id: P55084
gene_symbol: HADHB
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  HADHB encodes the beta subunit of the mitochondrial trifunctional protein (MTP/TFP),
  a heterotetrameric complex (alpha2-beta2) that catalyzes the last three steps of
  long-chain fatty acid beta-oxidation. The beta subunit specifically possesses ONLY
  3-ketoacyl-CoA thiolase activity (EC 2.3.1.155, 2.3.1.16), while the alpha subunit
  (HADHA) carries the enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase activities.
  The complex is located in the mitochondrial inner membrane, where it processes
  long-chain fatty acyl-CoA substrates (C10-C16). Mutations in HADHB cause mitochondrial
  trifunctional protein deficiency type 2 (MTPD2), an autosomal recessive disorder
  characterized by cardiomyopathy, myopathy, and peripheral neuropathy.
alternative_products:
- name: '1'
  id: P55084-1
- name: '2'
  id: P55084-2
  sequence_note: VSP_054426
existing_annotations:
# ============================================================================
# MOLECULAR FUNCTION - THIOLASE ACTIVITIES (CORE FUNCTIONS - CORRECT)
# ============================================================================
- term:
    id: GO:0003985
    label: acetyl-CoA C-acetyltransferase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      This IBA annotation correctly assigns acetyl-CoA C-acetyltransferase activity to HADHB.
      The beta subunit possesses 3-ketoacyl-CoA thiolase activity, which includes this
      acetyltransferase function. PMID:8135828 demonstrated that "Expression of this cDNA
      [beta-subunit] in mammalian cells yielded a polypeptide with the long-chain 3-ketoacyl-CoA
      thiolase activity."
    action: ACCEPT
    reason: >-
      Core molecular function of HADHB. The thiolase activity of the beta subunit is well
      established through direct expression studies (PMID:8135828) and confirmed by structural
      studies showing the thiolase active site in the beta subunit (PMID:30850536).
    supported_by:
      - reference_id: PMID:8135828
        supporting_text: "Expression of this cDNA in mammalian cells yielded a polypeptide with the long-chain 3-ketoacyl-CoA thiolase activity."

- term:
    id: GO:0003985
    label: acetyl-CoA C-acetyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation based on Ensembl ortholog transfer. Consistent with the IBA annotation
      and experimental evidence showing HADHB has thiolase activity.
    action: ACCEPT
    reason: >-
      Redundant with IBA but correctly captures the core thiolase function. Electronic
      annotation is consistent with experimental evidence.

- term:
    id: GO:0003988
    label: acetyl-CoA C-acyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      This IEA annotation correctly assigns acetyl-CoA C-acyltransferase activity to HADHB.
      This is essentially synonymous with 3-ketoacyl-CoA thiolase activity (EC 2.3.1.16).
      UniProt lists EC:2.3.1.16 for HADHB with evidence from multiple publications.
    action: ACCEPT
    reason: >-
      Core molecular function. The acyltransferase activity is the same as the thiolase
      activity that characterizes the beta subunit. UniProt EC annotation (EC:2.3.1.16)
      is supported by PMID:7958339, PMID:8135828, PMID:8163672, and PMID:8651282.

- term:
    id: GO:0003988
    label: acetyl-CoA C-acyltransferase activity
  evidence_type: TAS
  original_reference_id: PMID:8135828
  review:
    summary: >-
      This TAS annotation is correctly based on PMID:8135828, which directly demonstrated
      that expression of the beta-subunit cDNA yielded thiolase activity. This is a key
      paper that definitively assigned the thiolase activity to the beta subunit specifically.
    action: ACCEPT
    reason: >-
      Core molecular function with strong direct evidence. PMID:8135828 showed "Expression
      of this cDNA [beta-subunit] in mammalian cells yielded a polypeptide with the
      long-chain 3-ketoacyl-CoA thiolase activity" while the alpha-subunit expression
      yielded hydratase and dehydrogenase activities.
    supported_by:
      - reference_id: PMID:8135828
        supporting_text: "Expression of this cDNA in mammalian cells yielded a polypeptide with the long-chain 3-ketoacyl-CoA thiolase activity."

- term:
    id: GO:0050633
    label: acetyl-CoA C-myristoyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      This IEA annotation assigns a specific long-chain thiolase activity (EC 2.3.1.155)
      to HADHB. UniProt lists this EC number for HADHB. The MTP complex shows specificity
      for long-chain fatty acids (C10-C16), and myristoyl-CoA (C14) is within this range.
    action: ACCEPT
    reason: >-
      Appropriate specific thiolase activity. HADHB is annotated with EC:2.3.1.155 in
      UniProt based on PMID:7958339, PMID:8135828, PMID:8163672, and PMID:8651282.
      This reflects the long-chain substrate specificity of the enzyme.

# ============================================================================
# MOLECULAR FUNCTION - INCORRECT ANNOTATIONS (BELONG TO HADHA, NOT HADHB)
# ============================================================================
- term:
    id: GO:0003857
    label: (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity
  evidence_type: TAS
  original_reference_id: PMID:1550553
  review:
    summary: >-
      CRITICAL ERROR: This annotation incorrectly assigns 3-hydroxyacyl-CoA dehydrogenase
      activity to HADHB. PMID:1550553 (1992) characterized the whole trifunctional enzyme
      complex before the subunit-specific activities were determined. The subsequent study
      PMID:8135828 (1994) definitively showed that the ALPHA subunit (HADHA), not the beta
      subunit (HADHB), carries the dehydrogenase activity.
    action: REMOVE
    reason: >-
      This activity belongs to HADHA, not HADHB. PMID:8135828 clearly demonstrated:
      "Expression of this cDNA [alpha-subunit] in mammalian cells yielded a polypeptide
      with the long-chain enoyl-CoA hydratase and long-chain 3-hydroxyacyl-CoA dehydrogenase
      activities." The beta subunit expression only yielded thiolase activity. UniProt
      correctly notes that "the trifunctional enzyme subunit alpha/HADHA carries the
      2,3-enoyl-CoA hydratase and the 3-hydroxyacyl-CoA dehydrogenase activities."
    supported_by:
      - reference_id: PMID:8135828
        supporting_text: "Expression of this cDNA in mammalian cells yielded a polypeptide with the long-chain enoyl-CoA hydratase and long-chain 3-hydroxyacyl-CoA dehydrogenase activities. [referring to alpha-subunit]"

- term:
    id: GO:0004300
    label: enoyl-CoA hydratase activity
  evidence_type: TAS
  original_reference_id: PMID:1550553
  review:
    summary: >-
      CRITICAL ERROR: This annotation incorrectly assigns enoyl-CoA hydratase activity
      to HADHB. PMID:1550553 (1992) characterized the whole trifunctional enzyme complex
      before the subunit-specific activities were determined. The subsequent study
      PMID:8135828 (1994) definitively showed that the ALPHA subunit (HADHA), not the beta
      subunit (HADHB), carries the hydratase activity.
    action: REMOVE
    reason: >-
      This activity belongs to HADHA, not HADHB. PMID:8135828 clearly demonstrated:
      "Expression of this cDNA [alpha-subunit] in mammalian cells yielded a polypeptide
      with the long-chain enoyl-CoA hydratase and long-chain 3-hydroxyacyl-CoA dehydrogenase
      activities." The beta subunit expression only yielded thiolase activity.
      The crystal structure (PMID:30850536) confirms that ECH (hydratase) and HAD
      (dehydrogenase) active sites are in the alpha subunits.
    supported_by:
      - reference_id: PMID:8135828
        supporting_text: "Expression of this cDNA in mammalian cells yielded a polypeptide with the long-chain enoyl-CoA hydratase and long-chain 3-hydroxyacyl-CoA dehydrogenase activities. [referring to alpha-subunit]"
      - reference_id: PMID:30850536
        supporting_text: "The biological unit of the protein is alpha2beta2... employing 2-enoyl-CoA hydratase (ECH), 3-hydroxyl-CoA dehydrogenase (HAD), and 3-ketothiolase (KT) activities consecutively. [ECH and HAD are in alpha subunit, KT in beta]"

# ============================================================================
# MOLECULAR FUNCTION - GENERAL TRANSFERASE TERMS (NON-CORE)
# ============================================================================
- term:
    id: GO:0016740
    label: transferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      Very broad term based on UniProt keyword mapping. HADHB does have transferase
      activity (thiolase is a type of transferase), but this is too general to be
      informative.
    action: KEEP_AS_NON_CORE
    reason: >-
      Technically correct but uninformative. The more specific thiolase/acyltransferase
      terms (GO:0003985, GO:0003988) better capture the molecular function.

- term:
    id: GO:0016746
    label: acyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Parent term of the more specific acetyl-CoA C-acyltransferase activity. Correct
      but less informative than the specific child terms.
    action: KEEP_AS_NON_CORE
    reason: >-
      Technically correct parent term. The more specific terms (GO:0003988, GO:0003985)
      should be used as core function annotations.

- term:
    id: GO:0016747
    label: acyltransferase activity, transferring groups other than amino-acyl groups
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      InterPro-based annotation capturing the thiolase domain function. Correct but
      less specific than the acetyl-CoA C-acyltransferase terms.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct parent term based on thiolase domain (InterPro:IPR002155). More specific
      child terms should be used for core function.

# ============================================================================
# MOLECULAR FUNCTION - PROTEIN BINDING (NON-CORE)
# ============================================================================
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:20562859
  review:
    summary: >-
      IPI annotation based on interaction with GABARAPL1. The interaction was detected
      in a network study of the autophagy system.
    action: KEEP_AS_NON_CORE
    reason: >-
      Generic protein binding term. Does not inform about specific molecular function.
      However, the interaction with autophagy machinery may be biologically relevant
      for mitochondrial quality control.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28514442
  review:
    summary: >-
      IPI annotation based on interaction with HADHA (the alpha subunit). This reflects
      the obligate heterotetrameric complex formation between alpha and beta subunits.
    action: KEEP_AS_NON_CORE
    reason: >-
      While this is technically correct (HADHB must bind HADHA to form the functional
      complex), "protein binding" is uninformative. The key interaction is captured
      by the complex membership annotation (GO:0016507).

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:29915090
  review:
    summary: >-
      IPI annotation from cryo-EM structure study showing HADHB-HADHA interaction in
      the TFP complex.
    action: KEEP_AS_NON_CORE
    reason: >-
      Reflects obligate complex formation. Complex membership (GO:0016507) is more
      informative than generic protein binding.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:30850536
  review:
    summary: >-
      IPI annotation from crystal structure study showing HADHB-HADHA interaction.
    action: KEEP_AS_NON_CORE
    reason: >-
      Same as above - reflects obligate complex formation captured better by GO:0016507.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  review:
    summary: >-
      IPI annotation from interactome study showing HADHB-HADHA interaction.
    action: KEEP_AS_NON_CORE
    reason: >-
      Redundant generic protein binding annotation.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:40205054
  review:
    summary: >-
      IPI annotation from multimodal cell maps study showing HADHB-HADHA interaction.
    action: KEEP_AS_NON_CORE
    reason: >-
      Redundant generic protein binding annotation.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32243843
  review:
    summary: >-
      IPI annotation based on interaction with MTLN (mitoregulin). The study showed
      that the TFP complex interacts with MTLN to regulate beta-oxidation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Interesting regulatory interaction but generic term is uninformative. The
      biological significance is in the regulation of beta-oxidation.

- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21527675
  review:
    summary: >-
      IPI annotations based on interaction with RSAD2/viperin. HCMV-induced viperin
      relocalizes to mitochondria and interacts with TFP to reduce ATP generation.
    action: KEEP_AS_NON_CORE
    reason: >-
      This interaction represents viral subversion of host metabolism. Viperin
      interaction with TFP "reduced cellular ATP generation, which resulted in
      actin cytoskeleton disruption." Interesting but not a core function.
    supported_by:
      - reference_id: PMID:21527675
        supporting_text: "viperin interacted with the mitochondrial trifunctional protein that mediates beta-oxidation of fatty acids to generate adenosine triphosphate (ATP). This interaction with viperin... reduced cellular ATP generation"

# ============================================================================
# MOLECULAR FUNCTION - RNA BINDING (NON-CORE, POSSIBLE MOONLIGHTING)
# ============================================================================
- term:
    id: GO:0003723
    label: RNA binding
  evidence_type: HDA
  original_reference_id: PMID:22658674
  review:
    summary: >-
      HDA annotation from large-scale mRNA interactome capture study. HADHB was
      identified among 860 proteins that qualify as RNA-binding proteins in HeLa cells.
      The study noted that many metabolic enzymes unexpectedly bind RNA.
    action: KEEP_AS_NON_CORE
    reason: >-
      Possible moonlighting function. The interactome capture study identified many
      metabolic enzymes as RNA-binding proteins. This may represent a regulatory
      mechanism linking metabolism to RNA fate, but it is not the core function of HADHB.
    supported_by:
      - reference_id: PMID:22658674
        supporting_text: "shedding light on RBPs in disease, RNA-binding enzymes of intermediary metabolism"

- term:
    id: GO:0106222
    label: lncRNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation transferred from mouse ortholog. Related to the general RNA
      binding observed in interactome studies.
    action: KEEP_AS_NON_CORE
    reason: >-
      Possible moonlighting function transferred from ortholog. Not a core function.

- term:
    id: GO:0044877
    label: protein-containing complex binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation transferred from rat ortholog. Very generic term.
    action: KEEP_AS_NON_CORE
    reason: >-
      Too generic to be informative. The complex membership (GO:0016507) better
      captures the relevant biology.

# ============================================================================
# BIOLOGICAL PROCESS - FATTY ACID BETA-OXIDATION (CORE)
# ============================================================================
- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation correctly placing HADHB in the fatty acid beta-oxidation pathway.
      The TFP complex catalyzes the last three steps of mitochondrial long-chain
      fatty acid beta-oxidation.
    action: ACCEPT
    reason: >-
      Core biological process. HADHB is an essential subunit of the TFP complex that
      performs beta-oxidation. Multiple structural and functional studies confirm this
      (PMID:29915090, PMID:30850536, PMID:8135828).
    supported_by:
      - reference_id: PMID:29915090
        supporting_text: "The mitochondrial trifunctional protein (TFP) catalyzes three reactions in the fatty acid beta-oxidation process."
      - reference_id: PMID:8135828
        supporting_text: "Trifunctional protein deficiency, a typical mitochondrial long-chain fatty acid beta-oxidation defect"

- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation consistent with the IBA and experimental evidence.
    action: ACCEPT
    reason: >-
      Redundant with IBA but correctly captures core biological process.

- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: IDA
  original_reference_id: PMID:29915090
  review:
    summary: >-
      IDA annotation from the cryo-EM structure study. The study directly demonstrated
      TFP function in beta-oxidation through structural analysis.
    action: ACCEPT
    reason: >-
      Core biological process with direct structural evidence. The cryo-EM structure
      revealed the architecture of the functional beta-oxidation complex.
    supported_by:
      - reference_id: PMID:29915090
        supporting_text: "The mitochondrial trifunctional protein (TFP) catalyzes three reactions in the fatty acid beta-oxidation process."

- term:
    id: GO:0006635
    label: fatty acid beta-oxidation
  evidence_type: TAS
  original_reference_id: PMID:1550553
  review:
    summary: >-
      TAS annotation from early characterization of the trifunctional enzyme. While
      PMID:1550553 did not distinguish subunit-specific activities, the assignment
      of beta-oxidation to the whole complex (including HADHB) is correct.
    action: ACCEPT
    reason: >-
      Core biological process. The TFP complex including HADHB participates in
      beta-oxidation, even though this paper preceded the subunit-specific activity
      assignments.

# ============================================================================
# BIOLOGICAL PROCESS - GENERAL LIPID/FATTY ACID METABOLISM (NON-CORE)
# ============================================================================
- term:
    id: GO:0006629
    label: lipid metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      Very broad parent term of fatty acid beta-oxidation. Based on UniProt keyword
      mapping.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct but too general. The more specific term GO:0006635 (fatty acid
      beta-oxidation) should be used for core function.

- term:
    id: GO:0006631
    label: fatty acid metabolic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: >-
      Parent term of fatty acid beta-oxidation. Based on UniProt keyword mapping.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct but less specific than GO:0006635.

# ============================================================================
# BIOLOGICAL PROCESS - OTHER (NON-CORE OR QUESTIONABLE)
# ============================================================================
- term:
    id: GO:0010467
    label: gene expression
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation transferred from mouse ortholog. Unexpected term for a
      metabolic enzyme. May relate to RNA binding observations or indirect effects.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      This is likely an over-annotation. There is no clear mechanistic link between
      HADHB's thiolase activity and gene expression regulation. May be an artifact
      of the RNA binding observations or indirect metabolic effects.

- term:
    id: GO:0071222
    label: cellular response to lipopolysaccharide
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IEA annotation transferred from mouse ortholog. This may reflect changes in
      fatty acid metabolism during immune responses, but is unlikely to be a core
      function of HADHB.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      Likely over-annotation. HADHB's primary function is in fatty acid beta-oxidation,
      not immune signaling. Any involvement in LPS response would be indirect through
      metabolic changes.

# ============================================================================
# CELLULAR COMPONENT - MITOCHONDRIAL INNER MEMBRANE (CORE)
# ============================================================================
- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA annotation based on UniProt subcellular location. Correct localization
      supported by extensive experimental evidence.
    action: ACCEPT
    reason: >-
      Core cellular localization. The TFP complex is membrane-bound and associates
      with the mitochondrial inner membrane (PMID:29915090, PMID:30850536).

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IDA
  original_reference_id: PMID:29915090
  review:
    summary: >-
      IDA annotation from cryo-EM structure study. The structure revealed how the
      TFP complex associates with the mitochondrial inner membrane.
    action: ACCEPT
    reason: >-
      Core cellular localization with strong structural evidence. The cryo-EM study
      showed "A concave surface of the TFP tetramer interacts with the detergent
      molecules in the structure, suggesting that this region is involved in
      associating with the membrane."
    supported_by:
      - reference_id: PMID:29915090
        supporting_text: "A concave surface of the TFP tetramer interacts with the detergent molecules in the structure, suggesting that this region is involved in associating with the membrane."

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: IDA
  original_reference_id: PMID:21527675
  review:
    summary: >-
      IDA annotation from viperin interaction study. Subcellular fractionation
      confirmed HADHB localization.
    action: ACCEPT
    reason: >-
      Core cellular localization confirmed by multiple studies.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1482775
  review:
    summary: >-
      TAS annotation from Reactome pathway curation.
    action: ACCEPT
    reason: >-
      Correct localization from pathway database curation.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77271
  review:
    summary: >-
      TAS annotation from Reactome pathway for beta-oxidation of tetradecanoyl-CoA.
    action: ACCEPT
    reason: >-
      Correct localization for beta-oxidation reactions.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77277
  review:
    summary: >-
      TAS annotation from Reactome. Note this Reactome entry (hydratase reaction)
      would be more appropriate for HADHA, but the localization itself is correct
      for both subunits since they form an obligate complex.
    action: ACCEPT
    reason: >-
      Localization is correct even if the reaction annotation would be more
      appropriate for HADHA.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77283
  review:
    summary: >-
      TAS annotation from Reactome. Note this Reactome entry (dehydrogenase reaction)
      would be more appropriate for HADHA, but the localization is correct.
    action: ACCEPT
    reason: >-
      Localization is correct for both subunits.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77301
  review:
    summary: >-
      TAS annotation from Reactome pathway.
    action: ACCEPT
    reason: >-
      Correct localization.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77303
  review:
    summary: >-
      TAS annotation from Reactome pathway.
    action: ACCEPT
    reason: >-
      Correct localization.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77304
  review:
    summary: >-
      TAS annotation from Reactome pathway (thiolase reaction). This correctly
      reflects HADHB's thiolase activity at the inner membrane.
    action: ACCEPT
    reason: >-
      Correct localization for thiolase reaction.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77309
  review:
    summary: >-
      TAS annotation from Reactome pathway.
    action: ACCEPT
    reason: >-
      Correct localization.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77321
  review:
    summary: >-
      TAS annotation from Reactome pathway.
    action: ACCEPT
    reason: >-
      Correct localization.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77329
  review:
    summary: >-
      TAS annotation from Reactome pathway.
    action: ACCEPT
    reason: >-
      Correct localization.

- term:
    id: GO:0005743
    label: mitochondrial inner membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-77340
  review:
    summary: >-
      TAS annotation from Reactome pathway.
    action: ACCEPT
    reason: >-
      Correct localization.

# ============================================================================
# CELLULAR COMPONENT - MITOCHONDRIAL COMPLEX (CORE)
# ============================================================================
- term:
    id: GO:0016507
    label: mitochondrial fatty acid beta-oxidation multienzyme complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IBA annotation correctly placing HADHB as part of the mitochondrial TFP complex.
      HADHB is the beta subunit of the alpha2-beta2 heterotetrameric complex.
    action: ACCEPT
    reason: >-
      Core cellular component. HADHB is an obligate component of the TFP complex.
      The complex structure has been determined by cryo-EM (PMID:29915090) and
      X-ray crystallography (PMID:30850536).
    supported_by:
      - reference_id: PMID:29915090
        supporting_text: "Here we report a 4.2-Å cryo-electron microscopy α2β2 tetrameric structure of the human TFP"
      - reference_id: PMID:30850536
        supporting_text: "The biological unit of the protein is α2β2"

- term:
    id: GO:0016507
    label: mitochondrial fatty acid beta-oxidation multienzyme complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      IEA annotation consistent with IBA and experimental evidence.
    action: ACCEPT
    reason: >-
      Redundant with IBA but correctly captures core complex membership.

# ============================================================================
# CELLULAR COMPONENT - GENERAL MITOCHONDRION (NON-CORE)
# ============================================================================
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      General mitochondrial localization. Correct but less specific than inner
      membrane annotation.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct but more specific terms (GO:0005743, GO:0016507) better capture
      the localization.

- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: >-
      IDA annotation from HPA immunofluorescence data.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct but less specific than inner membrane annotation.

- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  review:
    summary: >-
      HTP annotation from quantitative mitochondrial proteome study.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct mitochondrial localization from proteomics.

- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: NAS
  original_reference_id: PMID:7958339
  review:
    summary: >-
      NAS annotation from early review paper on the trifunctional enzyme.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct but less specific than inner membrane annotation.

# ============================================================================
# CELLULAR COMPONENT - MITOCHONDRIAL ENVELOPE (LESS SPECIFIC)
# ============================================================================
- term:
    id: GO:0005740
    label: mitochondrial envelope
  evidence_type: TAS
  original_reference_id: PMID:1550553
  review:
    summary: >-
      TAS annotation from early characterization. This is a parent term of
      mitochondrial inner membrane. The paper described the enzyme as
      "membrane-bound" but did not specify inner vs outer membrane.
    action: KEEP_AS_NON_CORE
    reason: >-
      Correct but less specific than GO:0005743 (mitochondrial inner membrane).
      Subsequent studies confirmed inner membrane localization.

# ============================================================================
# CELLULAR COMPONENT - MITOCHONDRIAL OUTER MEMBRANE (ADDITIONAL LOCALIZATION)
# ============================================================================
- term:
    id: GO:0005741
    label: mitochondrial outer membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA annotation based on UniProt subcellular location. UniProt lists both
      inner and outer membrane localization.
    action: KEEP_AS_NON_CORE
    reason: >-
      The primary localization is the inner membrane where the complex is active.
      Outer membrane localization may reflect import intermediates or interactions
      with outer membrane proteins.

- term:
    id: GO:0005741
    label: mitochondrial outer membrane
  evidence_type: IDA
  original_reference_id: PMID:21527675
  review:
    summary: >-
      IDA annotation from viperin interaction study. The study used subcellular
      fractionation and found HADHB in both inner and outer membrane fractions.
    action: KEEP_AS_NON_CORE
    reason: >-
      May represent interaction with outer membrane during viral infection or
      import intermediates. The functional complex is at the inner membrane.

# ============================================================================
# CELLULAR COMPONENT - ENDOPLASMIC RETICULUM (NON-CORE)
# ============================================================================
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      IEA annotation based on UniProt subcellular location. UniProt lists ER
      localization based on PMID:21527675.
    action: KEEP_AS_NON_CORE
    reason: >-
      This likely represents ER localization during viral infection (HCMV-induced
      viperin causes relocalization) rather than normal function. The core
      localization is mitochondrial inner membrane.

- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:21527675
  review:
    summary: >-
      IDA annotation from viperin study. HCMV infection causes viperin-mediated
      redistribution of cellular proteins including TFP components.
    action: KEEP_AS_NON_CORE
    reason: >-
      This represents pathological/viral-induced localization, not the normal
      cellular localization. The paper showed viperin "relocalization from the
      endoplasmic reticulum to the mitochondria" during infection.
    supported_by:
      - reference_id: PMID:21527675
        supporting_text: "Viperin interaction with the viral protein vMIA resulted in viperin relocalization from the endoplasmic reticulum to the mitochondria."

# ============================================================================
# CELLULAR COMPONENT - MITOCHONDRIAL NUCLEOID (NON-CORE)
# ============================================================================
- term:
    id: GO:0042645
    label: mitochondrial nucleoid
  evidence_type: IDA
  original_reference_id: PMID:18063578
  review:
    summary: >-
      IDA annotation from nucleoid proteomics study. HADHB was identified in native
      nucleoid preparations but was not found to cross-link to mtDNA, suggesting it
      is in the peripheral region of nucleoids.
    action: KEEP_AS_NON_CORE
    reason: >-
      The study found HADHB in native nucleoids but noted that "Several other
      metabolic proteins and chaperones identified in native nucleoids... were
      not observed to cross-link to mtDNA." This suggests HADHB is in the peripheral
      region where "translation and complex assembly may occur" rather than being
      a core nucleoid component.
    supported_by:
      - reference_id: PMID:18063578
        supporting_text: "Several other metabolic proteins and chaperones identified in native nucleoids... were not observed to cross-link to mtDNA... translation and complex assembly may occur in the peripheral region."

references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to
    orthologs using Ensembl Compara
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:1550553
  title: Human liver long-chain 3-hydroxyacyl-coenzyme A dehydrogenase is a multifunctional
    membrane-bound beta-oxidation enzyme of mitochondria.
  findings:
    - statement: >-
        Early characterization of the trifunctional enzyme complex from human liver.
        Described the enzyme as having hydratase, dehydrogenase, and thiolase activities,
        but did NOT determine which subunit carries which activity. The subunit-specific
        activities were later determined by PMID:8135828.
- id: PMID:7958339
  title: 'The mitochondrial long-chain trifunctional enzyme: 2-enoyl-CoA hydratase,
    3-hydroxyacyl-CoA dehydrogenase and 3-oxoacyl-CoA thiolase.'
  findings:
    - statement: >-
        Review of the trifunctional enzyme. Provides protein sequence data and
        describes the enzyme activities.
- id: PMID:8135828
  title: Structural analysis of cDNAs for subunits of human mitochondrial fatty acid
    beta-oxidation trifunctional protein.
  findings:
    - statement: >-
        KEY PAPER: Definitively assigned activities to specific subunits. Expression of
        alpha-subunit cDNA yielded hydratase and dehydrogenase activities. Expression of
        beta-subunit cDNA yielded ONLY thiolase activity.
- id: PMID:18063578
  title: The layered structure of human mitochondrial DNA nucleoids.
  findings:
    - statement: >-
        Proteomics study of mitochondrial nucleoids. HADHB was found in native nucleoid
        preparations but did not cross-link to mtDNA, suggesting peripheral association.
- id: PMID:20562859
  title: Network organization of the human autophagy system.
  findings:
    - statement: >-
        Autophagy network study identifying HADHB-GABARAPL1 interaction.
- id: PMID:21527675
  title: Human cytomegalovirus directly induces the antiviral protein viperin to enhance
    infectivity.
  findings:
    - statement: >-
        HCMV-induced viperin interacts with TFP and reduces cellular ATP generation.
        Viperin relocalization affects TFP localization. Provides evidence for HADHB
        localization in mitochondria, outer membrane, and ER (during infection).
- id: PMID:22658674
  title: Insights into RNA biology from an atlas of mammalian mRNA-binding proteins.
  findings:
    - statement: >-
        Interactome capture study identified HADHB among 860 RNA-binding proteins in HeLa
        cells. Many metabolic enzymes were unexpectedly found to bind RNA.
- id: PMID:28514442
  title: Architecture of the human interactome defines protein communities and disease
    networks.
  findings:
    - statement: >-
        Large-scale interactome study showing HADHB-HADHA interaction.
- id: PMID:29915090
  title: Cryo-EM structure of human mitochondrial trifunctional protein.
  findings:
    - statement: >-
        4.2-A cryo-EM structure of TFP showing alpha2beta2 heterotetramer with V-shaped
        architecture. Demonstrates membrane association through concave surface.
- id: PMID:30850536
  title: Crystal structure of human mitochondrial trifunctional protein, a fatty acid
    β-oxidation metabolon.
  findings:
    - statement: >-
        3.6-A crystal structure of TFP. Confirms alpha2beta2 architecture. Shows substrate
        channeling pathway. Identifies active site residues for thiolase in beta subunit.
- id: PMID:32243843
  title: Mitoregulin Controls β-Oxidation in Human and Mouse Adipocytes.
  findings:
    - statement: >-
        MTLN (mitoregulin) interacts with TFP to regulate beta-oxidation.
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the human
    interactome.
  findings:
    - statement: >-
        Interactome study confirming HADHB-HADHA interaction.
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics
    in cellular context.
  findings:
    - statement: >-
        Mitochondrial proteome study confirming HADHB mitochondrial localization.
- id: PMID:40205054
  title: Multimodal cell maps as a foundation for structural and functional genomics.
  findings: []
- id: Reactome:R-HSA-1482775
  title: MLCL is acylated to CL by HADH (IM)
  findings: []
- id: Reactome:R-HSA-77271
  title: 3-Oxotetradecanoyl-CoA+CoA-SH<=>Lauroyl-CoA
  findings:
    - statement: >-
        Thiolase reaction in beta-oxidation pathway - appropriate for HADHB.
- id: Reactome:R-HSA-77277
  title: trans-Tetradec-2-enoyl-CoA+H2O<=>(S)-3-Hydroxytetradecanoyl-CoA
  findings:
    - statement: >-
        Hydratase reaction - this is actually HADHA's activity, but both subunits
        are annotated to the complex.
- id: Reactome:R-HSA-77283
  title: (S)-3-Hydroxytetradecanoyl-CoA+NAD<=>3-Oxotetradecanoyl-CoA+NADH+H
  findings:
    - statement: >-
        Dehydrogenase reaction - this is actually HADHA's activity.
- id: Reactome:R-HSA-77301
  title: trans-Hexadec-2-enoyl-CoA+H2O<=>(S)-3-Hydroxyhexadecanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77303
  title: (S)-3-Hydroxyhexadecanoyl-CoA+NAD<=>3-Oxopalmitoyl-CoA+NADH+H
  findings: []
- id: Reactome:R-HSA-77304
  title: 3-Oxopalmitoyl-CoA+CoA-SH<=>myristoyl-CoA
  findings:
    - statement: >-
        Thiolase reaction - appropriate for HADHB.
- id: Reactome:R-HSA-77309
  title: 3-Oxododecanoyl-CoA+CoA-SH<=>Decanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77321
  title: 3-Oxohexanoyl-CoA+CoA-SH<=>Butanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77329
  title: 3-Oxooctanoyl-CoA+CoA-SH<=>Hexanoyl-CoA
  findings: []
- id: Reactome:R-HSA-77340
  title: 3-Oxodecanoyl-CoA+CoA-SH<=>Octanoyl-CoA
  findings: []

core_functions:
  - description: >-
      Catalyzes thiolytic cleavage of 3-ketoacyl-CoA to acetyl-CoA and shortened acyl-CoA
      during long-chain fatty acid beta-oxidation (C10-C16 substrates). Functions as the
      beta subunit of the mitochondrial trifunctional protein (alpha2-beta2 heterotetramer
      with HADHA), providing the sole thiolase activity of the complex.
    supported_by:
      - reference_id: PMID:8135828
        supporting_text: "Expression of this cDNA [beta-subunit] in mammalian cells yielded a polypeptide with the long-chain 3-ketoacyl-CoA thiolase activity."
      - reference_id: PMID:29915090
        supporting_text: "The mitochondrial trifunctional protein (TFP) catalyzes three reactions in the fatty acid beta-oxidation process."
      - reference_id: PMID:30850536
        supporting_text: "The biological unit of the protein is alpha2beta2... employing 3-ketothiolase (KT) activity."
    molecular_function:
      id: GO:0003988
      label: acetyl-CoA C-acyltransferase activity
    directly_involved_in:
      - id: GO:0006635
        label: fatty acid beta-oxidation
    locations:
      - id: GO:0005743
        label: mitochondrial inner membrane
    in_complex:
      id: GO:0016507
      label: mitochondrial fatty acid beta-oxidation multienzyme complex

proposed_new_terms: []

suggested_questions:
  - question: >-
      Should the Reactome annotations for hydratase and dehydrogenase reactions be
      removed from HADHB and retained only for HADHA? Currently both subunits are
      annotated to all reactions in the beta-oxidation pathway.
  - question: >-
      What is the functional significance of HADHB's RNA binding activity detected
      in interactome capture studies (PMID:22658674)?

suggested_experiments:
  - description: >-
      Confirm that isolated recombinant HADHB (beta subunit alone) lacks hydratase
      and dehydrogenase activities to definitively rule out any residual activity.
    hypothesis: >-
      Recombinant HADHB expressed alone will have no detectable enoyl-CoA hydratase
      or 3-hydroxyacyl-CoA dehydrogenase activity, confirming these are HADHA-specific.
  - description: >-
      Investigate whether the RNA binding by HADHB detected in PMID:22658674 has
      any regulatory significance for fatty acid metabolism.
    hypothesis: >-
      RNA binding by HADHB may represent a moonlighting function that links
      metabolic state to post-transcriptional regulation of lipid metabolism genes.