Spermidine Biosynthesis and Metabolism

PathBank:SMP0002097

This record represents the complete current PathBank SMP0002097 map for Escherichia coli, not just its two spermidine-producing reactions. SpeD decarboxylates S-adenosyl-L-methionine (SAM); SpeE transfers the resulting aminopropyl group to putrescine to make spermidine and 5′-methylthioadenosine (MTA); Pfs/MtnN hydrolyzes MTA to adenine and methylthioribose (MTR). The current map also includes ATP-dependent glutathionylspermidine (Gsp) formation by Gss and cytosol-to-periplasm MTR transport. All four chemical reactions, the transport and their 22 explicit stoichiometric sides are retained. A separately represented SAM-biosynthesis interface is a source pathway connection, not a sixth resolved chemical equation. The map's native organism is species-level E. coli (NCBITaxon:562). Its four reviewed protein accessions refer to E. coli K-12 (NCBITaxon:83333), which does not demonstrate every reaction or physiological outcome in every derivative. PWML assigns the Gss chain to K-12 but its complex to species element 346, labelled E. coli K-12 while carrying taxon 679895. Current NCBI identifies 679895 as E. coli BW25113, a descendant of K-12; this native label/identifier conflict is preserved rather than silently reassigned. The Gss biochemical work uses recombinant expression and several cellular strains, not a whole-route validation in BW25113. The older archived PW002085 BioPAX contains the SpeD, SpeE, Pfs and transport branch but lacks the current Gss branch and SAM interface. The current whole download adds 69 native objects and changes pathway membership while preserving the older event definitions. PathBank's HTML/PWML narrative still describes the older three-enzyme route. Current membership and explicit equation slots take precedence for the scope of this record, while the archive and narrative disagreement remain documented. This is distinct from the existing yeast spermidine-biosynthesis-I record and from the bacterial SAM cycle, although substrates and Pfs are shared. SpeD/P0A7F6 is a 264-residue proenzyme that undergoes nonhydrolytic cleavage between Lys111 and Ser112, yielding beta residues 1–111 and alpha residues 112–264; Ser112 gives the covalently attached pyruvoyl group required for catalysis. The 1987 processing abstract (PMID:3316212) describes pulse-chase precursor/product evidence, and PMID:3546296 supports four alpha/beta pairs with one pyruvoyl per pair. PathBank instead encodes eight copies of a protein explicitly named proenzyme in complex 3895. That native coefficient is retained as an annotation with an unresolved precursor-versus-processed-chain mismatch, not asserted as eight active precursor molecules. The older 1982 abstract's six-subunit description is separately retained as historical conflicting evidence. PWML lists pyruvic acid and magnesium as SpeD cofactors without coefficients. Free pyruvic acid (CHEBI:32816) is chemically distinct from the covalent pyruvoyl substituent (CHEBI:45360); the mechanistic cofactor edge represents the latter and explicitly qualifies the mature molecular state. Mg2+ activates the studied E. coli enzyme, but 2007 assays also report activation by several alternative cations and salt-dependent cooperativity. These are alternative experimental activation conditions, not simultaneous metal requirements or direct proof of the cellular metal. Native magnesium's unrelated BioCyc 13-HYDROXY-MAGNESIUM-PROTOPORP cross-reference is rejected; its Mg2+ structure agrees with current CHEBI:18420. The complete 1986 speE/speD paper, including all five scanned pages, reports linked gene deletions, complementation and separate overexpression. A 1795-bp insert restores both measured activities, and deleting upstream sequence lowers both unless an external T7 promoter supplies transcription. Its note added in proof identifies the SpeE N-terminal sequence with the predicted gene product. This supports the biochemical entry module in the tested strains and constructs. The paper explicitly says deficient cells still grow on purified medium and does not establish universal spermidine essentiality or a new Gss/transport phenotype. SpeE/P09158 catalyzes aminopropyl transfer from decarboxylated SAM to putrescine. PathBank complex 3896 contains two SpeE chains; the 2010 structural-paper abstract reports a dimer in crystal and solution. Current UniProt names the protein polyamine aminopropyltransferase and annotates additional amine substrates, which are outside this exact map. Its Michaelis-constant annotation labels two donor entries S-adenosylmethionine even though the catalytic equation uses decarboxylated SAM; those ambiguous donor values are preserved in the kinetic ledger and are not silently relabelled or propagated as pathway-substrate constants. Pfs/MtnN/P0AF12 is assigned as a homodimer in PathBank complex 3419. Reviewed annotation and the 1998 cloning abstract support irreversible glycosidic cleavage of MTA; the distinct SAH and 5′-deoxyadenosine activities belong to adjacent pathways. The 1996 recombinant study's abstract distinguishes the full-length enzyme from an engineered N-terminal eight-residue deletion with altered MTA affinity; the truncation is not substituted for the native chain. The retained current sequence is 232 residues, and an old sequence-start caution remains separate from its current identity. Annotation-derived MTA kinetic values from different temperatures and references are assay-specific and do not establish cellular flux. The Gss reaction joins the glycine carboxyl group of reduced glutathione to spermidine's N1 aminopropyl terminal amino group while ATP is converted to ADP and phosphate. PathBank's equation is an ATP-dependent synthetase reaction, despite its native reaction label and enzyme-class slot being the amidase EC 3.5.1.78. The chain's PWML/UniProt records also list synthetase EC 6.3.1.8. The graph retains the native reaction identifier and written direction with a chemically descriptive label, without promoting the inconsistent amidase label to synthetase identity. The same bifunctional protein hydrolyzes Gsp through a separate amidase activity; this does not reverse ATP-dependent synthesis or regenerate ATP. The complete 2006 primary paper reports a dimeric 619-residue Gss structure with N-terminal amidase residues 1–195, a 196–205 linker and C-terminal synthetase residues 206–619. Its main text describes analytical ultracentrifugation near 138 kDa and a roughly 70-kDa polypeptide, but the cited supporting measurement itself was not acquired. The reported two-subunit complex agrees with PathBank's coefficient. Crystal structures reveal Mg2+-associated nucleotide binding and an ATP-grasp catalytic domain. GSH acylphosphate formation followed by spermidine attack is the proposed chemical mechanism; movement between two GSH sites is a mechanistic proposal, with direct binding at the productive site not excluded. Trapped Cys338–GSH disulfide and Lys607-linked material at crystallization pH are not obligatory catalytic intermediates. Experimental preparations remain distinct. The 2006 crystallographic protein was expressed in E. coli BL21(DE3) from the supplied plasmid and purified using cited earlier procedures; the accessible Methods do not establish its exact tag. The same paper explicitly describes pET28a N-terminal His6 constructs for the kinetic/mutant work. The 2010 study uses full-length GspSA and a separately expressed 1–197 amidase fragment; its fragment crystal is not a full-length native enzyme. The Gss magnesium edge therefore describes the synthetase structural/assay context without assigning a metal requirement to the amidase domain or inferring native-host metal occupancy. The 2006 Table 1 gives wild-type Gss apparent Km values of 218 ± 12 micromolar for GSH and 76 ± 1 micromolar for spermidine, with kcat 4.35 ± 0.30 s−1 under its coupled assay and saturating other substrates. The ten mutant rows, including the inactive R316E row, are separate constructs, not additional wild-type constants. Older UniProt kinetic annotations include different pH-dependent substrate values and synthetase/amidase turnover values attributed to 1995. Those older numbers are retained as annotation-tier evidence because the complete 1995 paper was not read. No numerical value is assigned to a PMID merely because that paper appears in a combined citation list. The complete 2010 paper supports selective oxidative inhibition of Gss amidase activity through Cys59 sulfenic-acid formation, while synthetase activity is relatively preserved under the tested peroxide conditions. It proposes a Gsp-linked protein-thiolation/redox cycle. Its Results state that the single gspSA deletion had viability similar to wild type in the tested comparison, whereas glutaredoxin/gspSA double mutants showed greater peroxide sensitivity. This narrower result is retained despite broader abstract wording. These findings explain adjacent Gsp physiology; the record does not expand the native four-reaction map into an unassigned redox or trypanothione pathway. PathBank transport 511 explicitly moves its MTR state from cytosol to periplasm and is marked nonspontaneous, but supplies no transporter, energy-coupling reaction or transport mechanism. The available 2006 export abstract (PMID:16788729) studies plasmid-directed coliphage-T3 SAM hydrolase, radiolabelled methionine and metK mutants, reporting enhanced extracellular MTR. It supports export in that experimental context, not a measured periplasmic step, identified transporter, universal lack of methionine salvage, or native whole-pathway flux in all E. coli strains. Its publisher full text remained inaccessible. The 1973 production citation has metadata only and is not used as mechanistic evidence. The source distinguishes unlocalized and cytosolic spermidine/SAM/MTR instances, and cytosolic from periplasmic MTR. These native states remain distinct. Connections between a produced unlocalized metabolite and a later cytosolic pool are explicit curation inferences of pathway continuity, not measured translocation or substrate channeling. The SAM interface has an output-marked cytosolic SAM state and generic Interaction 553236, with no enzyme or complete chemical sides; it is represented as a pathway interface and does not import the entire adjacent SAM-biosynthesis pathway. Chemical identities are checked against complete current ChEBI originals and the full native structures. MTA is stereo-unspecified in PathBank, so it is not exactly equated to stereospecific CHEBI:17509. Native MTR is cyclic and stereospecified, whereas current CHEBI:16895 explicitly depicts an open-chain structure; no exact mapping is made. Native phosphate has phosphoric-acid structure/formula but a phosphate(3−) cross-reference, so its source identity is retained with the contradiction. Reduced GSH agrees with CHEBI:16856 and conflicts with the source's OXIDIZED-GLUTATHIONE cross-reference. Native Gsp uses an imidic tautomer depiction; full InChI comparisons, rather than names alone, govern any chemical mapping. Source equations mix their own protonation conventions; no exact Rhea normalization or atom-balanced physiological equation is inferred. The complete 2009 physiological paper studied the specifically constructed HT765 strain with eight biosynthetic-gene deletions and a thiamine-prototrophy selection. It grew indefinitely in air without added polyamines at a reduced rate, remained sensitive to oxygen stress, and showed strong early anaerobic growth impairment. The main text also records anaerobic growth after several days, possibly following a bypass change. These conditions contradict a blanket assertion that spermidine is essential for all E. coli growth; they do not disprove the recorded enzyme reactions. Evidence coverage comprises complete main-text reading of the 2006 Gss, 2010 redox and 2009 physiology articles, all 19 corresponding figure images, and all five scanned pages of the 1986 speE/speD paper. Other primary articles are limited to the complete available abstracts or metadata, explicitly identified in their references. Two supplementary-file attempts returned HTML download challenges rather than scientific files; no supporting-file contents are claimed. The whole current BioPAX, relevant complete PWML biological frames, all four current UniProt scientific frames and current ChEBI/taxon identities were inspected. Independent scientific review, authority integration, native validation and public-release licensing remain later decisions.

Pathway type

polyamine biosynthesis and metabolism

Organism scope

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Pathway network

44 nodes · 58 asserted directed edges

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Escherichia coli `NCBITaxon:562`	taxon
Escherichia coli K-12 `NCBITaxon:83333`	taxon
Escherichia coli BW25113 `NCBITaxon:679895`	taxon
Spermidine `PathBank:SMP0002097/Compound/PW_C000971`	small molecule
5-Methylthioribose `PathBank:SMP0002097/Compound/PW_C000855`	small molecule
Adenine `PathBank:SMP0002097/Compound/PW_C000024`	small molecule
Hydrogen Ion `PathBank:SMP0002097/Compound/PW_C040034`	small molecule
Glutathione `PathBank:SMP0002097/Compound/PW_C000080_Cytosol`	small molecule
Hydrogen Ion `PathBank:SMP0002097/Compound/PW_C040034_Cytosol`	small molecule
Adenosine triphosphate `PathBank:SMP0002097/Compound/PW_C000414_Cytosol`	small molecule
Glutathionylspermidine `PathBank:SMP0002097/Compound/PW_C041211_Cytosol`	small molecule
Water `PathBank:SMP0002097/Compound/PW_C001420`	small molecule
5-Methylthioribose `PathBank:SMP0002097/Compound/PW_C000855_Periplasmic_Space`	small molecule
S-Adenosylmethionine `PathBank:SMP0002097/Compound/PW_C000921_Cytosol`	small molecule
Adenosine diphosphate `PathBank:SMP0002097/Compound/PW_C001034_Cytosol`	small molecule
Putrescine `PathBank:SMP0002097/Compound/PW_C001092`	small molecule
5'-S-methyl-5'-thioadenosine `PathBank:SMP0002097/Compound/PW_C042677`	small molecule
5-Methylthioribose `PathBank:SMP0002097/Compound/PW_C000855_Cytosol`	small molecule
S-Adenosylmethioninamine `PathBank:SMP0002097/Compound/PW_C000783`	small molecule
S-Adenosylmethionine `PathBank:SMP0002097/Compound/PW_C000921`	small molecule
Phosphate `PathBank:SMP0002097/Compound/PW_C001104_Cytosol`	small molecule
Spermidine `PathBank:SMP0002097/Compound/PW_C000971_Cytosol`	small molecule
Carbon dioxide `PathBank:SMP0002097/Compound/PW_C001316`	small molecule
adenosylmethionine decarboxylase `PathBank:SMP0002097/ProteinComplex/3895`	complex
Spermidine synthase `PathBank:SMP0002097/ProteinComplex/3896`	complex
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase `PathBank:SMP0002097/ProteinComplex/3419`	complex
Bifunctional glutathionylspermidine synthetase/amidase `PathBank:SMP0002097/ProteinComplex/416967_Cytosol`	complex
S-adenosylmethionine decarboxylase proenzyme `UniProtKB:P0A7F6`	protein
Polyamine aminopropyltransferase `UniProtKB:P09158`	protein
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase `UniProtKB:P0AF12`	protein
Bifunctional glutathionylspermidine synthetase/amidase `UniProtKB:P0AES0`	protein
pyruvoyl group `CHEBI:45360`	cofactor
magnesium(2+) `CHEBI:18420`	cofactor
Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	cellular component
Periplasmic Space `PathBank:SMP0002097/CellularLocation/Periplasmic_Space`	cellular component
S-Adenosyl-L-Methionine Biosynthesis `PathBank:SMP0000857`	pathway
SAM decarboxylation `PathBank:SMP0002097/Reactions/5165`	molecular activity	left to right
Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	molecular activity	left to right
MTA hydrolysis to adenine and methylthioribose `PathBank:SMP0002097/Reactions/5167`	molecular activity	left to right
ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	molecular activity	left to right
Methylthioribose transport from cytosol to periplasm `PathBank:SMP0002097/Transports/511`	molecular activity	left to right
SAM-biosynthesis pathway interface (unresolved chemical event) `PathBank:SMP0002097/SubPathwayInteractions/553236`	molecular activity

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
SAM decarboxylation `PathBank:SMP0002097/Reactions/5165`	part_of Explicit native pathway membership; transport is retained alongside all four chemical events.	`PathBank:SMP0002097`	PathBank:SMP0002097 Source assertion: Reactions/5165 is an explicit component of SMP0002097. Source location `/rdf:RDF/*[@rdf:about='http://identifiers.org/smpdb/SMP0002097']/bp:pathwayComponent[@rdf:resource='#Reactions/5165']`
Hydrogen Ion `PathBank:SMP0002097/Compound/PW_C040034`	consumes One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	SAM decarboxylation `PathBank:SMP0002097/Reactions/5165`	PathBank:SMP0002097 Source assertion: Hydrogen Ion is a left participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5165']/bp:left[1]` PathBank:SMP0002097 Source assertion:* Compound/PW_C040034 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C040034/Stoichiometry/1.0']`
S-Adenosylmethionine `PathBank:SMP0002097/Compound/PW_C000921`	consumes One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	SAM decarboxylation `PathBank:SMP0002097/Reactions/5165`	PathBank:SMP0002097 Source assertion: S-Adenosylmethionine is a left participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5165']/bp:left[2]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000921 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000921/Stoichiometry/1.0']`
SAM decarboxylation `PathBank:SMP0002097/Reactions/5165`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	S-Adenosylmethioninamine `PathBank:SMP0002097/Compound/PW_C000783`	PathBank:SMP0002097 Source assertion: S-Adenosylmethioninamine is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5165']/bp:right[1]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000783 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000783/Stoichiometry/1.0']`
SAM decarboxylation `PathBank:SMP0002097/Reactions/5165`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Carbon dioxide `PathBank:SMP0002097/Compound/PW_C001316`	PathBank:SMP0002097 Source assertion: Carbon dioxide is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5165']/bp:right[2]` PathBank:SMP0002097 Source assertion:* Compound/PW_C001316 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C001316/Stoichiometry/1.0']`
Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	part_of Explicit native pathway membership; transport is retained alongside all four chemical events.	`PathBank:SMP0002097`	PathBank:SMP0002097 Source assertion: Reactions/5166 is an explicit component of SMP0002097. Source location `/rdf:RDF/*[@rdf:about='http://identifiers.org/smpdb/SMP0002097']/bp:pathwayComponent[@rdf:resource='#Reactions/5166']`
S-Adenosylmethioninamine `PathBank:SMP0002097/Compound/PW_C000783`	consumes One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	PathBank:SMP0002097 Source assertion: S-Adenosylmethioninamine is a left participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5166']/bp:left[1]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000783 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000783/Stoichiometry/1.0']`
Putrescine `PathBank:SMP0002097/Compound/PW_C001092`	consumes One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	PathBank:SMP0002097 Source assertion: Putrescine is a left participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5166']/bp:left[2]` PathBank:SMP0002097 Source assertion:* Compound/PW_C001092 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C001092/Stoichiometry/1.0']`
Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	5'-S-methyl-5'-thioadenosine `PathBank:SMP0002097/Compound/PW_C042677`	PathBank:SMP0002097 Source assertion: 5'-S-methyl-5'-thioadenosine is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5166']/bp:right[1]` PathBank:SMP0002097 Source assertion:* Compound/PW_C042677 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C042677/Stoichiometry/1.0']`
Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Hydrogen Ion `PathBank:SMP0002097/Compound/PW_C040034`	PathBank:SMP0002097 Source assertion: Hydrogen Ion is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5166']/bp:right[2]` PathBank:SMP0002097 Source assertion:* Compound/PW_C040034 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C040034/Stoichiometry/1.0']`
Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Spermidine `PathBank:SMP0002097/Compound/PW_C000971`	PathBank:SMP0002097 Source assertion: Spermidine is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5166']/bp:right[3]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000971 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000971/Stoichiometry/1.0']`
MTA hydrolysis to adenine and methylthioribose `PathBank:SMP0002097/Reactions/5167`	part_of Explicit native pathway membership; transport is retained alongside all four chemical events.	`PathBank:SMP0002097`	PathBank:SMP0002097 Source assertion: Reactions/5167 is an explicit component of SMP0002097. Source location `/rdf:RDF/*[@rdf:about='http://identifiers.org/smpdb/SMP0002097']/bp:pathwayComponent[@rdf:resource='#Reactions/5167']`
5'-S-methyl-5'-thioadenosine `PathBank:SMP0002097/Compound/PW_C042677`	consumes One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	MTA hydrolysis to adenine and methylthioribose `PathBank:SMP0002097/Reactions/5167`	PathBank:SMP0002097 Source assertion: 5'-S-methyl-5'-thioadenosine is a left participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5167']/bp:left[1]` PathBank:SMP0002097 Source assertion:* Compound/PW_C042677 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C042677/Stoichiometry/1.0']`
Water `PathBank:SMP0002097/Compound/PW_C001420`	consumes One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	MTA hydrolysis to adenine and methylthioribose `PathBank:SMP0002097/Reactions/5167`	PathBank:SMP0002097 Source assertion: Water is a left participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5167']/bp:left[2]` PathBank:SMP0002097 Source assertion:* Compound/PW_C001420 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C001420/Stoichiometry/1.0']`
MTA hydrolysis to adenine and methylthioribose `PathBank:SMP0002097/Reactions/5167`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Adenine `PathBank:SMP0002097/Compound/PW_C000024`	PathBank:SMP0002097 Source assertion: Adenine is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5167']/bp:right[1]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000024 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000024/Stoichiometry/1.0']`
MTA hydrolysis to adenine and methylthioribose `PathBank:SMP0002097/Reactions/5167`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	5-Methylthioribose `PathBank:SMP0002097/Compound/PW_C000855`	PathBank:SMP0002097 Source assertion: 5-Methylthioribose is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/5167']/bp:right[2]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000855 has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000855/Stoichiometry/1.0']`
ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	part_of Explicit native pathway membership; transport is retained alongside all four chemical events.	`PathBank:SMP0002097`	PathBank:SMP0002097 Source assertion: Reactions/1960116 is an explicit component of SMP0002097. Source location `/rdf:RDF/*[@rdf:about='http://identifiers.org/smpdb/SMP0002097']/bp:pathwayComponent[@rdf:resource='#Reactions/1960116']`
Glutathione `PathBank:SMP0002097/Compound/PW_C000080_Cytosol`	consumes One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	PathBank:SMP0002097 Source assertion: Glutathione is a left participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/1960116']/bp:left[1]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000080_Cytosol has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000080_Cytosol/Stoichiometry/1.0']`
Adenosine triphosphate `PathBank:SMP0002097/Compound/PW_C000414_Cytosol`	consumes One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	PathBank:SMP0002097 Source assertion: Adenosine triphosphate is a left participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/1960116']/bp:left[2]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000414_Cytosol has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000414_Cytosol/Stoichiometry/1.0']`
Spermidine `PathBank:SMP0002097/Compound/PW_C000971_Cytosol`	consumes One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	PathBank:SMP0002097 Source assertion: Spermidine is a left participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/1960116']/bp:left[3]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000971_Cytosol has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000971_Cytosol/Stoichiometry/1.0']`
ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Phosphate `PathBank:SMP0002097/Compound/PW_C001104_Cytosol`	PathBank:SMP0002097 Source assertion: Phosphate is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/1960116']/bp:right[1]` PathBank:SMP0002097 Source assertion:* Compound/PW_C001104_Cytosol has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C001104_Cytosol/Stoichiometry/1.0']`
ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Adenosine diphosphate `PathBank:SMP0002097/Compound/PW_C001034_Cytosol`	PathBank:SMP0002097 Source assertion: Adenosine diphosphate is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/1960116']/bp:right[2]` PathBank:SMP0002097 Source assertion:* Compound/PW_C001034_Cytosol has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C001034_Cytosol/Stoichiometry/1.0']`
ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Hydrogen Ion `PathBank:SMP0002097/Compound/PW_C040034_Cytosol`	PathBank:SMP0002097 Source assertion: Hydrogen Ion is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/1960116']/bp:right[3]` PathBank:SMP0002097 Source assertion:* Compound/PW_C040034_Cytosol has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C040034_Cytosol/Stoichiometry/1.0']`
ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Glutathionylspermidine `PathBank:SMP0002097/Compound/PW_C041211_Cytosol`	PathBank:SMP0002097 Source assertion: Glutathionylspermidine is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Reactions/1960116']/bp:right[4]` PathBank:SMP0002097 Source assertion:* Compound/PW_C041211_Cytosol has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C041211_Cytosol/Stoichiometry/1.0']`
Methylthioribose transport from cytosol to periplasm `PathBank:SMP0002097/Transports/511`	part_of Explicit native pathway membership; transport is retained alongside all four chemical events.	`PathBank:SMP0002097`	PathBank:SMP0002097 Source assertion: Transports/511 is an explicit component of SMP0002097. Source location `/rdf:RDF/*[@rdf:about='http://identifiers.org/smpdb/SMP0002097']/bp:pathwayComponent[@rdf:resource='#Transports/511']`
5-Methylthioribose `PathBank:SMP0002097/Compound/PW_C000855_Cytosol`	consumes One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	Methylthioribose transport from cytosol to periplasm `PathBank:SMP0002097/Transports/511`	PathBank:SMP0002097 Source assertion: 5-Methylthioribose is a left participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Transports/511']/bp:left[1]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000855_Cytosol has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000855_Cytosol/Stoichiometry/1.0']`
Methylthioribose transport from cytosol to periplasm `PathBank:SMP0002097/Transports/511`	produces One native stoichiometric occurrence. Native chemical state and written protonation are retained; no normalized physiological balance is asserted.	5-Methylthioribose `PathBank:SMP0002097/Compound/PW_C000855_Periplasmic_Space`	PathBank:SMP0002097 Source assertion: 5-Methylthioribose is a right participant of the native written LEFT_TO_RIGHT event. Source location `/rdf:RDF/[@rdf:ID='Transports/511']/bp:right[1]` PathBank:SMP0002097 Source assertion:* Compound/PW_C000855_Periplasmic_Space has explicit stoichiometric coefficient 1.0. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000855_Periplasmic_Space/Stoichiometry/1.0']`
S-adenosylmethionine decarboxylase proenzyme `UniProtKB:P0A7F6`	part_of The source records 8 copies of the indicated protein component. This preserves the source annotation only: the native precursor label/coefficient conflicts with four processed alpha/beta pairs and is not an assertion of eight active proenzymes.	adenosylmethionine decarboxylase `PathBank:SMP0002097/ProteinComplex/3895`	PathBank:SMP0002097 Source assertion: Protein/6056 is the native component of ProteinComplex/3895. Source location `/rdf:RDF/[@rdf:ID='ProteinComplex/3895']/bp:component` PathBank:SMP0002097 Source assertion:* Native component coefficient is 8; the protein reference identifies UniProt P0A7F6. Source location `/rdf:RDF/[@rdf:ID='Protein/6056/Stoichiometry/8.0']` UniProtKB:P0A7F6 Source assertion:* The reviewed SUBUNIT annotation states four alpha and four beta chains, supported by PMID 3546296; this is distinct from eight complete precursors. Source location `$.comments[6]`
adenosylmethionine decarboxylase `PathBank:SMP0002097/ProteinComplex/3895` molecular state: Catalytically mature SpeD with a covalent pyruvoyl group formed at Ser112 after Lys111–Ser112 cleavage. Native complex membership encodes eight precursors; that conflicting coefficient is preserved separately, not interpreted as the mature assembly. Qualification evidence UniProtKB:P0A7F6 Source assertion: Autocatalytic cleavage generates the alpha-chain N-terminal pyruvoyl group; the unprocessed chain is the precursor. Source location `$.comments[7]`	catalyzes Native complex catalysis assignment. Reviewed protein evidence supports chemistry; conflicting native labels and preparation scope remain explicit in the description.	SAM decarboxylation `PathBank:SMP0002097/Reactions/5165`	PathBank:SMP0002097 Source assertion: ProteinComplex/3895 is the controller of Reactions/5165; the control type is ACTIVATION within a native Catalysis object. Source location `/rdf:RDF/*[@rdf:ID='ReactionCatalysis/5136']`
Polyamine aminopropyltransferase `UniProtKB:P09158`	part_of The source records 2 copies of the indicated protein component.	Spermidine synthase `PathBank:SMP0002097/ProteinComplex/3896`	PathBank:SMP0002097 Source assertion: Protein/5967 is the native component of ProteinComplex/3896. Source location `/rdf:RDF/[@rdf:ID='ProteinComplex/3896']/bp:component` PathBank:SMP0002097 Source assertion:* Native component coefficient is 2; the protein reference identifies UniProt P09158. Source location `/rdf:RDF/*[@rdf:ID='Protein/5967/Stoichiometry/2.0']`
Spermidine synthase `PathBank:SMP0002097/ProteinComplex/3896`	catalyzes Native complex catalysis assignment. Reviewed protein evidence supports chemistry; conflicting native labels and preparation scope remain explicit in the description.	Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	PathBank:SMP0002097 Source assertion: ProteinComplex/3896 is the controller of Reactions/5166; the control type is ACTIVATION within a native Catalysis object. Source location `/rdf:RDF/*[@rdf:ID='ReactionCatalysis/5137']`
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase `UniProtKB:P0AF12`	part_of The source records 2 copies of the indicated protein component.	5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase `PathBank:SMP0002097/ProteinComplex/3419`	PathBank:SMP0002097 Source assertion: Protein/9645 is the native component of ProteinComplex/3419. Source location `/rdf:RDF/[@rdf:ID='ProteinComplex/3419']/bp:component` PathBank:SMP0002097 Source assertion:* Native component coefficient is 2; the protein reference identifies UniProt P0AF12. Source location `/rdf:RDF/*[@rdf:ID='Protein/9645/Stoichiometry/2.0']`
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase `PathBank:SMP0002097/ProteinComplex/3419`	catalyzes Native complex catalysis assignment. Reviewed protein evidence supports chemistry; conflicting native labels and preparation scope remain explicit in the description.	MTA hydrolysis to adenine and methylthioribose `PathBank:SMP0002097/Reactions/5167`	PathBank:SMP0002097 Source assertion: ProteinComplex/3419 is the controller of Reactions/5167; the control type is ACTIVATION within a native Catalysis object. Source location `/rdf:RDF/*[@rdf:ID='ReactionCatalysis/5138']`
Bifunctional glutathionylspermidine synthetase/amidase `UniProtKB:P0AES0`	part_of The source records 2 copies of the indicated protein component.	Bifunctional glutathionylspermidine synthetase/amidase `PathBank:SMP0002097/ProteinComplex/416967_Cytosol`	PathBank:SMP0002097 Source assertion: Protein/107701_Cytosol is the native component of ProteinComplex/416967_Cytosol. Source location `/rdf:RDF/[@rdf:ID='ProteinComplex/416967_Cytosol']/bp:component` PathBank:SMP0002097 Source assertion:* Native component coefficient is 2; the protein reference identifies UniProt P0AES0. Source location `/rdf:RDF/*[@rdf:ID='Protein/107701_Cytosol/Stoichiometry/2.0']`
Bifunctional glutathionylspermidine synthetase/amidase `PathBank:SMP0002097/ProteinComplex/416967_Cytosol`	catalyzes Native complex catalysis assignment. Reviewed protein evidence supports chemistry; conflicting native labels and preparation scope remain explicit in the description.	ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	PathBank:SMP0002097 Source assertion: ProteinComplex/416967_Cytosol is the controller of Reactions/1960116; the control type is ACTIVATION within a native Catalysis object. Source location `/rdf:RDF/[@rdf:ID='ReactionCatalysis/1991917']` UniProtKB:P0AES0 Source assertion:* The synthetase catalytic annotation describes glutathione + spermidine + ATP forming glutathionylspermidine + ADP + phosphate + H+, distinct from the amidase activity. Source location `$.comments[1]`
S-adenosylmethionine decarboxylase proenzyme `UniProtKB:P0A7F6` molecular state: Processed SpeD alpha chain begins at original Ser112 converted into the covalently attached pyruvoyl group; this is a mature molecular state of the precursor accession. Qualification evidence UniProtKB:P0A7F6 Source assertion: Nonhydrolytic self-cleavage creates alpha and beta chains and the catalytic pyruvoyl group. Source location `$.comments[7]`	has_cofactor Covalently bound pyruvoyl group; free pyruvic acid listed in PWML is not the active attached moiety.	pyruvoyl group `CHEBI:45360`	UniProtKB:P0A7F6 Source assertion: The cofactor note specifies a covalently bound pyruvoyl group required for activity. Source location `$.comments[2]` CHEBI:45360 Source assertion: The released ChEBI entity is the pyruvoyl substituent, *C(=O)C(C)=O, not free pyruvic acid. Source location `$.default_structure`
S-adenosylmethionine decarboxylase proenzyme `UniProtKB:P0A7F6` molecular state: Mature pyruvoyl-containing E. coli SpeD in a Mg2+-activated experimental condition; the graph does not assign Mg2+ occupancy to an unprocessed chain or exclude alternative cations. Qualification evidence UniProtKB:P0A7F6 Source assertion: Activity is metal-activated in the reported assays; multiple alternative cations are listed. Source location `$.comments[3]`	has_cofactor Mg2+ is a demonstrated activating assay condition; alternative cations and salt-dependent cooperativity do not establish simultaneous requirements or native occupancy.	magnesium(2+) `CHEBI:18420`	UniProtKB:P0A7F6 Source assertion: Mg2+ activates the enzyme, with several other cations active in vitro; the physiological metal assignment is presumptive. Source location `$.comments[3]` PMID:17567041 Source assertion: The abstract describes alternative cation activation, cooperative Mg2+ effects and salt dependence; direct metal coordination is not required by its interpretation. Source location `/PubmedArticleSet/PubmedArticle[MedlineCitation/PMID='17567041']/MedlineCitation/Article/Abstract`
Bifunctional glutathionylspermidine synthetase/amidase `UniProtKB:P0AES0` experimental construct: Recombinant E. coli Gss studied in the 2006 work: crystal protein expressed in BL21(DE3), exact tag unspecified in accessible preparation text; kinetic/mutant constructs separately specified as pET28a N-terminal His6. This edge concerns synthetase, not amidase. Qualification evidence PMID:17124497 Source assertion: Methods distinguish crystallographic expression/purification from the explicitly N-terminal His6 pET28a kinetic/mutant preparations. Source location `//article//section[.//h2[contains(.,'Materials and methods')]]`	has_cofactor Mg2+ belongs to the Gss synthetase structural/assay context. The distinct amidase activity does not require a metal according to the separate primary abstract.	magnesium(2+) `CHEBI:18420`	PMID:17124497 Source assertion: Figure 4C and its caption describe two Mg2+ ions at the Gss synthetase active site in the nucleotide/GSH complex. Source location `//article//figure[@id='f4']` UniProtKB:P0AES0 Source assertion: Asp318 is annotated as a Mg2+-binding position in the synthetase portion. Source location `$.features[13]` PMID:8999955 Source assertion: The separately active amidase domain requires no metal ion; the full-length enzyme also contains a distinct ATP-dependent synthetase domain. Source location `/PubmedArticleSet/PubmedArticle[MedlineCitation/PMID='8999955']/MedlineCitation/Article/Abstract`
Bifunctional glutathionylspermidine synthetase/amidase `PathBank:SMP0002097/ProteinComplex/416967_Cytosol`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: ProteinComplex/416967_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='ProteinComplex/416967_Cytosol']/bp:cellularLocation`
Glutathione `PathBank:SMP0002097/Compound/PW_C000080_Cytosol`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: Compound/PW_C000080_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000080_Cytosol']/bp:cellularLocation`
Hydrogen Ion `PathBank:SMP0002097/Compound/PW_C040034_Cytosol`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: Compound/PW_C040034_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C040034_Cytosol']/bp:cellularLocation`
Adenosine triphosphate `PathBank:SMP0002097/Compound/PW_C000414_Cytosol`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: Compound/PW_C000414_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000414_Cytosol']/bp:cellularLocation`
Glutathionylspermidine `PathBank:SMP0002097/Compound/PW_C041211_Cytosol`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: Compound/PW_C041211_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C041211_Cytosol']/bp:cellularLocation`
5-Methylthioribose `PathBank:SMP0002097/Compound/PW_C000855_Periplasmic_Space`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Periplasmic Space `PathBank:SMP0002097/CellularLocation/Periplasmic_Space`	PathBank:SMP0002097 Source assertion: Compound/PW_C000855_Periplasmic_Space is localized to CellularLocation/Periplasmic_Space. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000855_Periplasmic_Space']/bp:cellularLocation`
S-Adenosylmethionine `PathBank:SMP0002097/Compound/PW_C000921_Cytosol`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: Compound/PW_C000921_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000921_Cytosol']/bp:cellularLocation`
Adenosine diphosphate `PathBank:SMP0002097/Compound/PW_C001034_Cytosol`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: Compound/PW_C001034_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C001034_Cytosol']/bp:cellularLocation`
5-Methylthioribose `PathBank:SMP0002097/Compound/PW_C000855_Cytosol`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: Compound/PW_C000855_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000855_Cytosol']/bp:cellularLocation`
Bifunctional glutathionylspermidine synthetase/amidase `UniProtKB:P0AES0`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: Protein/107701_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='Protein/107701_Cytosol']/bp:cellularLocation`
Phosphate `PathBank:SMP0002097/Compound/PW_C001104_Cytosol`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: Compound/PW_C001104_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C001104_Cytosol']/bp:cellularLocation`
Spermidine `PathBank:SMP0002097/Compound/PW_C000971_Cytosol`	located_in Explicit native compartment of this physical instance; unlocalized source instances remain separate.	Cytosol `PathBank:SMP0002097/CellularLocation/Cytosol`	PathBank:SMP0002097 Source assertion: Compound/PW_C000971_Cytosol is localized to CellularLocation/Cytosol. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000971_Cytosol']/bp:cellularLocation`
SAM decarboxylation `PathBank:SMP0002097/Reactions/5165`	provides_input_for Curated chemical continuity through decarboxylated SAM. Where the native unlocalized product and cytosolic input are distinct, their pool connection is an inference, not an extra measured transport or channeling event.	Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	PathBank:SMP0002097 Source assertion: Reactions/5165 produces the named intermediate in the native map. Source location `/rdf:RDF/[@rdf:ID='Reactions/5165']/bp:right` PathBank:SMP0002097 Source assertion:* Reactions/5166 consumes the corresponding named intermediate; the exact source physical instance is retained. Source location `/rdf:RDF/*[@rdf:ID='Reactions/5166']/bp:left`
Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	provides_input_for Curated chemical continuity through MTA. Where the native unlocalized product and cytosolic input are distinct, their pool connection is an inference, not an extra measured transport or channeling event.	MTA hydrolysis to adenine and methylthioribose `PathBank:SMP0002097/Reactions/5167`	PathBank:SMP0002097 Source assertion: Reactions/5166 produces the named intermediate in the native map. Source location `/rdf:RDF/[@rdf:ID='Reactions/5166']/bp:right` PathBank:SMP0002097 Source assertion:* Reactions/5167 consumes the corresponding named intermediate; the exact source physical instance is retained. Source location `/rdf:RDF/*[@rdf:ID='Reactions/5167']/bp:left`
Spermidine formation from putrescine and decarboxylated SAM `PathBank:SMP0002097/Reactions/5166`	provides_input_for Curated chemical continuity through spermidine. Where the native unlocalized product and cytosolic input are distinct, their pool connection is an inference, not an extra measured transport or channeling event.	ATP-dependent glutathionylspermidine synthesis `PathBank:SMP0002097/Reactions/1960116`	PathBank:SMP0002097 Source assertion: Reactions/5166 produces the named intermediate in the native map. Source location `/rdf:RDF/[@rdf:ID='Reactions/5166']/bp:right` PathBank:SMP0002097 Source assertion:* Reactions/1960116 consumes the corresponding named intermediate; the exact source physical instance is retained. Source location `/rdf:RDF/*[@rdf:ID='Reactions/1960116']/bp:left`
MTA hydrolysis to adenine and methylthioribose `PathBank:SMP0002097/Reactions/5167`	provides_input_for Curated chemical continuity through MTR. Where the native unlocalized product and cytosolic input are distinct, their pool connection is an inference, not an extra measured transport or channeling event.	Methylthioribose transport from cytosol to periplasm `PathBank:SMP0002097/Transports/511`	PathBank:SMP0002097 Source assertion: Reactions/5167 produces the named intermediate in the native map. Source location `/rdf:RDF/[@rdf:ID='Reactions/5167']/bp:right` PathBank:SMP0002097 Source assertion:* Transports/511 consumes the corresponding named intermediate; the exact source physical instance is retained. Source location `/rdf:RDF/*[@rdf:ID='Transports/511']/bp:left`
S-Adenosyl-L-Methionine Biosynthesis `PathBank:SMP0000857`	part_of Explicit source subpathway connection; no complete SAM-synthesis mechanism is imported.	`PathBank:SMP0002097`	PathBank:SMP0002097 Source assertion: SMP0000857 is explicitly attached as a subpathway of SMP0002097. Source location `/rdf:RDF/*[@rdf:about='http://identifiers.org/smpdb/SMP0002097']/bp:pathwayComponent[@rdf:resource='http://identifiers.org/smpdb/SMP0000857']`
SAM-biosynthesis pathway interface (unresolved chemical event) `PathBank:SMP0002097/SubPathwayInteractions/553236`	part_of Generic source Interaction supplies an interface, not a resolved biochemical conversion.	S-Adenosyl-L-Methionine Biosynthesis `PathBank:SMP0000857`	PathBank:SMP0002097 Source assertion: The SAM-biosynthesis subpathway contains Interaction 553236. Source location `/rdf:RDF/*[@rdf:about='http://identifiers.org/smpdb/SMP0000857']/bp:pathwayComponent`
SAM-biosynthesis pathway interface (unresolved chemical event) `PathBank:SMP0002097/SubPathwayInteractions/553236`	has_output The participant is separately marked SubPathwayOutput. No left side, enzyme, energy balance or additional chemical equation is inferred.	S-Adenosylmethionine `PathBank:SMP0002097/Compound/PW_C000921_Cytosol`	PathBank:SMP0002097 Source assertion: Interaction 553236 has the cytosolic SAM participant. Source location `/rdf:RDF/[@rdf:ID='SubPathwayInteractions/553236']/bp:participant` PathBank:SMP0002097 Source assertion:* The cytosolic SAM instance carries the native name SubPathwayOutput. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000921_Cytosol']/bp:name`
SAM-biosynthesis pathway interface (unresolved chemical event) `PathBank:SMP0002097/SubPathwayInteractions/553236`	provides_input_for Inferred pathway continuity between an output-marked cytosolic SAM pool and the native unlocalized SpeD input; not physical channeling.	SAM decarboxylation `PathBank:SMP0002097/Reactions/5165`	PathBank:SMP0002097 Source assertion: The interface output refers to the same SAM chemical reference as the SpeD input. Source location `/rdf:RDF/[@rdf:ID='Compound/PW_C000921_Cytosol']/bp:entityReference` PathBank:SMP0002097 Source assertion:* The SpeD input is the separate unlocalized SAM instance. Source location `/rdf:RDF/*[@rdf:ID='Compound/PW_C000921']/bp:entityReference`

References

PathBank:SMP0002097 Spermidine Biosynthesis and Metabolism (source version: Whole current PathBank BioPAX acquired 2026-10-12; SMP0002097, distinct PathWhiz PW002085. Four chemical reactions, one transport, and one SAM-pathway interface; source version is retrieval-specific, not inferred from the older archive.)
PathBank:PW002085 PathWhiz PW002085 complete PWML for PathBank SMP0002097 (source version: Whole PWML acquired 2026-10-12. The original has an undeclared drawing-only option prefix; XPath inspection adds an in-memory namespace declaration, with raw bytes unchanged. Biology and native conflicts are retained.)
UniProtKB:P0A7F6 S-adenosylmethionine decarboxylase proenzyme (source version: Complete reviewed UniProtKB JSON acquired 2026-10-12; entry version 140, sequence version 1, annotation updated 2026-06-10. Reviewed annotation evidence tiers and whole sequence retained; cited papers are not thereby full-text reads.)
UniProtKB:P09158 Polyamine aminopropyltransferase (source version: Complete reviewed UniProtKB JSON acquired 2026-10-12; entry version 198, sequence version 2, annotation updated 2026-09-02. Reviewed annotation evidence tiers and whole sequence retained; cited papers are not thereby full-text reads.)
UniProtKB:P0AF12 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (source version: Complete reviewed UniProtKB JSON acquired 2026-10-12; entry version 151, sequence version 1, annotation updated 2026-09-02. Reviewed annotation evidence tiers and whole sequence retained; cited papers are not thereby full-text reads.)
UniProtKB:P0AES0 Bifunctional glutathionylspermidine synthetase/amidase (source version: Complete reviewed UniProtKB JSON acquired 2026-10-12; entry version 141, sequence version 1, annotation updated 2026-09-02. Reviewed annotation evidence tiers and whole sequence retained; cited papers are not thereby full-text reads.)
CHEBI:15377 water (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:15378 hydron (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:15414 S-adenosyl-L-methionine (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:15422 ATP (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:15625 S-adenosylmethioninamine (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:16526 carbon dioxide (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:16610 spermidine (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:16613 glutathionylspermidine (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:16708 adenine (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:16761 ADP (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:16856 glutathione (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:16895 S-methyl-5-thio-D-ribose (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:17148 putrescine (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:17509 5'-S-methyl-5'-thioadenosine (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:18367 phosphate(3−) (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:18420 magnesium(2+) (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:32816 pyruvic acid (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
CHEBI:45360 pyruvoyl group (source version: Complete released ChEBI JSON acquired 2026-10-12; exact chemical form/charge/structure checked. This does not update the project ontology snapshot.)
NCBITaxon:562 Escherichia coli (source version: Whole NCBI Taxonomy three-taxon EFetch XML acquired 2026-10-12; exact selected taxon, rank and lineage checked. BW25113 is distinct from the parent K-12 taxon.)
NCBITaxon:83333 Escherichia coli K-12 (source version: Whole NCBI Taxonomy three-taxon EFetch XML acquired 2026-10-12; exact selected taxon, rank and lineage checked. BW25113 is distinct from the parent K-12 taxon.)
NCBITaxon:679895 Escherichia coli BW25113 (source version: Whole NCBI Taxonomy three-taxon EFetch XML acquired 2026-10-12; exact selected taxon, rank and lineage checked. BW25113 is distinct from the parent K-12 taxon.)
PMID:16788729 In vivo hydrolysis of S-adenosyl-L-methionine in Escherichia coli increases export of 5-methylthioribose. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred.)
PMID:4203512 Biological production of 5-methylthioribose. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred. This record has no abstract; metadata only and no mechanistic claim assigned to it.)
PMID:3316212 The speEspeD operon of Escherichia coli. Formation and processing of a proenzyme form of S-adenosylmethionine decarboxylase. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred.)
PMID:20051267 The crystal structure of Escherichia coli spermidine synthase SpeE reveals a unique substrate-binding pocket. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred.)
PMID:9524204 Cloning and expression of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase: identification of the pfs gene product. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred.)
PMID:8941345 Characterization of recombinant Eschericha coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase: analysis of enzymatic activity and substrate specificity. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred.)
PMID:3526348 Spermidine synthase of Escherichia coli: localization of the speE gene. (source version: Whole NCBI PMC HTML acquired 2026-10-12, plus all five complete scanned article pages independently acquired and visually read at original resolution, including Methods, four tables, two figures and note added in proof. The HTML alone contains only abstract/page links.)
PMID:19542271 Polyamines are not required for aerobic growth of Escherichia coli: preparation of a strain with deletions in all of the genes for polyamine biosynthesis. (source version: Whole NCBI PMC HTML acquired 2026-10-12; full main text, Methods, table, captions and reference list read. All four main-text figure images independently acquired and visually inspected. No supplementary-file contents are asserted.)
PMID:17124497 Dual binding sites for translocation catalysis by Escherichia coli glutathionylspermidine synthetase. (source version: Whole NCBI PMC HTML acquired 2026-10-12; full main text, Methods, tables, captions and reference list read. All main-text figure images independently acquired and visually inspected. Supporting-file download attempts returned HTML challenge pages; supplements were not read.)
PMID:20530482 Protein S-thiolation by Glutathionylspermidine (Gsp): the role of Escherichia coli Gsp synthetASE/amidase in redox regulation. (source version: Whole NCBI PMC HTML acquired 2026-10-12; full main text, Methods, tables, captions and reference list read. All main-text figure images independently acquired and visually inspected. Supporting-file download attempts returned HTML challenge pages; supplements were not read.)
PMID:7775463 Glutathionylspermidine metabolism in Escherichia coli. Purification, cloning, overproduction, and characterization of a bifunctional glutathionylspermidine synthetase/amidase. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred.)
PMID:8999955 Dissection of glutathionylspermidine synthetase/amidase from Escherichia coli into autonomously folding and functional synthetase and amidase domains. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred.)
PMID:3546296 Escherichia coli S-adenosylmethionine decarboxylase. Subunit structure, reductive amination, and NH2-terminal sequences. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred.)
PMID:6749853 S-adenosylmethionine decarboxylase of Escherichia coli. Studies on the covalently linked pyruvate required for activity. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred.)
PMID:17567041 Metal ion activation of S-adenosylmethionine decarboxylase reflects cation charge density. (source version: Whole NCBI PubMed EFetch original acquired 2026-10-12; exact article metadata and complete available abstract read. Full paper not acquired/read; no unsupported Methods, exact construct or numerical kinetic details inferred.)

Curation history

2026-10-12T23:51:36Z codex
- CREATE — Add complete evidence-backed E. coli spermidine biosynthesis and metabolism.
  Exact accepted scoped PathBank:SMP0002097:18 paragraphs,58 edges,4 qualifiers,43 IDs,42 references and4 mappings; all four biochemical events plus transport,22 sides and generic SAM interface retained. Native assembly, taxon/construct, chemical-identity, transport and source-access limits remain. Whole original bodies and all92 acquisition attempts retained in research/pathway_additions/2026-10-12-next-240. Maintained gates/native review remain pending.
Read this curation session