acetoacetate degradation (to acetyl CoA)

MetaCyc:ACETOACETATE-DEG-PWY

Acetoacetate degradation in Escherichia coli converts acetoacetate and free CoA to acetate and one net acetyl-CoA through two coupled transformations. AtoDA first transfers CoA from an acetyl-CoA donor to acetoacetate, giving acetoacetyl-CoA and acetate. AtoB then cleaves acetoacetyl-CoA with CoA to produce two acetyl-CoA molecules gross: one replaces the donor used in the first transformation and one is the net product. The regenerated donor is a material-balance inference, not evidence for an obligatory physical channel between the enzymes. The native transfer reaction is reversible and the pathway uses its left-to-right orientation; the reversible thiolase reaction is written as acetyl-CoA condensation in its native frame and is used right-to-left during degradation. Rhea 27807 and 21038 independently supply the corresponding oriented equations. They are alternative descriptions of the same two biological events. Their acetoacetate and acetate are monoanions and their acetyl-CoA, acetoacetyl-CoA and CoA are the explicitly represented tetraanions; acid-form PathBank cross-references are not substituted for these chemical identities. The native thiolase composite includes two reversible constituent reactions, RXN-20154 and RXN-20155. In their written condensation orientation, acetyl-CoA first acetylates a protein-bound cysteine and releases CoA; the S-acetylated residue then combines with a second acetyl-CoA to produce acetoacetyl-CoA and regenerate the protein-bound cysteine. All eight constituent side entries are retained as decomposition context, not two additional physiological pathway steps. Degradative cleavage traverses this chemistry in reverse. The two generic protein-residue classes do not identify an isolated free cysteine molecule or independently prove that a particular AtoB residue occupied that state in an experiment. The EcoCyc reference assembly for acetoacetyl-CoA transferase is nested: its unnamed parent contains one beta complex and one alpha complex, and those children contain two AtoA and two AtoD chains, respectively. Reciprocal component-of links support this hierarchy. Thus the reference composition is AtoA2AtoD2, not a single AtoA or AtoD enzyme and not an unspecified mixed controller. The unnamed AtoB reference complex contains four AtoB chains. These four assembly nodes and three leaf protein types are kept distinct from any individual assay preparation. The native transferase account associates a 97 kDa preparation with Sramek and Frerman (1975), while the 1987 genetic study reports atoD and atoA products of approximately 26.5 and 26 kDa and a 42 kDa atoB product. These experimental apparent masses are not replaced by current sequence-derived masses or used to recalculate assembly stoichiometry. Current UniProt entries describe the transferase as cytoplasmic and membrane-associated. The native AtoA and AtoD monomer comments separately retain an older sequence-based function prediction from the 2003 metabolic model; that annotation is not evidence that either isolated chain catalyzes the complete CoA-transfer reaction. The native transferase commentary describes two half-reactions involving a covalent enzyme-CoA intermediate, two detectable conformational changes and a likely ping-pong mechanism, citing the 1975 and 1977 studies. It also reports broad use of short-chain acyl-CoA donors and carboxylic acid acceptors, with strongest activity for normal and 3-keto substrates. UniProt gives apparent Km values of 0.26 mM for acetyl-CoA in acetoacetyl-CoA formation and 0.035 mM for acetoacetyl-CoA in acetyl-CoA formation, citing the 1975 kinetic study. These are source-attributed annotations because the complete original kinetic papers were not obtained here; they do not establish a universal rate law, identical assay conditions or a fixed in vivo flux ratio. Four native regulatory annotations are retained. Acetyl-CoA competitively inhibits the transferase in REG0-11728, which supplies no linked primary citation; CoA is a competitive inhibitor with respect to acyl-CoA in REG0-8779, citing the 1977 study; p-chloromercuribenzoate inhibits it in REG0-8781, citing the 1975 purification study; and acetoacetyl-CoA inhibits the AtoB reaction in REG0-7500, citing the 1976 thiolase study. Their concentrations and preparation-specific conditions are not supplied by these complete regulation frames, so the graph records source-qualified inhibitory relationships without a universal in vivo potency claim. Acetyl-CoA can be a substrate in one direction and an inhibitor in another assay context. The mercurial is the native anion with the verified PubChem 21226146 structure, not an acid-form substitution. The native pathway account describes growth on acetoacetate as sole carbon and energy source and reports a 200–300-fold increase in transferase and thiolase synthesis during growth on acetoacetate, citing Pauli and Overath (1972). The associated protein comment also attributes AtoB induction to this work. This historical quantitative statement is retained as a database-attributed account, because the complete 1972 paper and its exact strain, baseline and assay denominators were not acquired; it is not a prediction for every E. coli strain or growth condition. The complete 1975 thiolase study distinguishes two preparations that should not be collapsed into one strain attribution. Thiolase I was prepared from wild-type E. coli B ATCC 11775 grown on oleate, whereas thiolase II was prepared from a constitutive fadR16 fad-5 atoC49 mutant grown on acetate. The paper does not identify that mutant as the same wild-type B preparation. Accordingly, the native summary that the AtoB enzyme was initially purified from E. coli B is qualified by the primary Methods, and modern AtoB/FadA names are retrospective mappings rather than genes sequenced in that study. In that 1975 work, thiolase assays were performed at 25 °C in 0.6 ml containing 67 micromol Tris at pH 8.1, 0.134 micromol dithiothreitol, 15 micromol MgCl2, 58 nmol CoA and 12 nmol beta-ketoacyl-CoA, with CoA initiating the spectrophotometric reaction. Thiolase I acted on tested C4–C16 substrates, with medium-chain substrates preferred; the long-chain tests used lower concentrations because of substrate inhibition. Thiolase II activity on the tested C6 substrate was below 1% of its acetoacetyl-CoA activity. This supports strong substrate preference, not demonstrated zero activity on every possible substrate. Failure to detect thiolase II in the oleate-grown wild-type B preparation is conditional on that preparation and assay. The AtoB structure study is represented by its indexed abstract and the complete native annotation: apo and CoA-bound crystal structures support a tetramer described as a loosely associated pair of tight dimers. EcoCyc states that the gene was cloned from BL21(DE3) and that its sequence matches the K-12 protein. Those are attributed source statements, not a newly verified construct alignment, and the complete 2016 paper was not obtained. The native 166 kDa complex mass cites the separate 1976 study. A crystal assembly, a historical apparent mass and the K-12 reference sequence are complementary contexts, not interchangeable assay preparations. The native AtoB kinetic slots attribute Km values of 17.6 micromolar for acetoacetyl-CoA, 8.0 micromolar for CoA and 138.6 micromolar for acetyl-CoA, and kcat values of 220.5 s−1 for cleavage and 6.5 s−1 for condensation, to the 2016 study. A separate acetyl-CoA Km of 470 micromolar is imported from BRENDA with the 1976 citation. The 1976-linked native prose also lists apparent rates of 0.85 micromolar per minute for cleavage and 38 nanomolar per minute for condensation. These heterogeneous annotations retain their original directions, units and citations; unavailable complete assay contexts prevent combining them into one fitted enzyme model or treating their ratios as an in vivo directional constraint. Sequence annotations identify an AtoB acyl-thioester site at Cys88 by similarity and proton-acceptor sites at positions 349 and 379 by sequence-model evidence. AtoA position 46 and the AtoD CoA-binding region at positions 24–30 are also sequence-model annotations. These features are useful mechanistic context but are not new direct mutagenesis results or proof that the generic native protein-bound cysteine class is exclusively AtoB Cys88. Native Pfam and GO annotations retain their computational or curated evidence levels; family membership alone does not establish isolated-subunit catalysis. The 1987 genetic and expression studies support an atoDAB structural-gene operon and a separately expressed atoC regulator. Their indexed abstracts distinguish complementation and gene-product assignments from promoter-level regulation: atoD and atoA are both required for transferase activity, while galK promoter fusions and atoC allele behavior support transcriptional control. The early study left some synthesis-versus-activation interpretation open; it is not used to claim direct allosteric activation of purified transferase by AtoC. Later evidence is described specifically for the atoDAEB operon nomenclature used by those studies. AtoC regulates expression of the acetoacetate-utilization enzymes through the atoDAEB promoter. In the complete 2007 study, reporter assays used modified M9 glucose medium with 10 mM acetoacetate and compared promoter fragments extending from −206, −120 or −47 to +73 relative to the predicted transcription start. The upstream −206 to −120 region was required for strong AtoC binding and inducible reporter expression. Reporter constructs for atoS, atoC and rcsC did not show the same acetoacetate induction, providing assay-specific negative controls rather than a global statement about all regulation of those genes. The 2007 in vitro binding experiments used recombinant His10-tagged AtoC without an established phosphorylated preparation: the authors could not obtain significant phosphorylation under their tested in vitro conditions with AtoS or small phosphodonors. EMSA and footprinting therefore demonstrate DNA binding by that preparation, not that phosphorylation is unnecessary for physiological acetoacetate signaling. Added acetoacetate did not itself enhance the in vitro DNA-binding reaction. The possible failure to phosphorylate or rapid dephosphorylation was not resolved. Footprinting in the 2007 study identified two adjacent 20-base-pair AtoC-binding regions, −146 to −127 and −126 to −107 relative to a predicted, not experimentally mapped, transcription start. The protected region and hypersensitive positions were evaluated with tagged AtoC over a concentration series. Promoter mutations at positions including −111, −121, −130 and −140 strongly reduced induction; a −53 mutation could reduce induction without eliminating AtoC binding. These observations support a regulatory DNA mechanism, not direct changes to the catalytic chemistry of AtoDA or AtoB. The same study used chromatin immunoprecipitation of plasmid-borne promoter constructs in BW25113 and its atoSC-deletion derivative BW28878, with antibody and deletion controls, and observed increased AtoC association after acetoacetate induction. An IHF-deficient N7193 background compared with N99 markedly reduced induction, supporting an architectural contribution by IHF under those conditions. Neither plasmid-promoter occupancy nor an IHF-mutant response measures a fixed stoichiometric relation between AtoC abundance and metabolic flux. AtoC phosphorylation-site and mutant annotations require allele-specific interpretation. The indexed 2005 study examined His10-tagged AtoC and D55G/H73L substitutions, with single substitutions reducing but not abolishing phosphorylation and the double mutant failing to respond to acetoacetate. UniProt retains uncertainty about independent aspartate/histidine phosphorylation versus transfer between sites. Native and UniProt annotations connect D55G and H73L to approximately 40% and 70% lower complexed polyhydroxybutyrate accumulation, respectively, using a separate 2006 study. Those cPHB phenotypes are not measured acetoacetate-catabolic fluxes, and the mutant proteins are not treated as unmodified reference AtoC. AtoC also has source-supported ornithine-decarboxylase inhibition, cPHB, spermidine-response, motility and chemotaxis contexts. These remain distinct from the two-step degradation chemistry. The 1993 abstract reports decarboxylase inhibition without reduced decarboxylase protein abundance; the 2006–2007 cPHB work concerns specific overexpression and phosphomutant backgrounds; and the 2011 motility study uses atoSC deletion, complementation and an amino-terminally truncated constitutive regulator. Their phenotypes are retained as contextual evidence, not additional metabolites or obligatory steps of this pathway. The AtoC reference annotation includes a receiver region, a sigma-54 interaction region, predicted ATP-binding regions and a carboxy-terminal DNA-binding region. Legacy EcoCyc and current UniProt feature boundaries need not be identical: the native HTH annotation spans 433–452, whereas the current UniProt DNA-binding annotation spans 433–456. The old AAA23450.1 sequence carries a frameshift caution and a position-99 conflict. These sequence and evidence-version distinctions are preserved; they do not define a new wild-type allele or a directly observed nucleotide stoichiometry. YdiF is an alternative CoA-transferase context whose physiological contribution to this acetoacetate route remains unestablished by the evidence reviewed here. The older EcoCyc K-12 assignment and its enzymatic-reaction link are based on sequence/model inference. A separate 2005 study characterized the O157:H7 ortholog, which the native annotation describes as 99% identical to K-12, and reported a homotetramer arranged as a dimer of dimers. The ortholog and the current K-12 reference are kept separate; an annotation of broad catalytic capacity is not proof of acetoacetate-growth necessity. The O157:H7 YdiF account supports broad short-chain acyl-CoA specificity and a glutamyl-CoA thioester intermediate. Its curated donor/acceptor account includes acetoacetyl-, propionyl-, crotonoyl- and butyryl-CoA with acetate, and several short carboxylate acceptors with acetyl-CoA; isovalerate was not an effective tested acceptor. Activity falls with longer substrates. The K-12 Glu333 mechanism and tetramer annotations are transferred by similarity from that ortholog. These are source-qualified biochemical contexts because the complete 2005 paper was not obtained, and its historical uncertainty about physiological function is not presented as if no later work existed. The complete 2022 YdiF study adds direct biochemical evidence for the reverse of the assimilation transfer reaction and for lactyl-CoA formation. Its purified recombinant YdiF assay used 7.5 micrograms enzyme in 50 microlitres containing 1 mM acetoacetyl-CoA and 10 mM acetate or L-lactate, 50 mM each sodium dihydrogen phosphate and disodium hydrogen phosphate, and 5 mM MgCl2 at pH 7.0, incubated at 35 °C for 20 minutes after a five-minute preincubation. LC–MS detected acetyl-CoA or lactyl-CoA products. Thus the acetate assay starts with acetoacetyl-CoA plus acetate; it does not directly measure forward acetoacetate assimilation. In that 2022 work, YdiF was expressed using pET28a in BL21(lambdaDE3) and purified by nickel-affinity methods, while much of the physiology concerned MG1655. YdiF overexpression increased lysine acetylation and lactylation signals relative to an empty-vector control. This study does not establish that YdiF is necessary for growth on acetoacetate or that lactyl-CoA is an intermediate of the native two-step degradation route. The additional YiaC/CobB, PykF mutant, molecular-dynamics and glycolytic-growth experiments concern protein lactylation and are not added as pathway steps. Exact supplement-only cloning details and all supplemental datasets were not independently read. PathBank PW002090/SMP0002102 describes a broader acetate-metabolism diagram with five reactions and twenty-one side entries. Its phosphate-acetyltransferase and acetate-kinase segment overlaps an already represented acetate-production route, while acetyl-CoA synthetase is an alternative acetate-assimilation route outside the present native pathway. Its transferase reaction agrees with the two-step acetoacetate boundary, but its thiolase reaction incorrectly places CoA among the products and gives only one acetyl-CoA. That equation is not imported. The PathBank AtoB tetramer is explicit, whereas the transferase controller lists AtoD and AtoA without component coefficients; its missing stoichiometry does not replace the complete nested EcoCyc reference assembly. The acetyl-CoA product can feed central metabolism, including the TCA cycle, as described by the native pathway commentary. That interface is not an additional reaction in this record and does not quantify ATP yield or prove the same flux partition under all oxygen and growth conditions. The record has an E. coli species scope but preserves the distinct K-12/MG1655, BL21, wild-type B, constitutive mutant and O157:H7 evidence contexts instead of treating every observation as universal across the species. AtoB has also been used in engineered 1-butanol and medium-chain fuel production, and the native entries explain the historical ato gene-name derivation from acetoacetate. These annotations are preserved as application and nomenclature context. They do not change the physiological pathway boundary or establish an engineered product as a normal degradation endpoint. Evidence depth is explicit throughout this record: the complete 1975 thiolase, 2007 AtoC and 2022 YdiF papers were read, while inaccessible older transferase/thiolase papers, the 1987 genetic papers, the 2005 YdiF paper and the 2016 structure paper are represented by acquired indexed abstracts where available and clearly attributed database annotations. Missing full assay contexts are not supplied from titles, cross-references or metadata alone. The whole issuing pathway, reaction, assembly, regulation and protein originals are retained separately from primary-paper evidence.

Pathway type

degradation

Organism scope

Escherichia coli NCBITaxon:562

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Pathway network

25 nodes · 46 asserted directed edges

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Pathway
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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
unnamed protein complex ACETOACETYL-COA-TRANSFER-CPLX `EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX`	complex
β complex `EcoCyc:ATOA-CPLX`	complex
α complex `EcoCyc:ATOD-CPLX`	complex
unnamed protein complex ACETYL-COA-ACETYLTRANSFER-CPLX `EcoCyc:ACETYL-COA-ACETYLTRANSFER-CPLX`	complex
a [protein]-L-cysteine `MetaCyc:PROT-CYS`	chemical entity
a [protein] S-acetyl-L-cysteine `MetaCyc:Protein-S-Acetyl-Cysteines`	chemical entity
Acetate CoA-transferase subunit alpha `UniProtKB:P76458`	protein
Acetate CoA-transferase subunit beta `UniProtKB:P76459`	protein
Acetyl-CoA acetyltransferase `UniProtKB:P76461`	protein
Acetate CoA-transferase YdiF `UniProtKB:P37766`	protein
Regulatory protein AtoC `UniProtKB:Q06065`	protein
acetoacetate `CHEBI:13705`	small molecule
acetyl-CoA(4-) `CHEBI:57288`	small molecule
acetoacetyl-CoA(4-) `CHEBI:57286`	small molecule
acetate `CHEBI:30089`	small molecule
coenzyme A(4-) `CHEBI:57287`	small molecule
(4-Carboxyphenyl)-chloro-mercury `PubChem:21226146`	small molecule
ACETOACETYL-COA-TRANSFER-RXN `MetaCyc:ACETOACETYL-COA-TRANSFER-RXN`	molecular activity	reversible
ACETYL-COA-ACETYLTRANSFER-RXN `MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN`	molecular activity	reversible
RXN-20154 `MetaCyc:RXN-20154`	molecular activity	reversible
RXN-20155 `MetaCyc:RXN-20155`	molecular activity	reversible
acetoacetate + acetyl-CoA => acetoacetyl-CoA + acetate `RHEA:27807`	molecular activity	left to right
acetoacetyl-CoA + CoA => 2 acetyl-CoA `RHEA:21038`	molecular activity	right to left

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
acetyl-CoA(4-) `CHEBI:57288`	consumes Coefficient 1; native left-to-right orientation.	ACETOACETYL-COA-TRANSFER-RXN `MetaCyc:ACETOACETYL-COA-TRANSFER-RXN`	MetaCyc:ACETOACETYL-COA-TRANSFER-RXN Source assertion: Whole native left contains ACETYL-COA, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/left[1]; /reaction-direction` EcoCyc:ACETYL-COA Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:57288 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
acetoacetate `CHEBI:13705`	consumes Coefficient 1; native left-to-right orientation.	ACETOACETYL-COA-TRANSFER-RXN `MetaCyc:ACETOACETYL-COA-TRANSFER-RXN`	MetaCyc:ACETOACETYL-COA-TRANSFER-RXN Source assertion: Whole native left contains 3-KETOBUTYRATE, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/left[2]; /reaction-direction` EcoCyc:3-KETOBUTYRATE Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:13705 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
ACETOACETYL-COA-TRANSFER-RXN `MetaCyc:ACETOACETYL-COA-TRANSFER-RXN`	produces Coefficient 1; native left-to-right orientation.	acetate `CHEBI:30089`	MetaCyc:ACETOACETYL-COA-TRANSFER-RXN Source assertion: Whole native right contains ACET, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/right[1]; /reaction-direction` EcoCyc:ACET Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:30089 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
ACETOACETYL-COA-TRANSFER-RXN `MetaCyc:ACETOACETYL-COA-TRANSFER-RXN`	produces Coefficient 1; native left-to-right orientation.	acetoacetyl-CoA(4-) `CHEBI:57286`	MetaCyc:ACETOACETYL-COA-TRANSFER-RXN Source assertion: Whole native right contains ACETOACETYL-COA, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/right[2]; /reaction-direction` EcoCyc:ACETOACETYL-COA Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:57286 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
ACETYL-COA-ACETYLTRANSFER-RXN `MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN`	produces Coefficient 2; pathway degradation orientation, native right-to-left.	acetyl-CoA(4-) `CHEBI:57288`	MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN Source assertion: Whole native left contains ACETYL-COA, coefficient 2; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/left[1]; /reaction-direction` EcoCyc:ACETYL-COA Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:57288 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
acetoacetyl-CoA(4-) `CHEBI:57286`	consumes Coefficient 1; pathway degradation orientation, native right-to-left.	ACETYL-COA-ACETYLTRANSFER-RXN `MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN`	MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN Source assertion: Whole native right contains ACETOACETYL-COA, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/right[1]; /reaction-direction` EcoCyc:ACETOACETYL-COA Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:57286 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
coenzyme A(4-) `CHEBI:57287`	consumes Coefficient 1; pathway degradation orientation, native right-to-left.	ACETYL-COA-ACETYLTRANSFER-RXN `MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN`	MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN Source assertion: Whole native right contains CO-A, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/right[2]; /reaction-direction` EcoCyc:CO-A Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:57287 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
acetyl-CoA(4-) `CHEBI:57288`	consumes Coefficient 1; native left-to-right orientation. Written condensation constituent of the reversible thiolase composite; not another physiological pathway event.	RXN-20154 `MetaCyc:RXN-20154`	MetaCyc:RXN-20154 Source assertion: Whole native left contains ACETYL-COA, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/left[1]; /reaction-direction` EcoCyc:ACETYL-COA Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:57288 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
a [protein]-L-cysteine `MetaCyc:PROT-CYS`	consumes Coefficient 1; native left-to-right orientation. Written condensation constituent of the reversible thiolase composite; not another physiological pathway event.	RXN-20154 `MetaCyc:RXN-20154`	MetaCyc:RXN-20154 Source assertion: Whole native left contains PROT-CYS, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/left[2]; /reaction-direction` MetaCyc:PROT-CYS Source assertion: Whole native Compound is a generic protein-bound residue class, not a free amino acid or proved AtoB-specific state. Source location `/ptools-xml/Compound/@class; /parent; /common-name`
RXN-20154 `MetaCyc:RXN-20154`	produces Coefficient 1; native left-to-right orientation. Written condensation constituent of the reversible thiolase composite; not another physiological pathway event.	a [protein] S-acetyl-L-cysteine `MetaCyc:Protein-S-Acetyl-Cysteines`	MetaCyc:RXN-20154 Source assertion: Whole native right contains Protein-S-Acetyl-Cysteines, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/right[1]; /reaction-direction` MetaCyc:Protein-S-Acetyl-Cysteines Source assertion: Whole native Compound is a generic protein-bound residue class, not a free amino acid or proved AtoB-specific state. Source location `/ptools-xml/Compound/@class; /parent; /common-name`
RXN-20154 `MetaCyc:RXN-20154`	produces Coefficient 1; native left-to-right orientation. Written condensation constituent of the reversible thiolase composite; not another physiological pathway event.	coenzyme A(4-) `CHEBI:57287`	MetaCyc:RXN-20154 Source assertion: Whole native right contains CO-A, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/right[2]; /reaction-direction` EcoCyc:CO-A Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:57287 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
a [protein] S-acetyl-L-cysteine `MetaCyc:Protein-S-Acetyl-Cysteines`	consumes Coefficient 1; native left-to-right orientation. Written condensation constituent of the reversible thiolase composite; not another physiological pathway event.	RXN-20155 `MetaCyc:RXN-20155`	MetaCyc:RXN-20155 Source assertion: Whole native left contains Protein-S-Acetyl-Cysteines, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/left[1]; /reaction-direction` MetaCyc:Protein-S-Acetyl-Cysteines Source assertion: Whole native Compound is a generic protein-bound residue class, not a free amino acid or proved AtoB-specific state. Source location `/ptools-xml/Compound/@class; /parent; /common-name`
acetyl-CoA(4-) `CHEBI:57288`	consumes Coefficient 1; native left-to-right orientation. Written condensation constituent of the reversible thiolase composite; not another physiological pathway event.	RXN-20155 `MetaCyc:RXN-20155`	MetaCyc:RXN-20155 Source assertion: Whole native left contains ACETYL-COA, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/left[2]; /reaction-direction` EcoCyc:ACETYL-COA Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:57288 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
RXN-20155 `MetaCyc:RXN-20155`	produces Coefficient 1; native left-to-right orientation. Written condensation constituent of the reversible thiolase composite; not another physiological pathway event.	acetoacetyl-CoA(4-) `CHEBI:57286`	MetaCyc:RXN-20155 Source assertion: Whole native right contains ACETOACETYL-COA, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/right[1]; /reaction-direction` EcoCyc:ACETOACETYL-COA Source assertion: Whole native InChI exactly matches the selected issuing CHEBI:57286 subject, retaining charge/protonation. Source location `/ptools-xml/Compound/inchi`
RXN-20155 `MetaCyc:RXN-20155`	produces Coefficient 1; native left-to-right orientation. Written condensation constituent of the reversible thiolase composite; not another physiological pathway event.	a [protein]-L-cysteine `MetaCyc:PROT-CYS`	MetaCyc:RXN-20155 Source assertion: Whole native right contains PROT-CYS, coefficient 1; native reaction-direction is REVERSIBLE. Source location `/ptools-xml/Reaction/right[2]; /reaction-direction` MetaCyc:PROT-CYS Source assertion: Whole native Compound is a generic protein-bound residue class, not a free amino acid or proved AtoB-specific state. Source location `/ptools-xml/Compound/@class; /parent; /common-name`
acetoacetate `CHEBI:13705`	consumes Rhea oriented projection, coefficient 1; same native biological event, not an additional step.	acetoacetate + acetyl-CoA => acetoacetyl-CoA + acetate `RHEA:27807`	RHEA:27807 Source assertion: substrates include CHEBI:13705 with coefficient 1; complete compound charge and formula retained. Source location `http://rdf.rhea-db.org/27807 / rh:substrates; http://rdf.rhea-db.org/27806_L/rh:contains1; http://rdf.rhea-db.org/Participant_27806_compound_3307; http://rdf.rhea-db.org/Compound_3307`
acetyl-CoA(4-) `CHEBI:57288`	consumes Rhea oriented projection, coefficient 1; same native biological event, not an additional step.	acetoacetate + acetyl-CoA => acetoacetyl-CoA + acetate `RHEA:27807`	RHEA:27807 Source assertion: substrates include CHEBI:57288 with coefficient 1; complete compound charge and formula retained. Source location `http://rdf.rhea-db.org/27807 / rh:substrates; http://rdf.rhea-db.org/27806_L/rh:contains1; http://rdf.rhea-db.org/Participant_27806_compound_4271; http://rdf.rhea-db.org/Compound_4271`
acetoacetate + acetyl-CoA => acetoacetyl-CoA + acetate `RHEA:27807`	produces Rhea oriented projection, coefficient 1; same native biological event, not an additional step.	acetoacetyl-CoA(4-) `CHEBI:57286`	RHEA:27807 Source assertion: products include CHEBI:57286 with coefficient 1; complete compound charge and formula retained. Source location `http://rdf.rhea-db.org/27807 / rh:products; http://rdf.rhea-db.org/27806_R/rh:contains1; http://rdf.rhea-db.org/Participant_27806_compound_4872; http://rdf.rhea-db.org/Compound_4872`
acetoacetate + acetyl-CoA => acetoacetyl-CoA + acetate `RHEA:27807`	produces Rhea oriented projection, coefficient 1; same native biological event, not an additional step.	acetate `CHEBI:30089`	RHEA:27807 Source assertion: products include CHEBI:30089 with coefficient 1; complete compound charge and formula retained. Source location `http://rdf.rhea-db.org/27807 / rh:products; http://rdf.rhea-db.org/27806_R/rh:contains1; http://rdf.rhea-db.org/Participant_27806_compound_6051; http://rdf.rhea-db.org/Compound_6051`
acetoacetyl-CoA(4-) `CHEBI:57286`	consumes Rhea oriented projection, coefficient 1; same native biological event, not an additional step.	acetoacetyl-CoA + CoA => 2 acetyl-CoA `RHEA:21038`	RHEA:21038 Source assertion: substrates include CHEBI:57286 with coefficient 1; complete compound charge and formula retained. Source location `http://rdf.rhea-db.org/21038 / rh:substrates; http://rdf.rhea-db.org/21036_R/rh:contains1; http://rdf.rhea-db.org/Participant_21036_compound_4872; http://rdf.rhea-db.org/Compound_4872`
coenzyme A(4-) `CHEBI:57287`	consumes Rhea oriented projection, coefficient 1; same native biological event, not an additional step.	acetoacetyl-CoA + CoA => 2 acetyl-CoA `RHEA:21038`	RHEA:21038 Source assertion: substrates include CHEBI:57287 with coefficient 1; complete compound charge and formula retained. Source location `http://rdf.rhea-db.org/21038 / rh:substrates; http://rdf.rhea-db.org/21036_R/rh:contains1; http://rdf.rhea-db.org/Participant_21036_compound_1264; http://rdf.rhea-db.org/Compound_1264`
acetoacetyl-CoA + CoA => 2 acetyl-CoA `RHEA:21038`	produces Rhea oriented projection, coefficient 2; same native biological event, not an additional step.	acetyl-CoA(4-) `CHEBI:57288`	RHEA:21038 Source assertion: products include CHEBI:57288 with coefficient 2; complete compound charge and formula retained. Source location `http://rdf.rhea-db.org/21038 / rh:products; http://rdf.rhea-db.org/21036_L/rh:contains2; http://rdf.rhea-db.org/Participant_21036_compound_4271; http://rdf.rhea-db.org/Compound_4271`
ACETOACETYL-COA-TRANSFER-RXN `MetaCyc:ACETOACETYL-COA-TRANSFER-RXN`	part_of Pathway event membership.	`MetaCyc:ACETOACETATE-DEG-PWY`	MetaCyc:ACETOACETATE-DEG-PWY Source assertion: The complete pathway reaction-list contains the CoA-transfer and thiolase transformations. Source location `/ptools-xml/Pathway/reaction-list; /reaction-layout`
ACETYL-COA-ACETYLTRANSFER-RXN `MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN`	part_of Pathway event membership.	`MetaCyc:ACETOACETATE-DEG-PWY`	MetaCyc:ACETOACETATE-DEG-PWY Source assertion: The complete pathway reaction-list contains the CoA-transfer and thiolase transformations. Source location `/ptools-xml/Pathway/reaction-list; /reaction-layout`
acetoacetate + acetyl-CoA => acetoacetyl-CoA + acetate `RHEA:27807`	part_of Alternative equation projection of a native event, not another biological step.	`MetaCyc:ACETOACETATE-DEG-PWY`	MetaCyc:ACETOACETATE-DEG-PWY Source assertion: The complete pathway reaction-list contains the CoA-transfer and thiolase transformations. Source location `/ptools-xml/Pathway/reaction-list; /reaction-layout` RHEA:27807 Source assertion: Whole oriented Rhea equation projects the corresponding native pathway transformation. Source location `rh:equation; rh:substrates; rh:products`
acetoacetyl-CoA + CoA => 2 acetyl-CoA `RHEA:21038`	part_of Alternative equation projection of a native event, not another biological step.	`MetaCyc:ACETOACETATE-DEG-PWY`	MetaCyc:ACETOACETATE-DEG-PWY Source assertion: The complete pathway reaction-list contains the CoA-transfer and thiolase transformations. Source location `/ptools-xml/Pathway/reaction-list; /reaction-layout` RHEA:21038 Source assertion: Whole oriented Rhea equation projects the corresponding native pathway transformation. Source location `rh:equation; rh:substrates; rh:products`
RXN-20154 `MetaCyc:RXN-20154`	part_of Native reversible constituent in written condensation orientation; all sides retained and degradative traversal reversed.	ACETYL-COA-ACETYLTRANSFER-RXN `MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN`	MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN Source assertion: The composite reaction-list explicitly contains RXN-20154. Source location `/ptools-xml/Reaction/reaction-list` MetaCyc:RXN-20154 Source assertion: Whole constituent links back to the thiolase composite. Source location `/ptools-xml/Reaction/in-pathway`
RXN-20155 `MetaCyc:RXN-20155`	part_of Native reversible constituent in written condensation orientation; all sides retained and degradative traversal reversed.	ACETYL-COA-ACETYLTRANSFER-RXN `MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN`	MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN Source assertion: The composite reaction-list explicitly contains RXN-20155. Source location `/ptools-xml/Reaction/reaction-list` MetaCyc:RXN-20155 Source assertion: Whole constituent links back to the thiolase composite. Source location `/ptools-xml/Reaction/in-pathway`
ACETOACETYL-COA-TRANSFER-RXN `MetaCyc:ACETOACETYL-COA-TRANSFER-RXN`	provides_input_for Acetoacetyl-CoA from the transfer reaction feeds thiolytic cleavage; no physical channeling claim.	ACETYL-COA-ACETYLTRANSFER-RXN `MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN`	MetaCyc:ACETOACETYL-COA-TRANSFER-RXN Source assertion: Acetoacetyl-CoA is a product in route orientation. Source location `/ptools-xml/Reaction/right` MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN Source assertion: Acetoacetyl-CoA is consumed in the pathway right-to-left orientation. Source location `/ptools-xml/Reaction/right; native pathway direction`
ACETYL-COA-ACETYLTRANSFER-RXN `MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN`	provides_input_for Curated stoichiometric inference: one of two gross acetyl-CoA products replenishes the donor, leaving one net acetyl-CoA; no obligatory enzyme complex inferred.	ACETOACETYL-COA-TRANSFER-RXN `MetaCyc:ACETOACETYL-COA-TRANSFER-RXN`	MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN Source assertion: Native left side has coefficient two acetyl-CoA and is the product side during degradation. Source location `/ptools-xml/Reaction/left/coefficient` MetaCyc:ACETOACETYL-COA-TRANSFER-RXN Source assertion: The native left side consumes one acetyl-CoA in pathway orientation. Source location `/ptools-xml/Reaction/left`
unnamed protein complex ACETOACETYL-COA-TRANSFER-CPLX `EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX`	catalyzes Whole reference complex catalysis; native reversible chemistry and selected degradative orientation retained. No isolated-chain activity inferred.	ACETOACETYL-COA-TRANSFER-RXN `MetaCyc:ACETOACETYL-COA-TRANSFER-RXN`	EcoCyc:ACETOACETYL-COA-TRANSFER-ENZRXN Source assertion: Whole enzymatic-reaction links this assembled enzyme to the native reaction. Source location `/ptools-xml/Enzymatic-Reaction/enzyme; /reaction` MetaCyc:ACETOACETYL-COA-TRANSFER-RXN Source assertion: Complete native reaction sides support the selected chemical transformation. Source location `/ptools-xml/Reaction/left; /right; /reaction-direction`
unnamed protein complex ACETOACETYL-COA-TRANSFER-CPLX `EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX`	catalyzes Whole reference complex catalysis; native reversible chemistry and selected degradative orientation retained. No isolated-chain activity inferred.	acetoacetate + acetyl-CoA => acetoacetyl-CoA + acetate `RHEA:27807`	EcoCyc:ACETOACETYL-COA-TRANSFER-ENZRXN Source assertion: Whole enzymatic-reaction links this assembled enzyme to the native reaction. Source location `/ptools-xml/Enzymatic-Reaction/enzyme; /reaction` MetaCyc:ACETOACETYL-COA-TRANSFER-RXN Source assertion: Complete native reaction sides support the selected chemical transformation. Source location `/ptools-xml/Reaction/left; /right; /reaction-direction`
unnamed protein complex ACETYL-COA-ACETYLTRANSFER-CPLX `EcoCyc:ACETYL-COA-ACETYLTRANSFER-CPLX`	catalyzes Whole reference complex catalysis; native reversible chemistry and selected degradative orientation retained. No isolated-chain activity inferred.	ACETYL-COA-ACETYLTRANSFER-RXN `MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN`	EcoCyc:ACETYL-COA-ACETYLTRANSFER-ENZRXN Source assertion: Whole enzymatic-reaction links this assembled enzyme to the native reaction. Source location `/ptools-xml/Enzymatic-Reaction/enzyme; /reaction` MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN Source assertion: Complete native reaction sides support the selected chemical transformation. Source location `/ptools-xml/Reaction/left; /right; /reaction-direction`
unnamed protein complex ACETYL-COA-ACETYLTRANSFER-CPLX `EcoCyc:ACETYL-COA-ACETYLTRANSFER-CPLX`	catalyzes Whole reference complex catalysis; native reversible chemistry and selected degradative orientation retained. No isolated-chain activity inferred.	acetoacetyl-CoA + CoA => 2 acetyl-CoA `RHEA:21038`	EcoCyc:ACETYL-COA-ACETYLTRANSFER-ENZRXN Source assertion: Whole enzymatic-reaction links this assembled enzyme to the native reaction. Source location `/ptools-xml/Enzymatic-Reaction/enzyme; /reaction` MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN Source assertion: Complete native reaction sides support the selected chemical transformation. Source location `/ptools-xml/Reaction/left; /right; /reaction-direction`
unnamed protein complex ACETOACETYL-COA-TRANSFER-CPLX `EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX`	has_part Native reference assembly coefficient 1; nested parent/child levels and whole-complex activity retained.	β complex `EcoCyc:ATOA-CPLX`	EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX Source assertion: Direct component ATOA-CPLX, coefficient 1. Source location `/ptools-xml/Protein/component[Protein[@frameid="ATOA-CPLX"]]`
unnamed protein complex ACETOACETYL-COA-TRANSFER-CPLX `EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX`	has_part Native reference assembly coefficient 1; nested parent/child levels and whole-complex activity retained.	α complex `EcoCyc:ATOD-CPLX`	EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX Source assertion: Direct component ATOD-CPLX, coefficient 1. Source location `/ptools-xml/Protein/component[Protein[@frameid="ATOD-CPLX"]]`
β complex `EcoCyc:ATOA-CPLX`	has_part Native reference assembly coefficient 2; nested parent/child levels and whole-complex activity retained.	Acetate CoA-transferase subunit beta `UniProtKB:P76459`	EcoCyc:ATOA-CPLX Source assertion: Direct component ATOA-MONOMER, coefficient 2. Source location `/ptools-xml/Protein/component[Protein[@frameid="ATOA-MONOMER"]]` EcoCyc:ATOA-MONOMER Source assertion: Whole monomer unifies UniProtKB:P76459. Source location `/ptools-xml/Protein/dblink[dblink-db="UNIPROT"]`
α complex `EcoCyc:ATOD-CPLX`	has_part Native reference assembly coefficient 2; nested parent/child levels and whole-complex activity retained.	Acetate CoA-transferase subunit alpha `UniProtKB:P76458`	EcoCyc:ATOD-CPLX Source assertion: Direct component ATOD-MONOMER, coefficient 2. Source location `/ptools-xml/Protein/component[Protein[@frameid="ATOD-MONOMER"]]` EcoCyc:ATOD-MONOMER Source assertion: Whole monomer unifies UniProtKB:P76458. Source location `/ptools-xml/Protein/dblink[dblink-db="UNIPROT"]`
unnamed protein complex ACETYL-COA-ACETYLTRANSFER-CPLX `EcoCyc:ACETYL-COA-ACETYLTRANSFER-CPLX`	has_part Native reference assembly coefficient 4; nested parent/child levels and whole-complex activity retained.	Acetyl-CoA acetyltransferase `UniProtKB:P76461`	EcoCyc:ACETYL-COA-ACETYLTRANSFER-CPLX Source assertion: Direct component ACETYL-COA-ACETYLTRANSFER-MONOMER, coefficient 4. Source location `/ptools-xml/Protein/component[Protein[@frameid="ACETYL-COA-ACETYLTRANSFER-MONOMER"]]` EcoCyc:ACETYL-COA-ACETYLTRANSFER-MONOMER Source assertion: Whole monomer unifies UniProtKB:P76461. Source location `/ptools-xml/Protein/dblink[dblink-db="UNIPROT"]`
acetyl-CoA(4-) `CHEBI:57288`	inhibits Native inhibitory annotation; exact preparation and concentration unavailable in this regulation frame, no universal in vivo potency inferred. Source mechanism COMPETITIVE. Frame has no primary citation; substrate and inhibitory contexts are distinct.	unnamed protein complex ACETOACETYL-COA-TRANSFER-CPLX `EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX`	EcoCyc:REG0-11728 Source assertion: Whole regulation links ACETYL-COA, inhibitory mode minus, to the enzyme reaction; full mechanism/comment/citation context retained. Source location `/ptools-xml/Regulation/regulator; /mode; /regulated-entity; /mechanism; /comment; /citation`
coenzyme A(4-) `CHEBI:57287`	inhibits Native inhibitory annotation; exact preparation and concentration unavailable in this regulation frame, no universal in vivo potency inferred. Source mechanism COMPETITIVE. Competition is with respect to acyl-CoA.	unnamed protein complex ACETOACETYL-COA-TRANSFER-CPLX `EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX`	EcoCyc:REG0-8779 Source assertion: Whole regulation links CO-A, inhibitory mode minus, to the enzyme reaction; full mechanism/comment/citation context retained. Source location `/ptools-xml/Regulation/regulator; /mode; /regulated-entity; /mechanism; /comment; /citation`
(4-Carboxyphenyl)-chloro-mercury `PubChem:21226146`	inhibits Native inhibitory annotation; exact preparation and concentration unavailable in this regulation frame, no universal in vivo potency inferred.	unnamed protein complex ACETOACETYL-COA-TRANSFER-CPLX `EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX`	EcoCyc:REG0-8781 Source assertion: Whole regulation links CPD-29, inhibitory mode minus, to the enzyme reaction; full mechanism/comment/citation context retained. Source location `/ptools-xml/Regulation/regulator; /mode; /regulated-entity; /mechanism; /comment; /citation`
acetoacetyl-CoA(4-) `CHEBI:57286`	inhibits Native inhibitory annotation; exact preparation and concentration unavailable in this regulation frame, no universal in vivo potency inferred.	unnamed protein complex ACETYL-COA-ACETYLTRANSFER-CPLX `EcoCyc:ACETYL-COA-ACETYLTRANSFER-CPLX`	EcoCyc:REG0-7500 Source assertion: Whole regulation links ACETOACETYL-COA, inhibitory mode minus, to the enzyme reaction; full mechanism/comment/citation context retained. Source location `/ptools-xml/Regulation/regulator; /mode; /regulated-entity; /mechanism; /comment; /citation`
Regulatory protein AtoC `UniProtKB:Q06065`	regulates Expression-level control through atoDAEB promoter regulation; not direct allosteric activation of purified catalyst. Reporter, tagged binding and strain contexts remain separate.	unnamed protein complex ACETOACETYL-COA-TRANSFER-CPLX `EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX`	PMID:17616594 Source assertion: Promoter reporters and binding/ChIP experiments support AtoC-mediated atoDAEB transcriptional regulation with acetoacetate induction. Source location `Full Results Figs1–6; Methods strains/plasmids and binding assays` UniProtKB:Q06065 Source assertion: FUNCTION links AtoC to atoDAEB transcription. Source location `comments[commentType=FUNCTION]`
Regulatory protein AtoC `UniProtKB:Q06065`	regulates Expression-level control through atoDAEB promoter regulation; not direct allosteric activation of purified catalyst. Reporter, tagged binding and strain contexts remain separate.	unnamed protein complex ACETYL-COA-ACETYLTRANSFER-CPLX `EcoCyc:ACETYL-COA-ACETYLTRANSFER-CPLX`	PMID:17616594 Source assertion: Promoter reporters and binding/ChIP experiments support AtoC-mediated atoDAEB transcriptional regulation with acetoacetate induction. Source location `Full Results Figs1–6; Methods strains/plasmids and binding assays` UniProtKB:Q06065 Source assertion: FUNCTION links AtoC to atoDAEB transcription. Source location `comments[commentType=FUNCTION]`
Acetate CoA-transferase YdiF `UniProtKB:P37766` experimental construct: 2022 recombinant YdiF expressed from pET28a in BL21(lambdaDE3), purified by nickel affinity; 1 mM acetoacetyl-CoA plus10 mM acetate, pH7,35 °C,20 min. Exact supplement-only clone details not independently verified. Qualification evidence PMID:36333310 Source assertion: Methods describe pET28a/BL21(lambdaDE3) expression, nickel purification and the purified YdiF CoA-transfer assay. Source location `PDF pp11–12 expression/purification and CoA-transferase activity assay`	catalyzes Alternative YdiF catalytic context for this reversible chemistry. Direct 2022 assay runs acetoacetyl-CoA + acetate toward acetyl-CoA + acetoacetate; forward assimilation and growth necessity are not established.	ACETOACETYL-COA-TRANSFER-RXN `MetaCyc:ACETOACETYL-COA-TRANSFER-RXN`	PMID:36333310 Source assertion: Purified YdiF converts acetoacetyl-CoA plus acetate to acetyl-CoA in the stated LC–MS assay; lactate is tested separately. Source location `PDF p4 Fig2a/b; p12 CoA-transferase activity assay` EcoCyc:ENZRXN0-2778 Source assertion: The older whole native enzymatic-reaction links YdiF to the reversible CoA-transfer reaction with inference-level evidence. Source location `/ptools-xml/Enzymatic-Reaction/enzyme; /reaction; /evidence`

References

MetaCyc:ACETOACETYL-COA-TRANSFER-RXN MetaCyc:ACETOACETYL-COA-TRANSFER-RXN: ACETOACETYL-COA-TRANSFER-RXN (source version: Whole issuing Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ACETYL-COA EcoCyc:ACETYL-COA: acetyl-CoA (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:3-KETOBUTYRATE EcoCyc:3-KETOBUTYRATE: acetoacetate (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ACET EcoCyc:ACET: acetate (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ACETOACETYL-COA EcoCyc:ACETOACETYL-COA: acetoacetyl-CoA (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN MetaCyc:ACETYL-COA-ACETYLTRANSFER-RXN: ACETYL-COA-ACETYLTRANSFER-RXN (source version: Whole issuing Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:CO-A EcoCyc:CO-A: coenzyme A (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
MetaCyc:RXN-20154 MetaCyc:RXN-20154: RXN-20154 (source version: Whole issuing Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
MetaCyc:PROT-CYS MetaCyc:PROT-CYS: a [protein]-L-cysteine (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
MetaCyc:Protein-S-Acetyl-Cysteines MetaCyc:Protein-S-Acetyl-Cysteines: a [protein] S-acetyl-L-cysteine (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
MetaCyc:RXN-20155 MetaCyc:RXN-20155: RXN-20155 (source version: Whole issuing Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
RHEA:27807 acetoacetate + acetyl-CoA => acetoacetyl-CoA + acetate (source version: Whole frozen issuing Rhea release142 RDF; all selected subject fragments freshly replayed.)
RHEA:21038 acetoacetyl-CoA + CoA => 2 acetyl-CoA (source version: Whole frozen issuing Rhea release142 RDF; all selected subject fragments freshly replayed.)
MetaCyc:ACETOACETATE-DEG-PWY MetaCyc:ACETOACETATE-DEG-PWY: acetoacetate degradation (to acetyl CoA) (source version: Whole issuing Pathway XML, PGDB 22.5, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ACETOACETYL-COA-TRANSFER-ENZRXN EcoCyc:ACETOACETYL-COA-TRANSFER-ENZRXN: acetoacetyl-CoA transferase (source version: Whole issuing Enzymatic-Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ACETYL-COA-ACETYLTRANSFER-ENZRXN EcoCyc:ACETYL-COA-ACETYLTRANSFER-ENZRXN: acetyl-CoA acetyltransferase (source version: Whole issuing Enzymatic-Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX EcoCyc:ACETOACETYL-COA-TRANSFER-CPLX: ACETOACETYL-COA-TRANSFER-CPLX (source version: Whole issuing Protein XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ATOA-CPLX EcoCyc:ATOA-CPLX: β complex (source version: Whole issuing Protein XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ATOA-MONOMER EcoCyc:ATOA-MONOMER: acetyl-CoA:acetoacetyl-CoA transferase subunit β (source version: Whole issuing Protein XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ATOD-CPLX EcoCyc:ATOD-CPLX: α complex (source version: Whole issuing Protein XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ATOD-MONOMER EcoCyc:ATOD-MONOMER: acetyl-CoA:acetoacetyl-CoA transferase subunit α (source version: Whole issuing Protein XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ACETYL-COA-ACETYLTRANSFER-CPLX EcoCyc:ACETYL-COA-ACETYLTRANSFER-CPLX: ACETYL-COA-ACETYLTRANSFER-CPLX (source version: Whole issuing Protein XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ACETYL-COA-ACETYLTRANSFER-MONOMER EcoCyc:ACETYL-COA-ACETYLTRANSFER-MONOMER: acetyl-CoA acetyltransferase (source version: Whole issuing Protein XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:REG0-11728 EcoCyc:REG0-11728: REG0-11728 (source version: Whole issuing Regulation XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:REG0-8779 EcoCyc:REG0-8779: REG0-8779 (source version: Whole issuing Regulation XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:REG0-8781 EcoCyc:REG0-8781: REG0-8781 (source version: Whole issuing Regulation XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:REG0-7500 EcoCyc:REG0-7500: REG0-7500 (source version: Whole issuing Regulation XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
PMID:17616594 Interactions of the antizyme AtoC with regulatory elements of the Escherichia coli atoDAEB operon. (source version: Complete acquired primary PDF read, including Methods/Results/Discussion/references; selected scientific tables/figures visually inspected. Supplements not claimed fully read.)
UniProtKB:Q06065 Regulatory protein AtoC (source version: Whole reviewed UniProt JSON, retrieved 2026-10-12; organism, evidence codes, comments and features retained.)
PMID:36333310 YiaC and CobB regulate lysine lactylation in Escherichia coli. (source version: Complete acquired primary PDF read, including Methods/Results/Discussion/references; selected scientific tables/figures visually inspected. Supplements not claimed fully read.)
EcoCyc:ENZRXN0-2778 EcoCyc:ENZRXN0-2778: acetate CoA-transferase (source version: Whole issuing Enzymatic-Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
MetaCyc:Protein-L-amino-Acids MetaCyc:Protein-L-amino-Acids: a [protein]-L-amino acid (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
MetaCyc:Protein-S-Acyl-Cysteines MetaCyc:Protein-S-Acyl-Cysteines: a [protein] S-acyl-L-cysteine (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
UniProtKB:P76458 Acetate CoA-transferase subunit alpha (source version: Whole reviewed UniProt JSON, retrieved 2026-10-12; organism, evidence codes, comments and features retained.)
UniProtKB:P76459 Acetate CoA-transferase subunit beta (source version: Whole reviewed UniProt JSON, retrieved 2026-10-12; organism, evidence codes, comments and features retained.)
PMID:3025185 Genetic and molecular characterization of the genes involved in short-chain fatty acid degradation in Escherichia coli: the ato system. (source version: PubMed indexed abstract and metadata; complete primary body unavailable or not acquired. Native annotations cited separately.)
PMID:1103739 Purification and properties of Escherichia coli coenzyme A-transferase. (source version: PubMed indexed metadata only; complete primary body unavailable or not acquired. Native annotations cited separately.)
PMID:12952533 An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). (source version: PubMed indexed abstract and metadata; complete primary body unavailable or not acquired. Native annotations cited separately.)
PMID:1103741 Escherichia coli coenzyme A-transferase: kinetics, catalytic pathway and structure. (source version: PubMed indexed metadata only; complete primary body unavailable or not acquired. Native annotations cited separately.)
PMID:332081 Substrate-induced conformational changes and half-the-sites reactivity in the Escherichia coli CoA transferase. (source version: PubMed indexed metadata only; complete primary body unavailable or not acquired. Native annotations cited separately.)
EcoCyc:CPD-29 EcoCyc:CPD-29: p-chloromercuribenzoate (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
PubChem:21226146 (4-Carboxyphenyl)-chloro-mercury (source version: Whole issuing PubChem property JSON; exact native InChI, charge and formula comparison; immutable original reused.)
EcoCyc:ACETOACETATE-DEG-PWY EcoCyc:ACETOACETATE-DEG-PWY: acetoacetate degradation (to acetyl CoA) (source version: Whole issuing Pathway XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
PMID:4563344 ato Operon: a highly inducible system for acetoacetate and butyrate degradation in Escherichia coli. (source version: PubMed indexed metadata only; complete primary body unavailable or not acquired. Native annotations cited separately.)
PMID:236278 Thiolases of Escherichia coli: purification and chain length specificities. (source version: Complete acquired primary PDF read, including Methods/Results/Discussion/references; selected scientific tables/figures visually inspected. Supplements not claimed fully read.)
PMID:27380370 Crystal structure of a thiolase from Escherichia coli at 1.8 Å resolution. (source version: PubMed indexed abstract and metadata; complete primary body unavailable or not acquired. Native annotations cited separately.)
PMID:9904 Molecular and catalytic properties of the acetoacetyl-coenzyme A thiolase of Escherichia coli. (source version: PubMed indexed metadata only; complete primary body unavailable or not acquired. Native annotations cited separately.)
UniProtKB:P76461 Acetyl-CoA acetyltransferase (source version: Whole reviewed UniProt JSON, retrieved 2026-10-12; organism, evidence codes, comments and features retained.)
PMID:2883171 Regulation of the ato operon by the atoC gene in Escherichia coli. (source version: PubMed indexed abstract and metadata; complete primary body unavailable or not acquired. Native annotations cited separately.)
PMID:16153782 Phosphorylation activity of the response regulator of the two-component signal transduction system AtoS-AtoC in E. coli. (source version: PubMed indexed abstract and metadata; complete primary body unavailable or not acquired. Native annotations cited separately.)
PMID:16564134 Involvement of the AtoS-AtoC signal transduction system in poly-(R)-3-hydroxybutyrate biosynthesis in Escherichia coli. (source version: PubMed indexed abstract and metadata; complete primary body unavailable or not acquired. Native annotations cited separately.)
EcoCyc:ATOC-MONOMER EcoCyc:ATOC-MONOMER: DNA-binding transcriptional activator/ornithine decarboxylase inhibitor AtoC (source version: Whole issuing Protein XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
PMID:8346225 Identification, cloning, and nucleotide sequencing of the ornithine decarboxylase antizyme gene of Escherichia coli. (source version: PubMed indexed abstract and metadata; complete primary body unavailable or not acquired. Native annotations cited separately.)
PMID:17475408 Spermidine triggering effect to the signal transduction through the AtoS-AtoC/Az two-component system in Escherichia coli. (source version: PubMed indexed abstract and metadata; complete primary body unavailable or not acquired. Native annotations cited separately.)
PMID:22083893 Involvement of AtoSC two-component system in Escherichia coli flagellar regulon. (source version: PubMed indexed abstract and metadata; complete primary body unavailable or not acquired. Native annotations cited separately.)
EcoCyc:EG12432-MONOMER EcoCyc:EG12432-MONOMER: putative acetate-CoA transferase YdiF (source version: Whole issuing Protein XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
PMID:16253988 Crystallographic trapping of the glutamyl-CoA thioester intermediate of family I CoA transferases. (source version: PubMed indexed abstract and metadata; complete primary body unavailable or not acquired. Native annotations cited separately.)
UniProtKB:P37766 Acetate CoA-transferase YdiF (source version: Whole reviewed UniProt JSON, retrieved 2026-10-12; organism, evidence codes, comments and features retained.)
UniProtKB:Q8X5X6 Acetate CoA-transferase YdiF (source version: Whole reviewed UniProt JSON, retrieved 2026-10-12; organism, evidence codes, comments and features retained.)
PathBank:SMP0002102 Acetate Metabolism (PW002090/SMP0002102) (source version: Whole BioPAX original; all165 objects and all5 reactions/21 sides adjudicated; incompatible thiolase equation rejected.)
EcoCyc:ACETOACETYL-COA-TRANSFER-RXN EcoCyc:ACETOACETYL-COA-TRANSFER-RXN: ACETOACETYL-COA-TRANSFER-RXN (source version: Whole issuing Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:ACETYL-COA-ACETYLTRANSFER-RXN EcoCyc:ACETYL-COA-ACETYLTRANSFER-RXN: ACETYL-COA-ACETYLTRANSFER-RXN (source version: Whole issuing Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:PROT-CYS EcoCyc:PROT-CYS: a [protein]-L-cysteine (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:Protein-S-Acetyl-Cysteines EcoCyc:Protein-S-Acetyl-Cysteines: a [protein] S-acetyl-L-cysteine (source version: Whole issuing Compound XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:RXN-20154 EcoCyc:RXN-20154: RXN-20154 (source version: Whole issuing Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)
EcoCyc:RXN-20155 EcoCyc:RXN-20155: RXN-20155 (source version: Whole issuing Reaction XML, PGDB 27.0, retrieved 2026-10-12; native annotations are not blanket full-primary-paper claims.)

Curation history

2026-10-12T14:57:15.343147+00:00 Codex; draft; Complete external acetoacetate degradation scientific draft; independent scientific review and typed authority/runtime preparation remain pending.
2026-10-12T20:45:35Z codex
- CREATE — Add the complete evidence-backed acetoacetate degradation record.
  Adopted exact accepted MetaCyc:ACETOACETATE-DEG-PWY science: 29 paragraphs, 46 edges, 25 named identities, one construct qualifier, 66 references and five mappings. Whole native pathways/reactions, nested Ato assemblies, generic protein-residue classes, mechanism/assay/source limits and rejected alternative equation preserved in research/pathway_additions/2026-10-12-next-236. Actual native outputs independently reviewed and accepted. Fresh maintained gates and saved native review remain pending.
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2026-10-13T04:32:50Z codex
- EDIT — Correct RHEA:21038 source orientation
  The issuing Rhea release142 RDF SHA256 8ee48d7044cf3eef1001fa730dae2a491902ab25b259b519d6826796bb8acedf assigns 21038 substrates to 21036_R and products to 21036_L. Set direction right_to_left while preserving its oriented equation and all 46 mechanistic edges. Earlier aceto scientific/technical reviews and historical integration reports accepted the aggregate disagreement; preserve those immutable observations and append a bounded corrective review. Root and independent reviewer re-read the issuing RDF. Pages and KGX will be regenerated and checked in the publication review dossier.
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