IDH3B

id: O43837
gene_symbol: IDH3B
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: >-
  IDH3B encodes the beta subunit of mitochondrial NAD-dependent isocitrate dehydrogenase 3 (IDH3).
  The functional IDH3 enzyme is a heterotetramer with alpha2-beta-gamma stoichiometry (2alpha:1beta:1gamma),
  where the alpha subunits (IDH3A) are catalytic, while beta (IDH3B) and gamma (IDH3G) play structural
  and regulatory roles. IDH3B does NOT have intrinsic catalytic activity on its own - expression of
  beta subunit alone shows no detectable activity [PMID:10601238]. The alphabeta and alphagamma dimers
  exhibit significant IDH activity, but the full heterotetramer is required for maximal activity and
  proper allosteric regulation [PMID:14555658]. The IDH3 complex catalyzes the irreversible oxidative
  decarboxylation of isocitrate to alpha-ketoglutarate in the TCA cycle. Beta-Arg99 is required for
  normal ADP activation of the enzyme but is not essential for catalysis [PMID:14555658]. IDH3B localizes
  to the mitochondrial matrix. Biallelic variants cause retinitis pigmentosa 46 (RP46). IDH3B exists
  as multiple isoforms (beta1 and beta2) due to alternative splicing, with tissue-specific expression
  patterns affecting the pH optimum of the enzyme complex [PMID:10601238].
alternative_products:
- name: B
  id: O43837-1
- name: A
  id: O43837-2
  sequence_note: VSP_002462
- name: C
  id: O43837-3
  sequence_note: VSP_041335
existing_annotations:
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IDH3B is well-established as a mitochondrial protein. The IBA annotation is phylogenetically
      well-supported across eukaryotes. UniProt indicates a mitochondrial transit peptide (residues
      1-34) and documents mitochondrial localization. PMID:10601238 describes IDH3B as part of
      "mitochondrial NAD(+)-dependent isocitrate dehydrogenase" and discusses its function in
      the context of mitochondrial enzyme complexes.
    action: ACCEPT
    reason: >-
      Mitochondrial localization is correct and well-supported by phylogenetic inference, UniProt
      annotation, and experimental literature. While mitochondrial matrix (GO:0005759) is more
      precise, this broader term is acceptable for the IBA evidence type.
    supported_by:
      - reference_id: PMID:10601238
        supporting_text: "the interactions and functional role of each of the three mitochondrial NAD(+)-dependent isocitrate dehydrogenase (IDH) subunits (alpha, beta, and gamma)"
- term:
    id: GO:0006099
    label: tricarboxylic acid cycle
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IDH3B is a component of the NAD-dependent isocitrate dehydrogenase complex that catalyzes
      a key step of the TCA cycle. While the beta subunit is not itself catalytic, it is essential
      for proper complex assembly and function in the TCA cycle [PMID:10601238, PMID:14555658].
      The IBA annotation appropriately captures the involvement of IDH3B in this process.
    action: ACCEPT
    reason: >-
      As an essential structural component of the IDH3 complex, IDH3B participates in the TCA
      cycle even though it lacks intrinsic catalytic activity. The phylogenetic evidence
      supports this annotation across eukaryotes.
    supported_by:
      - reference_id: PMID:10601238
        supporting_text: "Among the various combinations of human IDH subunits co-expressed in bacteria, alphabetagamma, alphabeta, and alphagamma combinations exhibited significant amounts of IDH activity"
- term:
    id: GO:0006102
    label: isocitrate metabolic process
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: >-
      IDH3B participates in isocitrate metabolism as part of the IDH3 complex. The complex
      converts isocitrate to alpha-ketoglutarate. While IDH3B is not the catalytic subunit,
      it is required for proper complex assembly and activity [PMID:10601238].
    action: ACCEPT
    reason: >-
      The annotation correctly captures IDH3B's involvement in isocitrate metabolism through
      its role in the IDH3 complex. Well-supported by phylogenetic analysis.
    supported_by:
      - reference_id: PMID:10601238
        supporting_text: "the alpha is the catalytic subunit and that at least one of the other two subunits plays an essential supporting role for activity"
- term:
    id: GO:0000287
    label: magnesium ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      This annotation is inferred from InterPro domain IPR019818 (IsoCit/isopropylmalate_DH_CS).
      However, in the IDH3 complex, Mg2+ (or Mn2+) binding occurs at the active site in the
      catalytic alpha subunit, not in the structural beta subunit. The deep research notes
      that the enzyme "is a heterooctamer containing two copies of a heterotetramer of two
      IDH3A, one IDH3B, one IDH3G, and two Mn++" [Reactome:R-HSA-70967], suggesting metal
      binding is associated with the catalytic subunits. No direct evidence supports
      magnesium binding by IDH3B specifically. The crystal structures of the αβ heterodimer
      (PDB 6KDE Ca2+-bound, 6KDY NAD-bound) place the divalent metal site at the active-site
      cleft contributed by the α subunit; the β subunit does not provide a productive metal
      site, and in the αβ heterodimer the active site has a distorted geometry unable to bind
      the metal ion in a catalysis-relevant manner [PMID:31515270].
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      While the InterPro domain is present, the functional magnesium/metal binding site is
      located in the catalytic alpha subunit. IDH3B shares sequence/structural homology with
      dehydrogenases but its specific role is structural, not catalytic. This IEA annotation
      represents domain-based inference that does not reflect the actual function of this
      specific subunit.
    supported_by:
      - reference_id: PMID:31515270
        supporting_text: "the active site has a distorted geometry that is unable to bind the metal ion effectively or in a catalysis-relevant manner"
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: >-
      Mitochondrial localization inferred from UniProt subcellular location annotation.
      This is consistent with experimental evidence and the IBA annotation above.
    action: ACCEPT
    reason: >-
      Correct annotation based on UniProt curation. IDH3B has a mitochondrial transit
      peptide and functions in the mitochondrial matrix.
- term:
    id: GO:0006099
    label: tricarboxylic acid cycle
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: >-
      Combined automated annotation correctly identifies IDH3B's involvement in the TCA cycle.
      Consistent with IBA annotation and experimental literature.
    action: ACCEPT
    reason: >-
      Correct annotation. IDH3B is part of the IDH3 complex that catalyzes a key TCA cycle step.
- term:
    id: GO:0016616
    label: oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      This annotation is inferred from InterPro domain IPR019818. However, PMID:10601238
      demonstrates that "subunits produced alone ... showed no detectable activity" and
      establishes that "the alpha is the catalytic subunit." IDH3B shares the dehydrogenase
      domain but does not itself possess oxidoreductase activity - it is a structural/
      regulatory subunit of the complex.
    action: REMOVE
    reason: >-
      IDH3B does not have intrinsic oxidoreductase activity. The beta subunit alone shows
      no detectable enzymatic activity [PMID:10601238]. This annotation incorrectly attributes
      the catalytic activity of the complex to the non-catalytic beta subunit based solely
      on domain homology.
    supported_by:
      - reference_id: PMID:10601238
        supporting_text: "subunits produced alone and betagamma showed no detectable activity. These data suggest that the alpha is the catalytic subunit"
- term:
    id: GO:0051287
    label: NAD binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: >-
      This annotation is inferred from InterPro domain IPR019818. While IDH3B shares
      structural homology with NAD-binding dehydrogenases, the functional NAD binding and
      catalysis occurs in the alpha subunit. PMID:14555658 shows that mutations in the
      gamma subunit affect NAD binding (gamma-R97Q has 10-fold higher Km for NAD), but
      the beta subunit's role is in ADP activation, not NAD binding at the catalytic site.
      However, the beta subunit may contribute to the nucleotide binding pocket architecture.
    action: MARK_AS_OVER_ANNOTATED
    reason: >-
      The annotation is based on domain homology rather than demonstrated function.
      IDH3B contributes to the complex structure and ADP-mediated regulation but is not
      itself the primary NAD-binding subunit. The catalytic NAD binding site is in IDH3A.
      Crystal structures of the alphabeta heterodimer (PDB 6KDY NAD-bound, 6KE3 NADH-bound)
      show that the NAD cofactor binds in the active-site cleft built jointly from the alpha
      subunit and the small domain of the beta subunit, so the beta subunit contributes to
      the architecture of the holoenzyme NAD-binding/active site rather than binding NAD as
      an isolated subunit [PMID:31515270].
    supported_by:
      - reference_id: PMID:14555658
        supporting_text: "the beta and gamma subunits have roles in the nucleotide functions of this allosteric enzyme"
      - reference_id: PMID:31515270
        supporting_text: "We report here the crystal structures of the αβ heterodimer of human NAD-IDH with the α subunit in apo form and in Ca2+-bound, NAD-bound, and NADH-bound forms"
      - reference_id: PMID:31515270
        supporting_text: "The active site is located in the cleft formed by the large and small domains of the α subunit and the small domain of the β subunit"
      - reference_id: PMID:36375638
        supporting_text: "the αQ139AICT+Ca+NADβNAD structure presents the first pseudo-Michaelis complex of HsIDH3, which allows us to identify the key residues involved in the binding of cofactor, substrate, and metal ion"
- term:
    id: GO:0045242
    label: isocitrate dehydrogenase complex (NAD+)
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  review:
    summary: >-
      IDH3B is a core component of the NAD-dependent isocitrate dehydrogenase complex.
      The complex has 2alpha:1beta:1gamma stoichiometry [PMID:14555658]. This cellular
      component annotation is entirely appropriate for IDH3B. Crystal structures of the
      human IDH3 alphabeta heterodimer (PDB 6KDE/6KDF/6KDY/6KE3) and of the constitutively
      active (αβαγ)2 holoenzyme (PDB 8GRB) directly establish IDH3B (beta) as an assembled
      subunit of the IDH3 complex and define the alpha-beta heterodimer interface
      [PMID:31515270, PMID:36375638].
    action: ACCEPT
    reason: >-
      Correct annotation. IDH3B is an established subunit of the IDH3 complex, confirmed
      by co-expression studies and structural analysis.
    supported_by:
      - reference_id: PMID:14555658
        supporting_text: "Wild type (WT) and mutant enzymes ... were purified to homogeneity yielding enzymes with 2alpha:1beta:1gamma subunit composition"
      - reference_id: PMID:31515270
        supporting_text: "The α and β subunits form a heterodimer (αβ), and the α and γ subunits form another heterodimer (αγ), which are assembled into a heterotetramer (α2βγ) and further into a heterooctamer"
      - reference_id: PMID:36375638
        supporting_text: "It consists of three types of subunits (α, β, and γ) and exists and functions as the (αβαγ)2 heterooctamer"
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: >-
      Direct experimental evidence for mitochondrial localization from HPA immunofluorescence
      data. This provides direct experimental support for the mitochondrial localization.
    action: ACCEPT
    reason: >-
      Direct experimental evidence (IDA from immunofluorescence) confirms mitochondrial
      localization, consistent with all other evidence sources.
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: NAS
  original_reference_id: PMID:14555658
  review:
    summary: >-
      PMID:14555658 is a study of human NAD-dependent isocitrate dehydrogenase expressed
      in bacteria. The paper discusses the enzyme's function in the context of mitochondrial
      metabolism but does not directly demonstrate mitochondrial localization - hence NAS
      (non-traceable author statement) is appropriate.
    action: ACCEPT
    reason: >-
      While the evidence is indirect, mitochondrial localization is well-established from
      multiple other sources. This annotation is consistent with the overall body of evidence.
    supported_by:
      - reference_id: PMID:14555658
        supporting_text: "Mammalian NAD-dependent isocitrate dehydrogenase is an allosteric enzyme"
- term:
    id: GO:0006099
    label: tricarboxylic acid cycle
  evidence_type: IDA
  original_reference_id: PMID:14555658
  review:
    summary: >-
      PMID:14555658 demonstrates that the IDH3 complex including the beta subunit has
      isocitrate dehydrogenase activity, which is a key TCA cycle reaction. The study
      shows IDH activity of purified complexes containing beta subunit [PMID:14555658].
    action: ACCEPT
    reason: >-
      Direct experimental evidence that IDH3B-containing complexes have isocitrate
      dehydrogenase activity, supporting involvement in TCA cycle.
    supported_by:
      - reference_id: PMID:14555658
        supporting_text: "Specific activities of 22, 14, and 2 micromol of NADH/min/mg were measured, respectively, for WT, beta-R99Q, and gamma-R97Q enzymes"
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: HTP
  original_reference_id: PMID:34800366
  review:
    summary: >-
      PMID:34800366 is a high-throughput mitochondrial proteomics study that identified
      IDH3B in the human mitochondrial proteome. This provides orthogonal mass spectrometry-
      based evidence for mitochondrial localization.
    action: ACCEPT
    reason: >-
      High-quality proteomics study confirming IDH3B presence in the mitochondrial proteome.
    supported_by:
      - reference_id: PMID:34800366
        supporting_text: "Quantitative high-confidence human mitochondrial proteome"
- term:
    id: GO:0045242
    label: isocitrate dehydrogenase complex (NAD+)
  evidence_type: IDA
  original_reference_id: PMID:14555658
  review:
    summary: >-
      PMID:14555658 provides direct experimental evidence that IDH3B is a component of
      the IDH3 complex. The study purified the complex and demonstrated the 2alpha:1beta:1gamma
      stoichiometry through expression and biochemical analysis. Crystal structures of the
      human IDH3 alphabeta heterodimer (PDB 6KDE/6KDF/6KDY NAD-bound/6KE3 NADH-bound) and of the
      constitutively active (alphabeta-alphagamma)2 holoenzyme (PDB 8GRB) directly visualize
      IDH3B (beta) as an assembled subunit of the IDH3 complex and define the alpha-beta
      heterodimer interface [PMID:31515270, PMID:36375638].
    action: ACCEPT
    reason: >-
      Direct experimental demonstration that IDH3B is part of the IDH3 complex with
      defined stoichiometry.
    supported_by:
      - reference_id: PMID:14555658
        supporting_text: "Wild type (WT) and mutant enzymes (each containing 2 normal subunits plus a mutant subunit with alpha-R88Q, beta-R99Q, or gamma-R97Q) were purified to homogeneity yielding enzymes with 2alpha:1beta:1gamma subunit composition and a native molecular mass of 315 kDa"
      - reference_id: PMID:31515270
        supporting_text: "The α and β subunits form a heterodimer (αβ), and the α and γ subunits form another heterodimer (αγ), which are assembled into a heterotetramer (α2βγ) and further into a heterooctamer"
      - reference_id: PMID:36375638
        supporting_text: "It consists of three types of subunits (α, β, and γ) and exists and functions as the (αβαγ)2 heterooctamer"
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: HDA
  original_reference_id: PMID:21630459
  review:
    summary: >-
      PMID:21630459 is a proteomic study of the human sperm nucleus that identified IDH3B
      among 403 nuclear proteins. This is a specialized cell type where metabolic proteins
      may be present in the nuclear fraction during spermatogenesis. The nuclear localization
      is likely context-specific rather than representing a core localization.
    action: KEEP_AS_NON_CORE
    reason: >-
      The detection in sperm nuclear proteome may represent a specialized developmental
      context. IDH3B's primary localization is mitochondrial, and nuclear detection may
      reflect the unique chromatin remodeling during spermiogenesis or technical
      co-purification. This is not a core localization but should be retained.
    supported_by:
      - reference_id: PMID:21630459
        supporting_text: "403 different proteins have been identified from the isolated sperm nuclei"
- term:
    id: GO:0005759
    label: mitochondrial matrix
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-70967
  review:
    summary: >-
      Reactome pathway R-HSA-70967 "IDH3 complex decarboxylates isocitrate" places the
      IDH3 complex, including IDH3B, in the mitochondrial matrix. This is the most specific
      and accurate localization for IDH3B's function.
    action: ACCEPT
    reason: >-
      Mitochondrial matrix is the precise subcellular location where IDH3 functions in
      the TCA cycle. This is the most informative localization annotation for IDH3B.
- term:
    id: GO:0009055
    label: electron transfer activity
  evidence_type: TAS
  original_reference_id: PMID:10601238
  review:
    summary: >-
      PMID:10601238 does not support electron transfer activity for IDH3B. The paper
      demonstrates that the IDH3 complex has isocitrate dehydrogenase activity (reducing
      NAD+ to NADH), but this is not the same as electron transfer activity. Electron
      transfer activity (GO:0009055) refers to proteins that function as electron carriers
      (like cytochromes or ferredoxins), not dehydrogenases that use NAD+ as a cofactor.
      Furthermore, IDH3B specifically is the non-catalytic subunit.
    action: REMOVE
    reason: >-
      Incorrect annotation. GO:0009055 (electron transfer activity) is inappropriate for
      IDH3B. The NAD+-dependent dehydrogenase reaction is not electron transfer activity
      in the GO sense. Additionally, IDH3B is not catalytically active - the paper states
      "subunits produced alone ... showed no detectable activity."
    supported_by:
      - reference_id: PMID:10601238
        supporting_text: "subunits produced alone and betagamma showed no detectable activity"
- term:
    id: GO:0004449
    label: isocitrate dehydrogenase (NAD+) activity
  evidence_type: TAS
  original_reference_id: PMID:10601238
  review:
    summary: >-
      PMID:10601238 explicitly demonstrates that IDH3B alone does not have isocitrate
      dehydrogenase activity. The paper states "subunits produced alone and betagamma
      showed no detectable activity" and concludes that "the alpha is the catalytic subunit."
      While the alphabeta dimer has activity, this is due to the alpha subunit, not beta.
    action: REMOVE
    reason: >-
      The cited paper PMID:10601238 directly contradicts this annotation. IDH3B does not
      have intrinsic isocitrate dehydrogenase activity. The beta subunit is structural/
      regulatory, and attributing the catalytic activity to it is incorrect. This is a
      case where the annotation was likely made at the complex level and incorrectly
      propagated to the non-catalytic subunit.
    supported_by:
      - reference_id: PMID:10601238
        supporting_text: "subunits produced alone and betagamma showed no detectable activity. These data suggest that the alpha is the catalytic subunit and that at least one of the other two subunits plays an essential supporting role for activity"
- term:
    id: GO:0005739
    label: mitochondrion
  evidence_type: TAS
  original_reference_id: PMID:10601238
  review:
    summary: >-
      PMID:10601238 describes IDH3B as part of "mitochondrial NAD(+)-dependent isocitrate
      dehydrogenase" and discusses it in the context of mitochondrial function. The
      mitochondrial localization is well-supported.
    action: ACCEPT
    reason: >-
      The paper describes IDH3B as a mitochondrial protein. Consistent with all other
      evidence for mitochondrial localization.
    supported_by:
      - reference_id: PMID:10601238
        supporting_text: "the interactions and functional role of each of the three mitochondrial NAD(+)-dependent isocitrate dehydrogenase (IDH) subunits"
- term:
    id: GO:0006102
    label: isocitrate metabolic process
  evidence_type: TAS
  original_reference_id: PMID:10601238
  review:
    summary: >-
      PMID:10601238 demonstrates that IDH3B contributes to isocitrate metabolism as part
      of the IDH3 complex. While IDH3B is not catalytic, it plays "an essential supporting
      role for activity" in isocitrate oxidation.
    action: ACCEPT
    reason: >-
      IDH3B participates in isocitrate metabolism through its essential structural role
      in the IDH3 complex. The paper demonstrates that beta-containing complexes have
      isocitrate dehydrogenase activity.
    supported_by:
      - reference_id: PMID:10601238
        supporting_text: "alphabetagamma, alphabeta, and alphagamma combinations exhibited significant amounts of IDH activity"
- term:
    id: GO:0005198
    label: structural molecule activity
  evidence_type: NAS
  original_reference_id: PMID:10601238
  review:
    summary: >-
      IDH3B functions as a structural subunit of the IDH3 complex. PMID:10601238 demonstrates
      that the beta subunit alone has no catalytic activity ("subunits produced alone and
      betagamma showed no detectable activity") but plays "an essential supporting role for
      activity." The beta subunit is required for proper complex assembly and function. Deep
      research confirms that IDH3B plays a structural/regulatory role in the heterotetramer
      [file:human/IDH3B/IDH3B-deep-research-falcon.md].
    action: NEW
    reason: >-
      This annotation captures IDH3B's established role as a structural component of the
      IDH3 enzyme complex. The term GO:0005198 is defined as "The action of a molecule
      that contributes to the structural integrity of a complex" which accurately describes
      IDH3B's function. This is a more appropriate molecular function annotation than
      the catalytic activity terms that were incorrectly attributed to IDH3B.
    supported_by:
      - reference_id: PMID:10601238
        supporting_text: "These data suggest that the alpha is the catalytic subunit and that at least one of the other two subunits plays an essential supporting role for activity"
      - reference_id: file:human/IDH3B/IDH3B-deep-research-falcon.md
        supporting_text: "IDH3B appears to play a structural/regulatory role in the complex, as opposed to a catalytic one"
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings:
    - statement: InterPro domain IPR019818 (IsoCit/isopropylmalate_DH_CS) is present in IDH3B but catalytic residues are in the alpha subunit
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings:
    - statement: Phylogenetic analysis supports IDH3B mitochondrial localization and TCA cycle involvement across eukaryotes
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping
  findings:
    - statement: UniProt documents mitochondrial localization with transit peptide
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings:
    - statement: HPA immunofluorescence confirms mitochondrial localization
- id: GO_REF:0000107
  title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara
  findings:
    - statement: Complex membership annotation transferred from mouse ortholog
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings:
    - statement: Automated methods correctly identify TCA cycle involvement
- id: PMID:10601238
  title: Identification and functional characterization of a novel, tissue-specific NAD(+)-dependent isocitrate dehydrogenase beta subunit isoform.
  findings:
    - statement: IDH3B exists as two isoforms (beta1 and beta2) due to alternative splicing
      supporting_text: "the smaller beta(2) transcript (1.3 kilobases) is primarily expressed in heart and skeletal muscle, whereas the larger beta(1) mRNA (1.6 kilobases) is prevalent in nonmuscle tissues"
    - statement: Beta subunit alone has no detectable IDH activity
      supporting_text: "subunits produced alone and betagamma showed no detectable activity"
    - statement: Alpha is the catalytic subunit
      supporting_text: "These data suggest that the alpha is the catalytic subunit and that at least one of the other two subunits plays an essential supporting role for activity"
    - statement: Alphabeta and alphagamma dimers have IDH activity
      supporting_text: "alphabetagamma, alphabeta, and alphagamma combinations exhibited significant amounts of IDH activity"
    - statement: Beta isoforms affect pH optimum of enzyme activity
      supporting_text: "Substitution of beta(1) with beta(2) in the co-expression system lowered the pH optimum for IDH activity from 8.0 to 7.6"
- id: PMID:14555658
  title: Evaluation by mutagenesis of the importance of 3 arginines in alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase.
  findings:
    - statement: IDH3 complex has 2alpha:1beta:1gamma stoichiometry with 315 kDa molecular mass
      supporting_text: "Wild type (WT) and mutant enzymes ... were purified to homogeneity yielding enzymes with 2alpha:1beta:1gamma subunit composition and a native molecular mass of 315 kDa"
    - statement: Beta-R99Q mutant retains 64% of wild-type activity (14 vs 22 micromol NADH/min/mg)
      supporting_text: "Specific activities of 22, 14, and 2 micromol of NADH/min/mg were measured, respectively, for WT, beta-R99Q, and gamma-R97Q enzymes"
    - statement: Beta-Arg99 is required for normal ADP activation but not essential for catalysis
      supporting_text: "for beta-R99Q and gamma-R97Q enzymes, the Km for isocitrate is the same in the absence or presence of ADP, although all the enzymes bind ADP"
    - statement: Alpha-Arg88 is essential for catalysis (alpha-R88Q has no activity)
      supporting_text: "mutant enzymes with normal beta and gamma subunits and alpha-R88Q mutant subunit has no detectable activity, demonstrating that ... alpha-Arg88 is essential for catalysis"
    - statement: Beta and gamma subunits have roles in nucleotide functions of the allosteric enzyme
      supporting_text: "the beta and gamma subunits have roles in the nucleotide functions of this allosteric enzyme"
- id: PMID:31515270
  title: Molecular basis for the function of the αβ heterodimer of human NAD-dependent isocitrate dehydrogenase.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Crystal structures (PDB 6KDF apo, 6KDE Ca2+-bound, 6KDY NAD-bound, 6KE3 NADH-bound) of the human
      IDH3 αβ heterodimer establish IDH3B (β) as an assembled subunit whose small domain helps form the
      active-site cleft and whose β3-α3/β12-α8 loops build a pseudo-allosteric site, defining β's
      structural/regulatory contribution to NAD/NADH binding, metal-ion geometry, and allosteric control
      of the holoenzyme rather than any catalytic activity of β alone.
  findings:
    - statement: Crystal structures of the human NAD-IDH αβ heterodimer determined in apo, Ca2+-bound, NAD-bound, and NADH-bound forms
      supporting_text: "We report here the crystal structures of the αβ heterodimer of human NAD-IDH with the α subunit in apo form and in Ca2+-bound, NAD-bound, and NADH-bound forms"
    - statement: The active site is formed jointly by the α subunit large/small domains and the β subunit small domain
      supporting_text: "The active site is located in the cleft formed by the large and small domains of the α subunit and the small domain of the β subunit"
    - statement: In the αβ heterodimer the active site has a distorted geometry unable to bind the metal ion productively
      supporting_text: "the active site has a distorted geometry that is unable to bind the metal ion effectively or in a catalysis-relevant manner"
- id: PMID:36375638
  title: Structures of a constitutively active mutant of human IDH3 reveal new insights into the mechanisms of allosteric activation and the catalytic reaction.
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: >-
      Structures of the constitutively active α-Q139A mutant, including the (αβαγ)2 holoenzyme (PDB 8GRB)
      and the first pseudo-Michaelis complex of HsIDH3, place IDH3B as an integral β subunit of the active
      heterooctamer and define the cofactor/substrate/metal-binding residues at the complex level,
      supporting β's role in holoenzyme assembly, allosteric activation, and the catalytic reaction.
  findings:
    - statement: Human IDH3 functions as the (αβαγ)2 heterooctamer composed of α, β, and γ subunits
      supporting_text: "It consists of three types of subunits (α, β, and γ) and exists and functions as the (αβαγ)2 heterooctamer"
    - statement: Structures provide the first pseudo-Michaelis complex of HsIDH3 identifying cofactor, substrate, and metal-ion binding residues
      supporting_text: "the αQ139AICT+Ca+NADβNAD structure presents the first pseudo-Michaelis complex of HsIDH3, which allows us to identify the key residues involved in the binding of cofactor, substrate, and metal ion"
- id: PMID:21630459
  title: Proteomic characterization of the human sperm nucleus.
  findings:
    - statement: IDH3B detected in sperm nuclear proteome among 403 proteins
      supporting_text: "403 different proteins have been identified from the isolated sperm nuclei"
- id: PMID:34800366
  title: Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context.
  findings:
    - statement: High-throughput proteomics confirms IDH3B in mitochondrial proteome
      supporting_text: "Quantitative high-confidence human mitochondrial proteome"
- id: Reactome:R-HSA-70967
  title: IDH3 complex decarboxylates isocitrate
  findings:
    - statement: IDH3 complex catalyzes isocitrate + NAD+ to alpha-ketoglutarate + CO2 + NADH in mitochondrial matrix
      supporting_text: "Mitochondrial isocitrate dehydrogenase IDH3 catalyzes the irreversible reaction of isocitrate and NAD+ to form alpha-ketoglutarate, CO2, and NADH"
    - statement: Complex is heterooctamer with 2alpha:1beta:1gamma heterotetramer repeated twice plus Mn++
      supporting_text: "The enzyme is a heterooctamer containing two copies of a heterotetramer of two IDH3A, one IDH3B, one IDH3G, and two Mn++"
    - statement: Activated by ADP, inhibited by NADH and high ATP
      supporting_text: "It is activated by ADP (Soundar et al., 2003, 2006; Bzymek and Colman, 2007) and inhibited by NADH and high concentrations of ATP"
- id: file:human/IDH3B/IDH3B-deep-research-falcon.md
  title: Deep research summary for IDH3B
  findings:
    - statement: IDH3 complex has alpha2-beta-gamma stoichiometry where beta plays structural/regulatory role
    - statement: AlphaBeta dimer has ~16% of heterotetramer activity while AlphaGamma dimer has ~36%
    - statement: Allosteric regulation by citrate and ADP occurs through gamma subunit, not beta
    - statement: IDH3B required for spermiogenesis in mouse knockout studies
    - statement: Biallelic IDH3B variants cause retinitis pigmentosa 46
core_functions:
- description: >-
    IDH3B functions as a structural/regulatory subunit of the mitochondrial NAD-dependent
    isocitrate dehydrogenase complex. It does not have intrinsic catalytic activity but is
    essential for proper complex assembly, stability, and allosteric regulation. The beta
    subunit contributes to ADP-mediated activation of the enzyme.
  molecular_function:
    id: GO:0005198
    label: structural molecule activity
  directly_involved_in:
    - id: GO:0006099
      label: tricarboxylic acid cycle
  locations:
    - id: GO:0005759
      label: mitochondrial matrix
  in_complex:
    id: GO:0045242
    label: isocitrate dehydrogenase complex (NAD+)
  supported_by:
    - reference_id: PMID:14555658
      supporting_text: "Wild type (WT) and mutant enzymes ... were purified to homogeneity yielding enzymes with 2alpha:1beta:1gamma subunit composition"
    - reference_id: PMID:10601238
      supporting_text: "the alpha is the catalytic subunit and that at least one of the other two subunits plays an essential supporting role for activity"
suggested_questions:
  - question: >-
      Within the αβαγ heterotetramer (and its (αβαγ)2 holoenzyme), which IDH3B residues
      beyond β-Arg99 transmit the ADP allosteric signal to the IDH3A catalytic site, and
      does IDH3B contribute any direct interactions to substrate/cofactor binding in the
      pseudo-Michaelis complex captured by the αQ139A·ICT·Ca·NAD·βNAD structure (PMID:36375638)?
      Mapping these residues would justify more specific molecular-function annotations
      for IDH3B (e.g., positive regulation of isocitrate dehydrogenase activity).
  - question: >-
      What is the functional consequence of β1 vs β2 isoform switching in vivo? Beyond
      the shifted pH optimum from 8.0 to 7.6 in vitro (PMID:10601238), do heart and
      skeletal muscle preferentially run IDH3 at distinct intramitochondrial pH set
      points, and is this isoform exchange dynamic with physiological state (exercise,
      ischemia)?
  - question: >-
      Why does loss of IDH3B selectively manifest as retinitis pigmentosa 46 when IDH3
      operates ubiquitously? Is the retinal phenotype driven by a uniquely high
      photoreceptor TCA flux, by altered NADH/NAD+ balance affecting outer-segment
      lipid/visual-cycle pathways, or by α2γ-only complexes acting as a partial-loss-of-
      function background that other tissues tolerate?
suggested_experiments:
  - description: >-
      Reconstitute the recombinant (αβαγ)2 holoenzyme with IDH3B variants spanning the
      β3-α3 and β12-α8 loops identified in PMID:31515270 / PMID:36375638 as building the
      pseudo-allosteric site, and measure ADP-dependent k_cat / K_m for isocitrate plus
      ADP-binding affinity by ITC. Pair with cryo-EM of selected variants in the apo and
      ADP-bound states to confirm structural consequences.
    hypothesis: >-
      The pseudo-allosteric loops contributed by IDH3B (small domain plus β3-α3 / β12-α8)
      are the principal transducers of ADP activation, and engineered residue swaps in
      these loops can uncouple ADP binding from catalytic activation.
    experiment_type: biochemistry / structural biology
  - description: >-
      Generate isoform-specific β1 and β2 CRISPR knock-in HEK293, C2C12 (skeletal muscle)
      and HL-1 (cardiomyocyte) lines and measure intramitochondrial pH, TCA flux (13C
      isotopologue analysis of citrate/α-ketoglutarate), and oxygen consumption under
      basal and exercised/hypoxic conditions.
    hypothesis: >-
      β2 expression in muscle tissue tunes IDH3 activity to a lower, physiologically
      relevant matrix pH, supporting sustained TCA flux during high-workload conditions
      where matrix pH falls below the β1 optimum.
    experiment_type: cell biology / metabolomics
  - description: >-
      Patient-derived iPSC differentiation to retinal organoids from RP46 IDH3B
      patients vs. isogenic CRISPR-corrected controls, with assessment of photoreceptor
      survival, outer-segment morphology, NADH/NAD+ ratio, α-KG levels, and TCA flux.
      Compare to iPSC-derived cardiomyocytes and hepatocytes from the same patients to
      identify the metabolic axis that distinguishes the retina.
    hypothesis: >-
      Photoreceptor degeneration in RP46 is driven by NADH-dependent or α-KG-dependent
      processes uniquely sensitive to partial IDH3 activity (e.g., visual-cycle retinoid
      metabolism or HIF/2-oxoglutarate-dependent dioxygenase signalling) rather than by a
      generalized TCA failure.
    experiment_type: stem-cell biology / clinical model