ECHS1

Summary: Conserved mitochondrial localization is supported by the literal PAINT lineage and human localization evidence.

Reason: The exact human ECHS1 sequence occurs below the mitochondrial IBD at PTN000235143 in the current family tree. No intervening loss event was found on its lineage. Human mitochondrial proteomics and HPA mitochondrial immunofluorescence independently support this compartment. The mitochondrion assertion remains correct and core at its recorded resolution; matrix localization is established separately, rather than being attributed to every donor assay.

Summary: The PAINT fatty acid beta-oxidation assertion describes an established catalytic role.

Reason: The literal IBD at PTN000941828 is ancestral to human ECHS1. Its descendant evidence includes ECHS1 and other enzymes participating in beta-oxidation; ECI1 donors support this shared process, not transfer of their particular catalytic mechanism. Human ECHS1 hydrates beta-oxidation enoyl-CoA substrates. Neither a small donor set nor the target appearing among the descendant evidence invalidates this phylogenetic judgment.

Summary: The shared catalytic-site mapping is true but adds no reaction-specific information.

Reason: The shared InterPro hydratase/isomerase conserved site supports catalysis but does not select the specific reaction; independently accepted hydratase records already provide the informative activity. The root term is true and adds no mechanism.

Summary: A minor enoyl-CoA isomerase activity is positively supported in the rat ortholog and inferred for human ECHS1.

Reason: The current human UniProt reaction is explicitly inferred from rat P14604. PMID:10074351 reports rat wild-type hydratase-1 isomerization, with activity much lower than hydration, and catalytic-site mutant effects. This provides positive ortholog evidence for an accessory activity; it does not establish the quantitative rate or physiological flux of human ECHS1. The inherited PMID:9073515 excerpt supports ECHS1 identity and hydratase activity, not this specific isomerase assay. The literal GOA mapping identifiers are RHEA:45228, RHEA:45736 and EC:5.3.3.8; the human UniProt record traces their ortholog support to P14604.

Summary: The combined electronic mapping identifies the directly supported hydratase activity.

Reason: The official EC/Rhea-linked enoyl-CoA hydration assignment agrees with human ECHS1 substrate assays. Hydration is the defining catalytic function, independent of the electronic route by which this particular row was generated.

Summary: The mitochondrial matrix is the functional compartment of ECHS1.

Reason: The official localization mapping, cleavable mitochondrial precursor and curated matrix reaction models consistently place ECHS1 in the matrix. Human mitochondrial import and organelle proteomics corroborate mitochondrial residence. The GO_REF mapping is retained without pretending that organelle-wide immunofluorescence resolves the matrix or that the inaccessible 2025 Methods were inspected.

Summary: Branched-chain amino acid catabolism is a valid broader description of ECHS1 participation in valine degradation.

Reason: ARBA00091432 captures the branched-chain amino acid pathway. ECHS1 performs methacrylyl-CoA hydration in its valine branch, so this remains a useful pathway-level annotation. It does not assert comparable flux through leucine and isoleucine pathways.

Summary: The Rhea-derived dehydratase term expresses the reverse of ECHS1 enoyl-CoA hydration.

Reason: GO:0018812 describes the reversible 3-hydroxyacyl-CoA/enoyl-CoA reaction in the dehydration direction. The official Rhea cross-references and human hydration evidence identify the same enzyme chemistry. Reversed reaction wording does not make this an accessory or false activity; the core synthesis uses a single hydratase unit.

Summary: The acryloyl-CoA reaction is a directly supported substrate-specific activity.

Reason: The current GO definition is 3-hydroxypropionyl-CoA dehydration, the reverse of acryloyl-CoA hydration. Human ECHS1 was assayed with acryloyl-CoA in PMID:26251176. Acryloyl-CoA is not methacrylyl-CoA, and this reaction is not used as a substitute for the valine hydration step. The curated reaction mapping is corroborated by the independently read original Methods, Results and Table 2 of PMID:26251176 (PDF pages 4–6); the source guide records the archive URL and file hash. The unchanged normal cache supplies only the abstract.

Summary: Crotonyl-CoA hydration is a well-supported specific ECHS1 reaction.

Reason: The official Rhea-to-GO mapping describes hydration of crotonyl-CoA to 3-hydroxybutanoyl-CoA. Direct human substrate assays establish this activity. It is represented within the broader integrated hydratase core, without creating a separate biochemical unit for every accepted substrate.

Summary: Retired historical amino-acid catabolism mapping can be represented by the supported valine process.

Reason: GO:0170035 is currently obsolete as an unnecessary grouping term, and this exact historical electronic assertion is absent from the new GOA snapshot. The retired flag records that source lifecycle only. Biological participation remains positively supported: ECHS1 hydrates methacrylyl-CoA during L-valine catabolism, so GO:0006574 is an informative replacement. No inference of biological loss is made from snapshot absence.

Proposed replacements: L-valine catabolic process

Summary: ECHS1 binds the DNA-binding transcription factor STAT3.

Reason: The original Results/Figure 1 and curated interaction records support STAT3 association by yeast two-hybrid, GST pulldown and coimmunoprecipitation. Human STAT3 is represented in the library and endogenous HepG2 experiments; some tagged HEK293T experiments use mouse STAT3 despite the human host. The verified partner class supports DNA-binding transcription factor binding. This refinement does not assign DNA binding, transcription-factor activity or phosphatase activity to ECHS1, and it does not convert the partial original access into a complete Methods read. This partner-unspecified historical representation is retired because the same source contexts are explicitly represented by zero-based review indices 49 and 50; the positive interaction evidence is retained.

Proposed replacements: DNA-binding transcription factor binding

Summary: The curated ECHS1–LRRK2 protein-array interaction supports protein kinase binding.

Reason: The literal IntAct pair joins human P30084 and Q5S007 in a protein-array assay. The original Methods describe kinase-active GST-LRRK2 and a full-length Flag-LRRK2 screen with negative controls. LRRK2 is a verified protein kinase, so GO:0019901 is an informative partner-class refinement. The cited supplementary target table was not recovered; curated pair identity and the original assay method are distinguished from target-specific functional validation. No ECHS1 phosphorylation or kinase activity is inferred.

Proposed replacements: protein kinase binding

Summary: The LRRK1/LRRK2 interactome study supplies a curated ECHS1–LRRK2 array association.

Reason: The current source context and literal interaction record identify Q5S007/LRRK2 as the partner for this assertion. The original study used full-length Flag-tagged kinase baits on human protein arrays; its separate cell-based AP-MS and selected validation experiments are not presented as ECHS1-specific follow-up. The verified kinase partner supports protein kinase binding. The inaccessible target supplement does not justify rejecting the curator-supported pair, and the additional LRRK1 record is not substituted for the imported identity.

Proposed replacements: protein kinase binding

Summary: ECHS1 was identified in LRRK2 affinity-purification interaction records.

Reason: The literal records join human ECHS1 with wild-type and G2019S LRRK2 in affinity-purification mass spectrometry. The original Methods establish the human HEK293T/Myc-LRRK2 assay context; the published follow-up concerns SERCA rather than ECHS1. Verified protein-kinase identity supports GO:0019901 without requiring a purified interface or transferring kinase activity to ECHS1. The recovered Table S1 contains the 232 G2019S-enriched subset, not all 2,831 identified proteins; absence of an ECHS1 identifier from that subset does not refute the curated association.

Proposed replacements: protein kinase binding

Summary: The orthology-based valine-catabolism assertion agrees with direct human evidence.

Reason: The GO_REF:0000107 route transfers the process through Ensembl orthology. The exact human ECHS1 identity and mouse ortholog record were verified, while direct human methacrylyl-CoA hydration and ECHS1-deficiency evidence independently establish the same process. Mouse dietary-valine perturbations are supporting context, not a substitute for human catalytic evidence or a quantitative cross-species flux comparison.

Summary: The electronic beta-oxidation assignment matches the established ECHS1 hydration step.

Reason: ECHS1 catalyzes enoyl-CoA hydration within the mitochondrial fatty acid beta-oxidation spiral. The official keyword/reaction mapping is consistent with direct human crotonyl-CoA assays and the curated reaction models. This is direct catalytic participation rather than a downstream metabolic phenotype alone.

Summary: Reactome places ECHS1 in beta-oxidation of lauroyl-CoA to decanoyl-CoA.

Reason: The actual pathway R-HSA-77310 contains hydration event R-HSA-77256. Its catalyst chain resolves through activity 71049 and the ECHS1 hexamer to human P30084 residues 28–290 in the mitochondrial matrix. This supports participation in the modeled beta-oxidation cycle. The reaction-level model is retained as curated evidence, without treating its older enzyme literature as a newly verified purified-human assay at every chain length.

Summary: Reactome places ECHS1 in beta-oxidation of decanoyl-CoA to octanoyl-CoA.

Reason: The actual pathway R-HSA-77346 contains hydration event R-HSA-77344. Its catalyst chain resolves through activity 71049 and the ECHS1 hexamer to human P30084 residues 28–290 in the mitochondrial matrix. This supports participation in the modeled beta-oxidation cycle. The reaction-level model is retained as curated evidence, without treating its older enzyme literature as a newly verified purified-human assay at every chain length.

Summary: Reactome places ECHS1 in beta-oxidation of octanoyl-CoA to hexanoyl-CoA.

Reason: The actual pathway R-HSA-77348 contains hydration event R-HSA-77333. Its catalyst chain resolves through activity 71049 and the ECHS1 hexamer to human P30084 residues 28–290 in the mitochondrial matrix. This supports participation in the modeled beta-oxidation cycle. The reaction-level model is retained as curated evidence, without treating its older enzyme literature as a newly verified purified-human assay at every chain length.

Summary: Reactome places ECHS1 in beta-oxidation of hexanoyl-CoA to butanoyl-CoA.

Reason: The actual pathway R-HSA-77350 contains hydration event R-HSA-77325. Its catalyst chain resolves through activity 71049 and the ECHS1 hexamer to human P30084 residues 28–290 in the mitochondrial matrix. This supports participation in the modeled beta-oxidation cycle. The reaction-level model is retained as curated evidence, without treating its older enzyme literature as a newly verified purified-human assay at every chain length.

Summary: Reactome places ECHS1 in beta-oxidation of butanoyl-CoA to acetyl-CoA.

Reason: The actual pathway R-HSA-77352 contains hydration event R-HSA-77314. Its catalyst chain resolves through activity 71049 and the ECHS1 hexamer to human P30084 residues 28–290 in the mitochondrial matrix. This supports participation in the modeled beta-oxidation cycle. The reaction-level model is retained as curated evidence, without treating its older enzyme literature as a newly verified purified-human assay at every chain length.

Summary: The Reactome branched-chain amino-acid pathway contains the ECHS1 valine reaction.

Reason: Reactome R-HSA-70895 contains the ECHS1-catalyzed valine reaction R-HSA-70870. This positively establishes participation in the branched-chain pathway through its valine branch; the pathway-level context is retained alongside the specific valine process.

Summary: Human ECHS1 enzyme assays directly establish enoyl-CoA hydratase activity.

Reason: The original study expressed human ECHS1 in HEK293 cells and used a 51-fold partially purified preparation, rather than homogeneous protein. It measured direct hydration for several enoyl-CoA substrates; methacrylyl-CoA activity used a coupled assay with rat HIBCH. These assay distinctions preserve the direct evidence for ECHS1 hydration without attributing the downstream HIBCH hydrolysis to ECHS1.

Summary: Reactome assigns ECHS1 hydration of trans-dodec-2-enoyl-CoA.

Reason: R-HSA-77256 has enoyl-CoA hydratase catalyst 71049, linked to the human ECHS1 mature-chain hexamer in the mitochondrial matrix. Its input/output fields describe the appropriate enoyl-CoA hydration chemistry. Retain the curated reaction assignment while distinguishing model support from an independently reconstructed human kinetic assay for this particular substrate.

Summary: Reactome assigns ECHS1 hydration of crotonyl-CoA.

Reason: R-HSA-77314 has enoyl-CoA hydratase catalyst 71049, linked to the human ECHS1 mature-chain hexamer in the mitochondrial matrix. Its input/output fields describe the appropriate enoyl-CoA hydration chemistry. Retain the curated reaction assignment while distinguishing model support from an independently reconstructed human kinetic assay for this particular substrate.

Summary: Reactome assigns ECHS1 hydration of trans-hex-2-enoyl-CoA.

Reason: R-HSA-77325 has enoyl-CoA hydratase catalyst 71049, linked to the human ECHS1 mature-chain hexamer in the mitochondrial matrix. Its input/output fields describe the appropriate enoyl-CoA hydration chemistry. Retain the curated reaction assignment while distinguishing model support from an independently reconstructed human kinetic assay for this particular substrate.

Summary: Reactome assigns ECHS1 hydration of trans-oct-2-enoyl-CoA.

Reason: R-HSA-77333 has enoyl-CoA hydratase catalyst 71049, linked to the human ECHS1 mature-chain hexamer in the mitochondrial matrix. Its input/output fields describe the appropriate enoyl-CoA hydration chemistry. Retain the curated reaction assignment while distinguishing model support from an independently reconstructed human kinetic assay for this particular substrate.

Summary: Reactome assigns ECHS1 hydration of trans-dec-2-enoyl-CoA.

Reason: R-HSA-77344 has enoyl-CoA hydratase catalyst 71049, linked to the human ECHS1 mature-chain hexamer in the mitochondrial matrix. Its input/output fields describe the appropriate enoyl-CoA hydration chemistry. Retain the curated reaction assignment while distinguishing model support from an independently reconstructed human kinetic assay for this particular substrate.

Summary: The disease reaction refers to loss of the normal ECHS1 hydratase activity.

Reason: R-HSA-9916717 is explicitly a FailedReaction, with normalReaction R-HSA-70870. Its mutant ECHS1 catalyst is associated with loss-of-function status, so it must not be read as evidence that inactive variants carry out hydration. The record describes which normal activity is deficient, and independent human enzyme assays establish that activity for ECHS1. Retain the imported gene-level hydratase assertion with the disease-source scope made explicit.

Summary: ECHS1 affects lysine-derived crotonyl-CoA metabolism in glioma stem-cell experiments.

Reason: The original human glioma study combines lysine tracing with ECHS1 expression perturbations and GCDH/CBP dependencies. Increasing ECHS1 reduces crotonyl-CoA-associated histone crotonylation and stem-cell growth, whereas depletion produces the converse context-dependent effects. These findings positively connect ECHS1 consumption of a lysine-derived crotonyl-CoA pool to lysine catabolism; they are not dismissed merely because the metabolite is shared with other pathways. Retain this experimental process as contextual to the glioma metabolic program. CBP/P300 and related enzymes perform histone crotonylation; the findings do not give ECHS1 a nuclear histone-modifying activity.

Summary: HPA immunofluorescence positively supports mitochondrial localization.

Reason: The actual HPA target record labels mitochondria as enhanced at the individual-location level. The saved XML includes mitochondrial staining in A-431, U-251 MG and U2OS contexts. This is positive evidence for a core compartment, retained at the resolution of the assay; it does not itself distinguish matrix from mitochondrial membranes or prove absence from every other pool.

Summary: The curated 2025 matrix-localization assertion agrees with established ECHS1 compartmentalization.

Reason: The current source is an experimental IDA annotation, and matrix residence is independently consistent with official precursor processing and curated matrix reactions. Only the abstract of PMID:40056416 was recovered, so its target-specific localization experiment is not claimed as independently inspected. Retain the correct established compartment with curator deference rather than rejecting an unseen assay or inventing its imaging details.

Summary: ECHS1 loss perturbs the valine-associated methacrylyl-CoA pathway.

Reason: The 2025 abstract reports increased lysine methacrylation in ECHS1- and HIBCH-deficient cells and fly tissues. This supports the curated perturbation-based valine-process assertion and is consistent with independent human methacrylyl-CoA hydration evidence. The original body was not recovered, so no unobserved construct, cell-line or localization-method detail is supplied; necessity evidence is accompanied here by an independently demonstrated catalytic step.

Summary: Human ECHS1 directly hydrates acryloyl-CoA.

Reason: The existing IDA annotation is retained on curator evidence together with an independent reading of the original study, rather than on the general abstract excerpt alone. The externally recovered PMID:26251176 original (DOI:10.1136/jmedgenet-2015-103231; SHA256 0b1c96c82e0b44dea4118463eed88d0387466147a7a4fbb9879cdff1588c1d2b) describes the human ECHS1 preparation and direct acryloyl-CoA hydration assay in Methods and Results on PDF pages 4–6, with substrate kinetics in Table 2 on page 6. The local source guide records its archived public URL and these locators; the normal publication cache remains abstract-only. GO:0043956 describes the reverse 3-hydroxypropionyl-CoA dehydration reaction. Acryloyl-CoA is distinct from the methacrylyl-CoA used in valine catabolism, and the acryloyl assay did not use the rat-HIBCH coupling needed for methacrylyl-CoA measurement.

Summary: The ECHS1 disease reaction is modeled in the mitochondrial matrix.

Reason: R-HSA-9916717 and its ECHS1 mutant hexamer carry the mitochondrial matrix compartment. The event is a failed reaction, not a positive catalytic measurement in the variants. Its localization is consistent with the normal ECHS1 matrix reaction and retained as curated compartment evidence, without claiming direct variant-by-variant microscopy.

Summary: The MitoCoP measurements positively identify human ECHS1 in mitochondria.

Reason: The Table S1 workbook contains the exact P30084/ECHS1 group in sheet A, physical row 337, and the MitoCoP gene inventory in sheet B, row 305. The study combines subtractive and spatial proteomics with importomics; its Methods specify human cell fractionation and quantitative mass spectrometry. Retain this positive mitochondrial observation as core localization at the assay resolution, without converting organelle enrichment into an independently measured matrix-specific or isoform-specific result.

Summary: The IDA record captures direct human enoyl-CoA hydration.

Reason: The original human ECHS1 preparation and substrate assays directly support the enzyme activity. The preparation was partially purified from HEK293 cells; direct hydration measurements and the rat-HIBCH-coupled methacrylyl assay are distinguished. This is the defining activity, represented once in the integrated core.

Summary: Human substrate assays establish ECHS1 catalytic participation in fatty acid beta-oxidation.

Reason: ECHS1 directly hydrates crotonyl-CoA and other tested enoyl-CoA substrates, performing the hydration step of beta-oxidation. The annotation is supported by catalytic participation, not solely by mitochondrial disease or a downstream energy phenotype. Substrate breadth in vitro is not interpreted as equal physiological flux through every chain length.

Summary: The normal valine hydration reaction places ECHS1 in the mitochondrial matrix.

Reason: R-HSA-70870 resolves through catalyst 71049 to an ECHS1 hexamer containing human P30084 residues 28–290, with the matrix compartment on the reaction and protein entities. This is curated model evidence consistent with precursor import and official localization, not a new imaging experiment.

Summary: The modeled dodecenoyl-CoA hydration reaction locates ECHS1 in the matrix.

Reason: The actual R-HSA-77256 reaction has a mitochondrial matrix compartment and shares catalyst 71049, which resolves to the human ECHS1 mature-chain hexamer. The source therefore supports the specific compartment in which this modeled hydration occurs. Preserve this curated reaction-level assertion separately from direct localization experiments.

Summary: The modeled crotonyl-CoA hydration reaction locates ECHS1 in the matrix.

Reason: The actual R-HSA-77314 reaction has a mitochondrial matrix compartment and shares catalyst 71049, which resolves to the human ECHS1 mature-chain hexamer. The source therefore supports the specific compartment in which this modeled hydration occurs. Preserve this curated reaction-level assertion separately from direct localization experiments.

Summary: The modeled hexenoyl-CoA hydration reaction locates ECHS1 in the matrix.

Reason: The actual R-HSA-77325 reaction has a mitochondrial matrix compartment and shares catalyst 71049, which resolves to the human ECHS1 mature-chain hexamer. The source therefore supports the specific compartment in which this modeled hydration occurs. Preserve this curated reaction-level assertion separately from direct localization experiments.

Summary: The modeled octenoyl-CoA hydration reaction locates ECHS1 in the matrix.

Reason: The actual R-HSA-77333 reaction has a mitochondrial matrix compartment and shares catalyst 71049, which resolves to the human ECHS1 mature-chain hexamer. The source therefore supports the specific compartment in which this modeled hydration occurs. Preserve this curated reaction-level assertion separately from direct localization experiments.

Summary: The modeled decenoyl-CoA hydration reaction locates ECHS1 in the matrix.

Reason: The actual R-HSA-77344 reaction has a mitochondrial matrix compartment and shares catalyst 71049, which resolves to the human ECHS1 mature-chain hexamer. The source therefore supports the specific compartment in which this modeled hydration occurs. Preserve this curated reaction-level assertion separately from direct localization experiments.

Summary: ECHS1 precursor binding to mitochondrial import receptors is experimentally supported.

Reason: The original human ECHS1 library and translated-precursor experiments show binding to Tom20 and Tom22 receptor fragments, with GST controls. These are positive import-recognition interactions, not evidence that ECHS1 itself acts as an import receptor or chaperone. The verified partners are mitochondrial import receptors rather than signaling receptors as defined by GO:0005102; no supported informative binding class was established in this bounded assessment. Retain generic protein binding as non-core under the project-specific policy, preserving the true interaction. This partner-unspecified historical representation is retired because the same source contexts are explicitly represented by zero-based review indices 51 and 52; the positive interaction evidence is retained.

Summary: The historical endothelial-proteomics localization is consistent with the established mitochondrial pool.

Reason: The abstract describes a HUVEC proteomic survey; its target-specific full-text table was not recovered. This TAS compartment assertion is retained with that access limit and with independent human ECHS1 mitochondrial proteomics and import evidence. It is not rejected solely because the abstract foregrounds other proteins, nor is it demoted merely because mitochondrion is broader than matrix.

Summary: The human cloning paper attributes the expected hydratase activity to ECHS1.

Reason: The verified abstract identifies ECHS1 as the enzyme catalyzing the second beta-oxidation step. This supports the statement-level TAS annotation; the paper is not described as a purified-human kinetic study. Independent human biochemical work supplies direct confirmation.

Summary: The human cloning paper places ECHS1 in mitochondrial fatty acid beta-oxidation.

Reason: The abstract explicitly describes the ECHS1-catalyzed second step of mitochondrial beta-oxidation. Retain the TAS process assertion while distinguishing that statement from the later direct substrate assays. The enzyme performs a reaction within the pathway rather than merely changing its downstream output.

Summary: The restored explicit human STAT3 context supports transcription-factor binding.

Reason: This current source record specifies P40763, human STAT3. The literal MINT records and original Figure 1 Results include human STAT3 yeast two-hybrid and endogenous HepG2 coimmunoprecipitation evidence. STAT3 is a verified DNA-binding transcription factor, supporting GO:0140297. This is partner-class binding, not ECHS1 transcription-factor activity; the broader historical source row is preserved as a retired aggregate. This partner context was already present in the archived GOA and is restored explicitly here.

Proposed replacements: DNA-binding transcription factor binding

Summary: The restored mouse Stat3 partner context preserves the documented cross-species assay.

Reason: The imported partner P42227 is mouse Stat3. Literal MINT records specify mouse Stat3 in tagged HEK293T coimmunoprecipitation and GST pulldown experiments; human assay cells do not change the construct species. Stat3 has the verified DNA-binding transcription-factor class, so GO:0140297 describes the tested binding activity. No native human–human interaction is inferred from this particular record alone. This partner context was already present in the archived GOA; the broader historical source row is retained as a retired aggregate.

Proposed replacements: DNA-binding transcription factor binding

Summary: The explicit TOMM20 partner records positive ECHS1 precursor recognition.

Reason: Q15388 is human TOMM20. Original yeast two-hybrid and translated human ECHS1/GST-receptor experiments support precursor binding to TOMM20 fragments. This is a mitochondrial import-recognition interaction, and TOMM20 is not a signaling receptor under GO:0005102. Retain the positive generic interaction as non-core under the project-specific policy; ECHS1 being imported does not make it an import receptor or transport adaptor.

Summary: The explicit TOMM22 partner records positive ECHS1 precursor recognition.

Reason: Q9NS69 is human TOMM22. Figure 1C and the original Methods describe translated human ECHS1 binding to GST-Tom22 residues 1–82 with GST controls. The prey was produced in reticulocyte lysate, so this is not represented as a homogeneous purified-pair assay. No informative signaling-receptor or chaperone class is established for this interaction; retain the positive generic binding as non-core under the project-specific policy.