UniProt: P11310 | HGNC:89 | EC 1.3.8.7 | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial.
MCAD catalyzes the first (rate-committed) step of each cycle of mitochondrial fatty acid
beta-oxidation for medium-chain acyl-CoA esters: the FAD-dependent alpha,beta-dehydrogenation
of a saturated acyl-CoA to the corresponding trans-2-enoyl-CoA, with electrons passed to the
electron-transfer flavoprotein (ETF).
This section supersedes conflicting interpretations in the earlier notes, while preserving
that earlier record. All 50 original GOA assertions, including their terms, qualifiers,
evidence codes and original references, remain unchanged. The final revised actions are 38 ACCEPT,
6 KEEP_AS_NON_CORE, 4 UNDECIDED, 1 MARK_AS_OVER_ANNOTATED and 1 MODIFY. No new annotation is proposed.
ACADM is the HGNC-approved human symbol (HGNC:89; UniProt P11310; aliases MCAD,
MCADH and ACAD1), checked against the HGNC-provided NCBI gene record.
The baseline review matches main commit 21121fc735d20bcb2dbf8328aa82d5da30185e5e,
Git blob 9e3c0f399451c3b041c58b61aa6f66ee064c28e4. An open-PR search found no overlapping
ACADM PR before editing. This was a substantive re-review of an existing COMPLETE file,
not a new seeded review.
A genuine default Falcon attempt with the prescribed perplexity-lite fallback ran alongside
publication caching. Both provider commands failed before reaching a research provider:
uvx could not fetch deep-research-client[cyberian]==0.2.7rc1 from PyPI because DNS lookup
failed, returning code 2 for each provider and wrapper code 1. The attempt used writable
process-local UV tool/cache directories. No provider report was produced, and no manual
text was labeled as provider output. All 13 cited publications were already cached;
fetch-gene-pmids completed 13/13 without replacing source files. This manual source review
uses those caches plus the primary-source reads identified below. No machine source was edited.
The single core function is FAD-dependent, ETF-coupled acyl-CoA dehydrogenation in the
mitochondrial matrix. FAD binding remains a valid annotation but is a component of that
catalytic mechanism, not an independent core function. Human liver enzyme purification
identifies the octanoyl-CoA product, ETF use, one FAD per subunit and homotetrameric structure
PMID:3597357. Recombinant human enzyme mutagenesis establishes the catalytic glutamate
and FAD content PMID:1970566. The reaction is the first step of a beta-oxidation cycle;
the earlier description as a rate-committed step was not justified by these sources.
The C14/C16 long-chain reactions in the unchanged human UniProt record have explicit
Rhea assignments, RHEA:47316/RHEA:43448, and human-literature provenance. Their existence is
compatible with a C6/C8 activity optimum [PMID:8823175; PMID:21237683]. These activities are
retained as non-core rather than rejected from the protein's name. The earlier high-Km
argument was incorrect: the curated record lists C8 3.4, C14 2.3 and C16 1.6 micromolar;
Km alone does not establish turnover or catalytic efficiency. The original full kinetic
panel was not independently re-extracted.
The RHEA:43456 pentanoyl-CoA reaction is assigned in human UniProt by similarity to rat
Acadm P08503, whose identity was checked in UniProt. GO:0016937 covers substrates with
fewer than six carbons and is not exclusive to the protein named SCAD. Retain this
secondary activity with its orthology limitation; neither butyryl-CoA kinetics nor an
activity optimum directly measures human C5 turnover. The underlying rat C5 assay remains
unrecovered. Broad acyl-CoA dehydrogenase/oxidoreductase terms describe the core chemistry
and are accepted rather than demoted solely for their breadth.
The earlier statement that PMID:16020546 contains only indirect MCAD context is withdrawn.
The author-uploaded full primary article
was inspected at Figure 5 and the submitochondrial localization results. It directly tests
MCAD in fractionated human muscle mitochondria and detects it in both matrix and membrane
fractions. The authors interpret the membrane signal as loose association or nonspecific
adherence typical of matrix ACADs. Matrix is accepted as core and membrane association is
retained as non-core, without claiming an integral or stable membrane-resident protein.
The local PMID cache remains abstract-only; primary full-text access is not relabeled as
complete local caching.
The primary ACAD10/11 study
includes MCAD comparator activity and immunostaining data in sections 3.7/3.8. Its axon
observation is retained as non-core PMID:21237683. The staining does not by itself resolve
every molecule to mitochondria or define an axon-specific molecular function. General
mitochondrion annotations correctly describe the core compartment. Cytoplasm is compatible
but less informative and is refined to matrix, without asserting that the PAINT inference
is biologically false.
The sperm-nucleus source reports extensive removal of mitochondrial and other non-nuclear
structures [PMID:21630459; publisher record].
The full ACADM-specific identification/supplement was not recovered. The earlier confident
contamination claim is withdrawn; the nucleus HDA remains UNDECIDED. The MitoCoP main article
was inspected PMID:34800366, but its individual ACADM supplementary entry was not re-extracted;
mitochondrion is accepted with curator deference and independent targeted evidence.
All 19 electronic/phylogenetic assertions have source-entity assessments. PAINT inference
is evaluated as ancestral-node propagation, not as pairwise donor counting; no reconstructed
tree or IBD placement is claimed. The underlying ARBA predicates were not inspected and
are explicitly UNRESOLVED even where independent human evidence supports the annotation.
InterPro domain/site compatibility is distinguished from experimental proof of chemistry.
Rhea and EC mappings are checked against the unchanged curated catalytic record.
The Ensembl process transfers identify mouse Acadm P45952 / ENSMUSP00000072483 / MGI:87867.
Their exact term-specific donor evidence chain for glycogen biosynthesis, regulation of
gluconeogenesis and CoA-linked carnitine metabolism was not recovered. QuickGO retrieval
failed on DNS and MGI page access was incomplete; no matching ACADM/Acadm entry was found
in the local GO-CAM index. The mouse identity is corroborated by the
Reactome ortholog reaction.
These three assertions are UNDECIDED rather than rejected as spurious transfers. A mouse
knockout article read as a lead (primary article)
was not established as the donor source and is not substituted for that missing chain.
The patient exercise study
measures carnitine-related plasma/urine changes and infers compensatory biosynthesis. Its
full text was not recovered. The CoA-linked carnitine and carnitine-biosynthesis IMP
assertions therefore remain UNDECIDED: the abstract alone does not show ACADM performing
a step in these processes. The FAO annotation is retained using independent human enzyme
evidence; increased octanoylcarnitine is not relabeled as directly quantified successful
MCAD flux. No additional process is proposed from metabolic necessity alone.
All 13 PMID references received manual source-scope assessments. VERIFIED refers to
citation identity and the support explicitly described, not to complete full-text access
or resolution of every annotation. PMID:25416781 supplies ETF-dependent electron-transfer
evidence, but its locally recovered text lacks complete assay methods. PMID:1731887 supports
a mitochondrial location by a traceable statement. PMID:2393404 establishes a human disease
variant, not a purified-enzyme assay. Reactome expression-event location is the location of
the mature protein, not the site of transcription or translation.
The earlier variant numbering is reversed: c.985A>G is precursor p.Lys329Glu, conventionally
K304E after removal of the 25-residue targeting peptide. Likewise, mature Glu376 corresponds
to precursor Glu401. PMID:1902818 describes tetramer failure as a probable explanation for
variant inactivity. Full-text PMID:19224950 shows variant-dependent differences in assembly,
stability and kinetics, including variants with preserved tetramer assembly; it does not
justify assigning one identical mechanism to all missense alleles. Identical-protein binding
is retained as non-core based on measured wild-type homotetramers.
The draft preserves all original source fields across 50 annotations and adds no NEW rows.
Initial just validate human ACADM passes without warnings or errors. History and rendered
HTML are generated from the final draft; an independent annotation review is requested before
publication. No Git state or shared project tracker was changed by this task.
Independent annotation review by the sibling annotation-reviewer found stale reference
findings concerning sperm-nucleus contamination, inferred exercise flux, probable tetramer
failure and a generic MitoCoP quote. These reviewer-authored statements were corrected to
match the source-scoped judgments above. Variant heterogeneity and cohort-specific allele
frequency were also clarified. IBA source-entity blocks retain the PTN ancestral node, as
the annotation-reviewer skill specifies, rather than templated extant-descendant lists.
The earlier unresolved-donor paragraph is superseded by a newly accessible
MGI comparative Acadm graph,
generated 2023-03-10. It explicitly lists mouse IMP evidence from PMID:18459129 / MGI:4412440
for all three disputed process annotations. The present web footer is newer than that
snapshot; no current GOA export or exact current Ensembl evidence selection is claimed.
The primary PubMed abstract was independently
verified. The sibling reviewer could additionally inspect methods/results through page 10
of an author thesis chapter reproducing the study.
Subsequent PDF requests timed out for both reviewers; the discussion was not read and no
complete full-paper access is claimed.
The source establishes stress-dependent metabolic effects. De novo G6P formation decreases
by about 20% during the LPS-induced acute phase response, while fasting alone has no such
reduction. G6P partitioning shifts toward glycogen. The glycogen-biosynthesis assertion is
therefore MARK_AS_OVER_ANNOTATED as a process-role overstatement; regulation of gluconeogenesis
is retained as a contextual non-core role. The partial methods/results include carnitine
pool assays; carnitine-process participation remains UNDECIDED because an unresolved
mechanism is not settled by altered metabolites. These are source-based judgments, not
an assertion that the mouse ortholog was misidentified.
Normal caching of the newly required PMID failed DNS (0/1 publications, no artifact), both
in the parent's canonical request and in an overlapping temporary-output probe initiated
before the parent's pending request was known. Neither source cache was fabricated. The
bibliographic entry is retained honestly; final publication must stay a draft until this
missing cache can be recovered normally. There are now 14 cited PMIDs, of which the original
13 remain cached and unchanged. Initial validation passed before adding the newly identified
source; the final validation report must be interpreted with this cache limitation.
Final targeted validation passes with one reference warning: Could not fetch reference: PMID:18459129. Rendering completes successfully. This operational limitation remains explicit; there are no schema, ontology, quotation or source-assertion errors.
Final independent signoff found no remaining blocking biological concern across all 50 rows, core functions, reference findings and notes. The missing PMID cache remains the publication limitation.
The earlier glycogen-biosynthesis OVER_ANNOTATED decision is superseded by REMOVE. This electronic transfer assigns ACADM to glycogen synthesis, whereas the recovered source describes G6P flux repartitioning and no ACADM-performed synthesis step. The reason and ROLE_CONFLATION assessment therefore support removing this process assertion. Regulation of gluconeogenesis remains a separate, context-dependent claim. Final counts are 38 ACCEPT, 6 KEEP_AS_NON_CORE, 4 UNDECIDED, 1 REMOVE and 1 MODIFY; all 50 source assertions are unchanged. PMID:18459129 still requires its normal cache fetch before this draft can become ready.
Recovered required PMID:18459129 through standard fetch-pmid in read-only Actions run 36286975328 (job 108529455048, artifact 10920674630), transported unchanged by read-only run 36288441414. Verified artifact SHA256 c0ffe4a66b80278af34b44aab6a3ae354ffd5699236b3a486ca95527be5e9713 and every record SHA256/Git blob before importing. Re-read this abstract, confirmed exact citation title and retained full_text_unavailable=true. All annotation decisions, source objects, core functions, reference identities and alternative products remain unchanged from 786055049e98d6df533cb981a2bffedc9b8a8148. Targeted validation passed with 0 warnings; YAML status is COMPLETE. The machine cache requirement is satisfied; source-limited UNDECIDED judgments remain explicit.
This supersedes the earlier missing-cache publication gate. The recovered record is abstract-only; neither its presence nor successful validation establishes access to the full paper. Zero remaining validation warnings permit COMPLETE status and a ready PR.
Final checks: just validate human ACADM, just render human ACADM and the new history validation all passed. The parsed review differs only in source-access notes and, where applicable, status; every biological decision and source field is preserved.