPLX-9560 Source assertion: CPLX-9560 explicitly contains 2 copies of MONOMER-21381. Source location `/ptools-xml/Protein[@frameid='CPLX-9560']/component[Protein/@frameid='MONOMER-21381']` MetaCyc:MONOMER-21381 Source assertion: MONOMER-21381 has reciprocal membership in CPLX-9560. Source location `/ptools-xml/Protein[@frameid='MONOMER-21381']/component-of` PMID:41140912 Source assertion: Separate purified MarH2 and Mar(DK)2 components are supported by mass photometry. Source location `/article/body/sec[2]/sec[1]/p[1]` PMID:41140912 Source assertion: Trapped one/two-dimer association and refined MarDK2H2 are distinct structural contexts. Source location `/article/body/sec[2]/sec[1]/p[4]`
methylthio-alkane reductase catalytic subunit α `MetaCyc:MONOMER-21380`	part_of Native component coefficient 2. Complete nested topology is retained; ATP-analogue-trapped docking states and the refined structural fragment are distinct contexts.	methylthio-alkane reductase catalytic component `MetaCyc:CPLX-9560`	MetaCyc:CPLX-9560 Source assertion: CPLX-9560 explicitly contains 2 copies of MONOMER-21380. Source location `/ptools-xml/Protein[@frameid='CPLX-9560']/component[Protein/@frameid='MONOMER-21380']` MetaCyc:MONOMER-21380 Source assertion: MONOMER-21380 has reciprocal membership in CPLX-9560. Source location `/ptools-xml/Protein[@frameid='MONOMER-21380']/component-of` PMID:41140912 Source assertion: Separate purified MarH2 and Mar(DK)2 components are supported by mass photometry. Source location `/article/body/sec[2]/sec[1]/p[1]` PMID:41140912 Source assertion: Trapped one/two-dimer association and refined MarDK2H2 are distinct structural contexts. Source location `/article/body/sec[2]/sec[1]/p[4]`
Methylthioribose-1-phosphate isomerase `UniProtKB:Q2RXI0` experimental construct: R. rubrum recombinant MtnA expressed in E. coli. The2020 Methods specify pET28/Rosetta(DE3)pLysS nickel purification; His10 is an older native database attribution. Exact tag orientation is unresolved. Qualification evidence PMID:31950558 Source assertion: pET28 recombinant R. rubrum proteins were expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Source location `//passage[41]` MetaCyc:MONOMER-17870 Source assertion: Native commentary attributes a His10 construct to earlier work. Source location `/ptools-xml/Protein[@frameid='MONOMER-17870']/comment`	catalyzes Substrate-specific activity; construct-qualified biochemical evidence is distinct from native physiology.	MTR1P isomerization `MetaCyc:5.3.1.23-RXN`	MetaCyc:ENZRXN-21245 Source assertion: The native activity assigns this protein to the specified reaction. Source location `/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-21245']/enzyme \| /ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-21245']/reaction` MetaCyc:ENZRXN-21245 Source assertion: Native evidence supports heterologous purified-protein activity; additional stated mutant evidence remains separate. Source location `/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-21245']/evidence` MetaCyc:MONOMER-17870 Source assertion: The native protein cross-reference identifies UniProtKB:Q2RXI0. Source location `/ptools-xml/Protein[@frameid='MONOMER-17870']/dblink` PMID:31950558 Source assertion: Table1 reports MTR1P-specific0.1s−1 and134micromolar as literature values. Source location `//passage[119]` MetaCyc:ENZRXN-21245 Source assertion: The native kinetic slots cite2012 for134micromolar and0.1s−1. Source location `/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-21245']/km \| /ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-21245']/kcat`
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase `UniProtKB:Q2RXI1` experimental construct: R. rubrum His6 Ald2 recombinantly expressed in E. coli and purified anaerobically in2017;2020 assays use pET28/Rosetta(DE3)pLysS nickel purification. Exact tag orientation and cellular metal occupancy are not established. Qualification evidence PMID:31950558 Source assertion: pET28 recombinant R. rubrum proteins were expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Source location `//passage[41]` DOI:10.1073/pnas.1711625114 Source assertion: SI Methods describe recombinant Ald2 production/purification. Source location `PDF page 2` DOI:10.1073/pnas.1711625114 Source assertion: TableS1 connects the His6-tagged pET28a vector to pET28-RuAld2. Source location `PDF page 11` MetaCyc:MONOMER-21152 Source assertion: Native commentary attributes His6 expression and anaerobic purification. Source location `/ptools-xml/Protein[@frameid='MONOMER-21152']/comment`	catalyzes Substrate-specific activity; construct-qualified biochemical evidence is distinct from native physiology.	MTRu1P aldol cleavage `MetaCyc:RXN-21318`	MetaCyc:ENZRXN-29277 Source assertion: The native activity assigns this protein to the specified reaction. Source location `/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29277']/enzyme \| /ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29277']/reaction` MetaCyc:ENZRXN-29277 Source assertion: Native evidence supports heterologous purified-protein activity; additional stated mutant evidence remains separate. Source location `/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29277']/evidence` MetaCyc:MONOMER-21152 Source assertion: The native protein cross-reference identifies UniProtKB:Q2RXI1. Source location `/ptools-xml/Protein[@frameid='MONOMER-21152']/dblink` PMID:29133429 Source assertion: Purified recombinant Ald2 cleaves MTRu1P to DHAP and methylthioacetaldehyde. Source location `/article/body/sec[1]/sec[3]/p[1]` PMID:31950558 Source assertion: Table1 reports0.94s−1 and288micromolar for R. rubrum Ald2 with MTRu1P. Source location `//passage[119]`
O-acetylhomoserine/O-acetylserine sulfhydrylase `UniProtKB:Q2RWB7` experimental construct: R. rubrum Oah recombinantly expressed in E. coli; His10 and detailed purification are native database attributions to2012, whose SI is unavailable here. Exact tag orientation is unresolved; this is not native-host purification. Qualification evidence MetaCyc:MONOMER-17873 Source assertion: His10 recombinant expression and purification are database-attributed to the2012 work. Source location `/ptools-xml/Protein[@frameid='MONOMER-17873']/comment`	catalyzes Substrate-specific activity; construct-qualified biochemical evidence is distinct from native physiology.	Methanethiol incorporation into methionine `MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN`	MetaCyc:ENZRXN-21248 Source assertion: The native activity assigns this protein to the specified reaction. Source location `/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-21248']/enzyme \| /ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-21248']/reaction` MetaCyc:ENZRXN-21248 Source assertion: Native evidence supports heterologous purified-protein activity; additional stated mutant evidence remains separate. Source location `/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-21248']/evidence` MetaCyc:MONOMER-17873 Source assertion: The native protein cross-reference identifies UniProtKB:Q2RWB7. Source location `/ptools-xml/Protein[@frameid='MONOMER-17873']/dblink` PMID:23042035 Source assertion: Heterologously expressed Rru_A0774 is methanethiol-specific O-acetylhomoserine sulfhydrylase. Source location `//passage[19]`
methylthio-alkane reductase `MetaCyc:CPLX-9562` experimental construct: R. rubrum MarBHDK expressed in engineered R. capsulatus MM0422/pMM0181: N-terminal His6 MarH and C-terminal Strep-tagII MarD. Separate MarH2 and Mar(DK)2 were combined with ATP/dithionite; native and trapped docking stoichiometries are distinct. Qualification evidence PMID:41140912 Source assertion: MarH bears an N-terminal His6 tag and MarD a C-terminal Strep-tagII. Source location `/article/body/sec[4]/sec[3]/p` PMID:41140912 Source assertion: Components were purified from engineered R. capsulatus MM0422. Source location `/article/body/sec[4]/sec[4]/p` PMID:41140912 Source assertion: Activity requires the stated reconstitution conditions. Source location `/article/body/sec[4]/sec[6]/p` DOI:10.1038/s41929-025-01426-2 Source assertion: The SI specifies MM0422 genotype andpMM0181. Source location `PDF page 7`	catalyzes Mar-dependent native sulfur assimilation is supported by deletion/complementation and radiotracing; purified2025 preparations independently catalyze MT-EtOH cleavage under ATP/dithionite conditions. Native donor and ATP stoichiometry remain unknown.	MT-EtOH reductive C–S cleavage `MetaCyc:RXN-21320`	MetaCyc:ENZRXN-29661 Source assertion: Native activity assigns CPLX9562 to RXN21320. Source location `/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29661']/enzyme \| /ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29661']/reaction` MetaCyc:ENZRXN-29661 Source assertion: Native evidence is reaction-blocked mutant support fromPMID32855335. Source location `/ptools-xml/Enzymatic-Reaction[@frameid='ENZRXN-29661']/evidence` PMID:32855335 Source assertion: Figure2 establishes native Mar-dependent MT-EtOH sulfur assimilation. Source location `PDF page 18` PMID:41140912 Source assertion: Both purified components, ATP and dithionite support MT-EtOH-to-ethylene activity. Source location `/article/body/sec[2]/sec[1]/p[2]` PMID:41140912 Source assertion: Methods retain the full activity conditions. Source location `/article/body/sec[4]/sec[6]/p`
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase `UniProtKB:Q2RXI1` molecular state: Recombinant R. rubrum Ald2 apoenzyme after EDTA dialysis, separately reconstituted for one hour with0.1mM Co2+. This is one alternative assay condition; cellular metal identity and occupancy are unresolved. Qualification evidence PMID:31950558 Source assertion: pET28 recombinant R. rubrum proteins were expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Source location `//passage[41]` PMID:31950558 Source assertion: EDTA and Chelex dialysis precede0.1mM metal incubation for one hour. Source location `//passage[54]`	has_cofactor Alternative high-activity reconstitution condition, not simultaneous Co/Ni binding or proven cellular occupancy.	cobalt(2+) `CHEBI:48828`	PMID:31950558 Source assertion: Separately reconstituted R. rubrum Ald2 gives maximal tested activities with Co2+ andNi2+. Source location `//passage[17]` PMID:31950558 Source assertion: EDTA and Chelex dialysis precede0.1mM metal incubation for one hour. Source location `//passage[54]` CHEBI:48828 Source assertion: The current issuing identity is the specified divalent ion. Source location `$.chebi_accession`
5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase `UniProtKB:Q2RXI1` molecular state: Recombinant R. rubrum Ald2 apoenzyme after EDTA dialysis, separately reconstituted for one hour with0.1mM Ni2+. This is one alternative assay condition; cellular metal identity and occupancy are unresolved. Qualification evidence PMID:31950558 Source assertion: pET28 recombinant R. rubrum proteins were expressed in E. coli Rosetta(DE3) pLysS and purified by nickel chromatography. Source location `//passage[41]` PMID:31950558 Source assertion: EDTA and Chelex dialysis precede0.1mM metal incubation for one hour. Source location `//passage[54]`	has_cofactor Alternative high-activity reconstitution condition, not simultaneous Co/Ni binding or proven cellular occupancy.	nickel(2+) `CHEBI:49786`	PMID:31950558 Source assertion: Separately reconstituted R. rubrum Ald2 gives maximal tested activities with Co2+ andNi2+. Source location `//passage[17]` PMID:31950558 Source assertion: EDTA and Chelex dialysis precede0.1mM metal incubation for one hour. Source location `//passage[54]` CHEBI:49786 Source assertion: The current issuing identity is the specified divalent ion. Source location `$.chebi_accession`
O-acetylhomoserine/O-acetylserine sulfhydrylase `UniProtKB:Q2RWB7`	has_cofactor Current UniProt PLP annotation is automated inference, not a direct R. rubrum occupancy determination or proof of a particular bound protonation state.	pyridoxal 5'-phosphate(2−) `CHEBI:597326`	UniProtKB:Q2RWB7 Source assertion: The PLP cofactor is linked toCHEBI597326 with ECO0000256 evidence. Source location `$.comments[0]` CHEBI:597326 Source assertion: ChEBI independently identifies pyridoxal5′-phosphate(2−). Source location `$.chebi_accession`
methylthio-alkane reductase reductase component dimer `MetaCyc:CPLX-9561` experimental construct: N-terminal His6-tagged R. rubrum MarH2 purified from engineered R. capsulatus MM0422. Structural samples were MgADP–AlF3-trapped; EPR samples used specified redox/ATP conditions. The generic cluster identity is not an exact redox-state assignment. Qualification evidence PMID:41140912 Source assertion: MarH bears an N-terminal His6 tag. Source location `/article/body/sec[4]/sec[3]/p` PMID:41140912 Source assertion: Cryo-EM samples were trapped with MgADP–AlF3. Source location `/article/body/sec[4]/sec[8]/p[1]` PMID:41140912 Source assertion: EPR samples have separately defined dithionite,ATP and oxidation conditions. Source location `/article/body/sec[4]/sec[11]/p[3]`	has_cofactor One interfacial[4Fe4S] cluster per MarH2 dimer is supported in the2025 preparation. The generic cluster identity does not fix its experimental redox state.	tetra-μ3-sulfido-tetrairon `CHEBI:49883`	PMID:41140912 Source assertion: MarH2 coordinates one[Fe4S4]cluster through residues from both chains. Source location `/article/body/sec[2]/sec[2]/p` PMID:41140912 Source assertion: EPR characterizes the reduced MarH2 cluster and ATP dependence. Source location `/article/body/sec[2]/sec[6]/p` UniProtKB:Q2RW96 Source assertion: Current UniProt linksCHEBI49883 and describes one cluster per dimer by similarity; that tier is separate from2025 experiments. Source location `$.comments[4]`

References

MetaCyc:5.3.1.23-RXN MetaCyc:5.3.1.23-RXN (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN MetaCyc:O-ACETYLHOMOSERINE-THIOL-LYASE-RXN (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:PWY-8132 S-methyl-5-thio-α-D-ribose 1-phosphate degradation III (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:RXN-21318 MetaCyc:RXN-21318 (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:RXN-21319 MetaCyc:RXN-21319 (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:RXN-21320 MetaCyc:RXN-21320 (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ACET acetate (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPD-1063 S-methyl-5-thio-D-ribulose 1-phosphate (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPD-23221 (2-methylsulfanyl)acetaldehyde (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPD-444 S-methyl-5-thio-α-D-ribose 1-phosphate (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPD-667 O-acetyl-L-homoserine (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPD-7671 methanethiol (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPD-7677 (2-methylsulfanyl)ethanol (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:DIHYDROXY-ACETONE-PHOSPHATE glycerone phosphate (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ENZRXN-1502 5-methylthioribose-1-phosphate isomerase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ENZRXN-18754 O-acetyl-L-homoserine sulfhydrylase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ENZRXN-21245 methylthioribose-1-phosphate isomerase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ENZRXN-21248 O-acetylhomoserine aminocarboxypropyltransferase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ENZRXN-29277 5-(methyltsulfanyl)ribulose-1-phosphate aldolase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ENZRXN-29283 methylthioribose-1-phosphate isomerase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ENZRXN-29286 5-(methylsulfanyl)-ribulose 1-phosphate aldolase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ENZRXN-29661 (2-methylsulfanyl)ethanol reductase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ENZRXNQT-13272 5-methylthioribose-1-phosphate isomerase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:ETHYLENE-CMPD ethene (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:MET L-methionine (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:NAD NAD+ (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:NADH NADH (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:Oxidized-ferredoxins an oxidized ferredoxin [iron-sulfur] cluster (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:PROTON H+ (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:Reduced-ferredoxins a reduced ferredoxin [iron-sulfur] cluster (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:WATER H2O (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:AT2G05830-MONOMER 5-methylthioribose-1-phosphate isomerase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPLX-1182 5-methylthioribose-1-phosphate isomerase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPLX-8242 MetaCyc:CPLX-8242 (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPLX-9562 methylthio-alkane reductase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:MONOMER-17870 methylthioribose-1-phosphate isomerase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:MONOMER-17873 O-acetylhomoserine aminocarboxypropyltransferase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:MONOMER-21152 5-(methylthio)ribulose-1-phosphate aldolase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:MONOMER-21153 MetaCyc:MONOMER-21153 (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:MONOMER-21154 methylthioribose-1-phosphate isomerase (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:AT2G05830 MTI1 (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPLX-9560 methylthio-alkane reductase catalytic component (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:CPLX-9561 methylthio-alkane reductase reductase component dimer (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:G-15512 mtnA (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:G-15515 oah (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:G-80668 ald2 (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:G-80669 ald2 (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:G-80670 mtnA (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:MONOMER-1341 5-methylthioribose-1-phosphate isomerase monomer (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:MONOMER-16245 O-acetyl-L-homoserine sulfhydrylase monomer (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
UniProtKB:Q2RWB7 O-acetylhomoserine/O-acetylserine sulfhydrylase (source version: UniProtKB unreviewed (TrEMBL); entry version 108, sequence version 1, annotation update 2026-09-02. Whole sequence and evidence codes retained.)
MetaCyc:MONOMER-21380 methylthio-alkane reductase catalytic subunit α (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:MONOMER-21381 methylthio-alkane reductase catalytic subunit β (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:MONOMER-21382 methylthio-alkane reductase reductase component (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
CHEBI:141184 (methylsulfanyl)acetaldehyde (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:15377 water (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:15378 hydron (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:16007 methanethiol (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:18153 ethene (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:30089 acetate (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:57540 NAD(1−) (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:57642 glycerone phosphate(2−) (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:57716 O-acetyl-L-homoserine zwitterion (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:57844 L-methionine zwitterion (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:57945 NADH(2−) (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:58533 S-methyl-5-thio-α-D-ribose 1-phosphate(2−) (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:58548 S-methyl-5-thio-D-ribulose 1-phosphate(2−) (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:63861 2-methylthioethanol (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
MetaCyc:G-80900 marD (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:G-80901 marK (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
MetaCyc:G-80902 marH (source version: MetaCyc 27.0 full Pathway Tools XML, META PGDB, INSA Lyon mirror. Whole types, context and evidence slots retained.)
NCBITaxon:1085 Rhodospirillum rubrum (source version: Complete original retrieved 2026-10-12; exact metadata and acquisition lineage retained.)
NCBITaxon:269796 Rhodospirillum rubrum ATCC 11170 (source version: Complete original retrieved 2026-10-12; exact metadata and acquisition lineage retained.)
UniProtKB:Q2RW96 Methylthio-alkane reductase iron protein (source version: UniProtKB reviewed (Swiss-Prot); entry version 125, sequence version 1, annotation update 2026-09-02. Whole sequence and evidence codes retained.)
UniProtKB:Q2RW97 Methylthio-alkane reductase catalytic subunit alpha (source version: UniProtKB reviewed (Swiss-Prot); entry version 97, sequence version 1, annotation update 2026-09-02. Whole sequence and evidence codes retained.)
UniProtKB:Q2RW98 Methylthio-alkane reductase catalytic subunit beta (source version: UniProtKB reviewed (Swiss-Prot); entry version 92, sequence version 1, annotation update 2026-09-02. Whole sequence and evidence codes retained.)
CHEBI:49883 tetra-μ3-sulfido-tetrairon (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:597326 pyridoxal 5'-phosphate(2−) (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
NCBITaxon:1076 Rhodopseudomonas palustris (source version: Complete original retrieved 2026-10-12; exact metadata and acquisition lineage retained.)
CHEBI:17513 reduced ferredoxin (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:17908 oxidized ferredoxin (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
UniProtKB:Q2RXI0 Methylthioribose-1-phosphate isomerase (source version: UniProtKB reviewed (Swiss-Prot); entry version 115, sequence version 1, annotation update 2026-09-02. Whole sequence and evidence codes retained.)
UniProtKB:Q2RXI1 5-methylthioribulose-1-phosphate/5-deoxyribulose-1-phosphate aldolase (source version: UniProtKB reviewed (Swiss-Prot); entry version 99, sequence version 1, annotation update 2026-09-02. Whole sequence and evidence codes retained.)
CHEBI:48828 cobalt(2+) (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
CHEBI:49786 nickel(2+) (source version: ChEBI complete released entry JSON acquired 2026-10-12. Chemical structure, charge and generic-class status retained; no ontology release upgrade.)
PMID:29133429 Microbial pathway for anaerobic 5′-methylthioadenosine metabolism coupled to ethylene formation. (source version: PNAS 2017;114:E10455–E10464, DOI 10.1073/pnas.1711625114. Complete primary JATS XML; available main figures and SI separately retained.)
PMID:29636438 Two Distinct Aerobic Methionine Salvage Pathways Generate Volatile Methanethiol in Rhodopseudomonas palustris. (source version: mBio 2018;9:e00407-18, DOI 10.1128/mBio.00407-18. Complete JATS primary text, methods, tables and captions; original supplemental bodies not acquired here.)
PMID:41140912 Methylthio-alkane reductases use nitrogenase metalloclusters for carbon–sulfur bond cleavage. (source version: Nature Catalysis 2025, DOI 10.1038/s41929-025-01426-2. Complete JATS main/method/extended-caption original; supplementary originals and figures separately retained.)
PMID:32855335 A nitrogenase-like enzyme system catalyzes methionine, ethylene, and methane biogenesis. (source version: Science 2020;369:1094–1098, DOI 10.1126/science.abb6310. Complete 54-page OSTI manuscript PDF including supporting text, figures and Table S1; external spreadsheets/databases not acquired.)
PMID:23042035 A RubisCO-like protein links SAM metabolism with isoprenoid biosynthesis. (source version: Nat Chem Biol 2012;8:926–932, DOI 10.1038/nchembio.1087. Complete NCBI BioC main text, 91 passages. Original figure bodies and SI unavailable through previously tested routes; prior full reading explicitly inherited.)
PMID:31950558 A bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coli. (source version: Mol Microbiol 2020;113:923–937, DOI 10.1111/mmi.14459. Complete NCBI BioC main text,122 passages, Table1 and captions. Full prior reading inherited; selected kinetic and scope passages reread. Original figures/SI inaccessible through tested routes.)
DOI:10.1073/pnas.1711625114 Supplementary information to Microbial pathway for anaerobic 5′-methylthioadenosine metabolism coupled to ethylene formation. (source version: Complete original PDF member extracted from the retained publisher/PMC supplementary ZIP; member bytes and full archive acquisition lineage bound.)
DOI:10.1038/s41929-025-01426-2 Supplementary information to Methylthio-alkane reductases use nitrogenase metalloclusters for carbon–sulfur bond cleavage. (source version: Complete original PDF member extracted from the retained publisher/PMC supplementary ZIP; member bytes and full archive acquisition lineage bound.)

Curation history

2026-10-12T23:03:48Z codex
- CREATE — Add complete evidence-backed S-methyl-5-thio-alpha-D-ribose 1-phosphate degradation III.
  Exact accepted MetaCyc:PWY-8132:21 paragraphs,44 edges,7 qualifications,38 IDs,93 references and20 mappings; all five events,22 sides and whole Mar nested assembly retained. Formal ferredoxin chemistry does not identify physiological donor or ATP stoichiometry; native R2L reduction lacks a named cellular catalyst. Construct/kinetic/source limits and98 whole scientific originals remain in research/pathway_additions/2026-10-12-next-239. Actual maintained gates/native review remain pending.
Read this curation session