SDHD

---
id: O14521
gene_symbol: SDHD
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: SDHD encodes the small cytochrome b-like membrane anchor subunit (CybS)
  of succinate dehydrogenase (SDH, Complex II), a heterotetrameric enzyme (SDHA/SDHB/SDHC/SDHD)
  embedded in the mitochondrial inner membrane. SDHD has three transmembrane helices
  and, together with SDHC, forms the membrane anchor domain that attaches the hydrophilic
  SDHA/SDHB catalytic head to the inner membrane. SDHD and SDHC together coordinate
  one heme b group (with His102 of SDHD serving as an axial ligand) and form the ubiquinone-binding
  entrance channel (involving SDHD TM2 helix and Tyr114 directly contacting ubiquinone).
  Complex II is unique among OXPHOS complexes in that it does NOT pump protons across
  the inner membrane. SDHD has no independent catalytic activity but contributes structurally
  to the ubiquinone binding site and electron sink function of heme b. SDHD functions
  as a tumor suppressor; heterozygous loss-of-function germline mutations cause hereditary
  paraganglioma/pheochromocytoma syndrome type 1 (PPGL1) via succinate accumulation
  acting as an oncometabolite. Biallelic mutations cause mitochondrial complex II
  deficiency type 3 (MC2DN3) with encephalomyopathy and cardiomyopathy.
alternative_products:
  - name: '1'
    id: O14521-1
  - name: '2'
    id: O14521-2
    sequence_note: VSP_054744
  - name: '3'
    id: O14521-3
    sequence_note: VSP_054745
  - name: '4'
    id: O14521-4
    sequence_note: VSP_054746, VSP_054747
existing_annotations:
  - term:
      id: GO:0006099
      label: tricarboxylic acid cycle
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: IBA annotation for TCA cycle involvement. Complex II is the only membrane-bound
        enzyme of the TCA cycle, catalyzing the oxidation of succinate to fumarate.
        SDHD is essential as the membrane anchor subunit. The IBA is phylogenetically
        well-supported with evidence from orthologous SDH subunits across multiple
        species. Confirmed by the original cDNA cloning study (PMID:9533030) which
        established SDHD as part of the succinate-ubiquinone oxidoreductase complex.
      action: ACCEPT
      reason: TCA cycle involvement is a core biological process for SDHD as part
        of Complex II. The IBA is phylogenetically sound and well-supported by biochemical
        evidence.
      supported_by:
        - reference_id: PMID:9533030
          supporting_text: Complex II (succinate-ubiquinone oxidoreductase) is an
            important enzyme complex in both the tricarboxylic acid cycle and the
            aerobic respiratory chains of mitochondria in eukaryotic cells and prokaryotic
            organisms
        - reference_id: PMID:37098072
          supporting_text: 'Human complex II is a key protein complex that links two
            essential energy-producing processes: the tricarboxylic acid cycle and
            oxidative phosphorylation'
        - reference_id: file:human/SDHD/SDHD-deep-research-falcon.md
          supporting_text: The SDHD gene (chromosome 11q23.1) encodes the small cytochrome
            b-like membrane subunit of mitochondrial Complex II (succinate dehydrogenase;
            SQR), partnering with SDHC to anchor the catalytic SDHA/SDHB dimer, harbor
            heme b, and form the ubiquinone-binding/channel region
  - term:
      id: GO:0006121
      label: mitochondrial electron transport, succinate to ubiquinone
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: IBA annotation for the specific electron transport process from succinate
        to ubiquinone. SDHD forms part of the ubiquinone-binding entrance channel
        (via TM2 helix and Tyr114) and coordinates heme b (via His102) which serves
        as an electron sink facilitating ubiquinone reduction. The cryo-EM structure
        (PMID:37098072) directly demonstrates SDHD residues at the quinone binding
        site.
      action: ACCEPT
      reason: This is a core biological process for SDHD. The SDHD subunit directly
        contributes to the ubiquinone-binding site and heme b coordination that enable
        electron transfer from succinate to ubiquinone. Phylogenetically well-supported
        and confirmed by structural data.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: UQ is also observed to bind at the entrance of the pocket
            formed by the transmembrane helix I of SDHC, transmembrane helix II of
            SDHD, and the C-terminal segment of SDHB. It interacts with Pro-SDHB197,
            Trp-SDHB201, Ile-SDHB246, Ile-SDHC56, Trp-SDHC61, Met-SDHC65, Ile-SDHC69,
            and Tyr-SDHD114
  - term:
      id: GO:0045273
      label: respiratory chain complex II (succinate dehydrogenase)
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: IBA annotation for Complex II membership. SDHD is one of the four core
        subunits of Complex II, forming the membrane anchor together with SDHC. The
        IBA is strongly supported phylogenetically. The cryo-EM structure (PMID:37098072)
        directly demonstrates SDHD as an integral subunit of the complex.
      action: ACCEPT
      reason: Localization to respiratory chain complex II is the most fundamental
        cellular component annotation for SDHD. Well-supported by IBA phylogenetic
        inference and confirmed by cryo-EM structure showing all four subunits.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: All the four subunits (SDHA, SDHB, SDHC, and SDHD) were
            detected by SDS-PAGE (SI Appendix, Fig. S1D) and mass spectrometry (MS)
        - reference_id: PMID:9533030
          supporting_text: the amino acid sequences of the large (cybL) and small
            (cybS) subunits of cytochrome b in human liver complex II were deduced
            from cDNAs
  - term:
      id: GO:0020037
      label: heme binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: IBA annotation for heme binding. SDHD coordinates heme b together with
        SDHC at the interface between the two membrane-spanning subunits. His102 of
        SDHD serves as an axial binding residue for the heme b iron (PMID:37098072,
        UniProt FT BINDING 102). Histidine residues predicted as heme axial ligands
        were identified in the second transmembrane segment of each subunit in the
        original cloning study (PMID:9533030).
      action: ACCEPT
      reason: Heme binding is a core molecular function of SDHD. His102 directly coordinates
        the heme b iron atom as an axial ligand, confirmed by the cryo-EM structure
        at 2.86 angstrom resolution. The heme b functions as an electron sink stabilizing
        semiquinone intermediates during ubiquinone reduction.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: Electron paramagnetic resonance (EPR) spectra revealed
            the presence of redox centers
        - reference_id: PMID:9533030
          supporting_text: Histidine residues, which are possible heme axial ligands
            in cytochrome b of complex II, were found in the second transmembrane
            segment of each subunit
  - term:
      id: GO:0048039
      label: ubiquinone binding
    evidence_type: IBA
    original_reference_id: GO_REF:0000033
    review:
      summary: IBA annotation for ubiquinone binding. SDHD directly contributes to
        the ubiquinone-binding site via Tyr114, which contacts ubiquinone in the entrance
        pocket formed by SDHC TM1, SDHD TM2, and the SDHB C-terminus (PMID:37098072).
        UniProt annotates SDHD Tyr114 as a ubiquinone-binding residue (ligand shared
        with SDHB).
      action: ACCEPT
      reason: Ubiquinone binding is a core molecular function of SDHD. Structural
        evidence from cryo-EM directly shows Tyr-SDHD114 contacting ubiquinone at
        the binding entrance. This is one of the key subunit-specific contributions
        of SDHD to the complex.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: UQ is also observed to bind at the entrance of the pocket
            formed by the transmembrane helix I of SDHC, transmembrane helix II of
            SDHD, and the C-terminal segment of SDHB. It interacts with Pro-SDHB197,
            Trp-SDHB201, Ile-SDHB246, Ile-SDHC56, Trp-SDHC61, Met-SDHC65, Ile-SDHC69,
            and Tyr-SDHD114
  - term:
      id: GO:0005740
      label: mitochondrial envelope
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: IEA annotation from InterPro (IPR007992 CybS) mapping to mitochondrial
        envelope. SDHD is an integral protein of the inner mitochondrial membrane.
        This term is correct but less specific than GO:0005743 (mitochondrial inner
        membrane) which is also annotated from multiple evidence codes.
      action: ACCEPT
      reason: Correct localization. SDHD is embedded in the inner mitochondrial membrane,
        which is part of the mitochondrial envelope. The more specific GO:0005743
        is also present from IDA, NAS, TAS, ISS, and IEA evidence. Acceptable for
        an IEA to be at this broader level.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: 'The entire hydrophobic domain contains two membrane-anchored
            subunits: SDHC and SDHD'
  - 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 vocabulary mapping.
        SDHD is a multi-pass integral protein of the inner mitochondrial membrane
        with three transmembrane helices, confirmed by the cryo-EM structure (PMID:37098072)
        and the original cloning study (PMID:9533030).
      action: ACCEPT
      reason: Correct localization. SDHD is an integral inner mitochondrial membrane
        protein. Well-supported by multiple experimental evidence sources.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: The two membrane-anchored proteins (SDHC and SDHD) in human
            CII, each with three transmembrane helices, contain only one heme b group
  - term:
      id: GO:0006099
      label: tricarboxylic acid cycle
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: IEA annotation for TCA cycle involvement from combined automated methods
        including ortholog transfer from mouse (UniProtKB:Q9CXV1) and UniProt keyword/UniPathway
        mapping. Consistent with the IBA and IDA annotations for the same term.
      action: ACCEPT
      reason: Correct. Duplicate of the IBA and IDA annotations for the same GO term.
        TCA cycle involvement is a core function of SDHD as part of Complex II.
  - term:
      id: GO:0016020
      label: membrane
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    review:
      summary: IEA annotation from InterPro (IPR007992, IPR034804) mapping to the
        generic 'membrane' term. SDHD is a multi-pass integral membrane protein with
        three transmembrane helices. This term is correct but very broad; more specific
        terms (GO:0005743, GO:0005740) are also annotated.
      action: ACCEPT
      reason: Correct but very general. Acceptable for an IEA to be at this broad
        level. The more specific GO:0005743 (mitochondrial inner membrane) is also
        annotated.
  - term:
      id: GO:0046872
      label: metal ion binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: IEA annotation from UniProt keyword (KW-0479 Metal-binding) mapping.
        SDHD binds iron as part of the heme b group coordinated between SDHC and SDHD.
        His102 of SDHD is an axial binding residue for the heme iron. This is correct
        but very general; the more informative GO:0020037 (heme binding) is also annotated.
      action: ACCEPT
      reason: Correct but general. SDHD coordinates iron as part of heme b via His102.
        The more specific GO:0020037 (heme binding) is also annotated and provides
        more informative description of the actual binding function.
  - term:
      id: GO:0005515
      label: protein binding
    evidence_type: IPI
    original_reference_id: PMID:32296183
    review:
      summary: IPI annotation for protein binding based on the HuRI high-throughput
        binary interactome study (PMID:32296183). The IntAct record indicates SDHD
        interacts with RHBDD2 (Q6NTF9-3), an interaction detected by yeast two-hybrid.
        UniProt also records this as the only documented binary interaction for SDHD
        outside of Complex II subunit-subunit interactions. RHBDD2 is a rhomboid-like
        protease with uncertain functional relevance to SDHD.
      action: MARK_AS_OVER_ANNOTATED
      reason: "'Protein binding' is an uninformative term per GO curation guidelines.\
        \ The interaction with RHBDD2 was detected in a high-throughput Y2H screen\
        \ and its biological relevance to SDHD function is unclear. SDHD binds SDHC\
        \ as its primary protein partner within Complex II, but this interaction is\
        \ already captured by the Complex II component annotations. The generic 'protein\
        \ binding' term does not inform about SDHD function."
      supported_by:
        - reference_id: PMID:32296183
          supporting_text: Here we present a human 'all-by-all' reference interactome
            map of human binary protein interactions, or 'HuRI'
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    review:
      summary: IEA annotation for mitochondrion localization from combined automated
        methods including ortholog transfer and ARBA rules. SDHD is a mitochondrial
        protein as part of Complex II in the inner mitochondrial membrane. This is
        correct but less specific than GO:0005743 (mitochondrial inner membrane).
      action: ACCEPT
      reason: Correct localization. SDHD resides in the mitochondrion. Acceptable
        for an IEA to be at this broader level when more specific terms are also annotated.
  - term:
      id: GO:0005759
      label: mitochondrial matrix
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: IEA annotation for mitochondrial matrix localization from Ensembl Compara
        ortholog transfer (mouse Q9CXV1). The GOA qualifier is 'is_active_in'. SDHD
        is an integral inner membrane protein with a short N-terminal region (residues
        57-63) in the matrix and the bulk of the protein spanning the membrane. The
        cryo-EM structure (PMID:37098072) maps SDHD topology showing matrix-facing
        and IMS-facing regions. This annotation is misleading because SDHD is not
        primarily active in the matrix; its functional role is within the membrane
        and at the quinone-binding site.
      action: MODIFY
      reason: SDHD is an integral membrane protein of the inner mitochondrial membrane.
        While a small N-terminal loop faces the matrix, calling SDHD 'is_active_in'
        the mitochondrial matrix is inaccurate. The appropriate localization for SDHD
        is the inner mitochondrial membrane (GO:0005743) which is already well-annotated.
        This IEA likely results from a blanket ortholog transfer that does not distinguish
        membrane-spanning from soluble subunits of the complex.
      proposed_replacement_terms:
        - id: GO:0005743
          label: mitochondrial inner membrane
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: 'The entire hydrophobic domain contains two membrane-anchored
            subunits: SDHC and SDHD'
  - term:
      id: GO:0008177
      label: succinate dehydrogenase (quinone) activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: IEA annotation for SDH quinone activity from Ensembl Compara ortholog
        transfer (mouse Q9CXV1). The GOA qualifier is 'enables'. GO:0008177 represents
        the overall reaction of the SDH complex (succinate + quinone -> fumarate +
        quinol, EC 1.3.5.1). SDHD alone cannot catalyze this reaction; it provides
        the membrane anchor and contributes to the ubiquinone-binding site via Tyr114
        (PMID:37098072). The qualifier should be 'contributes_to' rather than 'enables'
        for a non-catalytic subunit that participates in the quinone binding site.
      action: ACCEPT
      reason: SDHD contributes to the overall SDH quinone activity by providing part
        of the ubiquinone-binding site (Tyr114) and anchoring the complex in the membrane.
        The IEA mapping is not incorrect per se, though ideally the qualifier would
        be 'contributes_to'. As an IEA, accepting this broader annotation is appropriate
        since the complex-level activity does depend on SDHD.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: UQ is also observed to bind at the entrance of the pocket
            formed by the transmembrane helix I of SDHC, transmembrane helix II of
            SDHD, and the C-terminal segment of SDHB
  - term:
      id: GO:0045273
      label: respiratory chain complex II (succinate dehydrogenase)
    evidence_type: IEA
    original_reference_id: GO_REF:0000107
    review:
      summary: IEA annotation for Complex II membership from Ensembl Compara ortholog
        transfer (mouse Q9CXV1). Consistent with IBA, ISS, IDA, and TAS annotations
        for the same term. SDHD is unequivocally a core subunit of Complex II.
      action: ACCEPT
      reason: Correct. Duplicate of multiple other annotations for this well-established
        Complex II membership. SDHD is one of the four core subunits.
  - term:
      id: GO:0005743
      label: mitochondrial inner membrane
    evidence_type: NAS
    original_reference_id: PMID:30030361
    review:
      summary: NAS annotation from ComplexPortal citing the OXPHOS assembly review
        by Signes and Fernandez-Vizarra (2018). SDHD is an integral inner mitochondrial
        membrane protein with three transmembrane helices. This review covers the
        assembly of OXPHOS complexes I-V including Complex II.
      action: ACCEPT
      reason: Correct localization. Inner mitochondrial membrane is the well-established
        localization for SDHD. Consistent with IDA and structural evidence.
      supported_by:
        - reference_id: PMID:30030361
          supporting_text: The assembly of the five oxidative phosphorylation system
            (OXPHOS) complexes in the inner mitochondrial membrane is an intricate
            process
  - term:
      id: GO:0006099
      label: tricarboxylic acid cycle
    evidence_type: NAS
    original_reference_id: PMID:30030361
    review:
      summary: NAS annotation from ComplexPortal for TCA cycle involvement, citing
        the OXPHOS assembly review. Complex II uniquely functions in both the TCA
        cycle and the electron transport chain. Consistent with IBA and IDA annotations
        for the same term.
      action: ACCEPT
      reason: Correct. TCA cycle involvement is a core function of Complex II and
        therefore of SDHD. Consistent with multiple other evidence lines.
      supported_by:
        - reference_id: PMID:30030361
          supporting_text: The assembly of the five oxidative phosphorylation system
            (OXPHOS) complexes in the inner mitochondrial membrane is an intricate
            process
  - term:
      id: GO:0006121
      label: mitochondrial electron transport, succinate to ubiquinone
    evidence_type: NAS
    original_reference_id: PMID:30030361
    review:
      summary: NAS annotation from ComplexPortal for the specific electron transport
        process. SDHD contributes to the ubiquinone-binding site and heme b coordination
        that are essential for electron transfer from succinate to ubiquinone. Consistent
        with IBA annotation for the same term.
      action: ACCEPT
      reason: Correct. SDHD directly contributes to electron transfer by forming part
        of the quinone-binding entrance and coordinating heme b. Consistent with structural
        evidence.
      supported_by:
        - reference_id: PMID:30030361
          supporting_text: The assembly of the five oxidative phosphorylation system
            (OXPHOS) complexes in the inner mitochondrial membrane is an intricate
            process
  - term:
      id: GO:0042776
      label: proton motive force-driven mitochondrial ATP synthesis
    evidence_type: NAS
    original_reference_id: PMID:30030361
    review:
      summary: NAS annotation from ComplexPortal for proton motive force-driven ATP
        synthesis. Complex II transfers electrons from succinate to ubiquinone, contributing
        to the overall electron flow that drives proton pumping by Complexes I, III,
        and IV, which in turn drives ATP synthesis by Complex V. However, Complex
        II itself does NOT pump protons. This annotation attributes a downstream consequence
        of Complex II activity to SDHD rather than a direct function.
      action: MARK_AS_OVER_ANNOTATED
      reason: Complex II does NOT pump protons across the inner membrane. While it
        does feed electrons into the ubiquinone pool, contributing indirectly to the
        proton motive force via Complexes III and IV, annotating SDHD with 'proton
        motive force-driven mitochondrial ATP synthesis' overstates the direct role.
        The direct contributions of SDHD are better captured by GO:0006121 (electron
        transport, succinate to ubiquinone) and the Complex II component annotation.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: 'Respiratory complex II plays a crucial role in the two
            primary key metabolic pathways for generating ATP: the Krebs cycle (also
            known as tricarboxylic acid, TCA) and the OXPHOS pathway [Complex II does
            not directly pump protons but contributes electrons to the ubiquinone
            pool]'
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: HTP
    original_reference_id: PMID:34800366
    review:
      summary: HTP annotation for mitochondrion localization from the high-confidence
        human mitochondrial proteome study by Morgenstern et al. (2021). SDHD was
        detected as part of the high-confidence mitochondrial proteome by quantitative
        mass spectrometry. Consistent with all other localization evidence.
      action: ACCEPT
      reason: Correct. Mitochondrial localization of SDHD is confirmed by high-throughput
        proteomics and consistent with all other evidence. Broader than GO:0005743
        but acceptable for HTP evidence.
      supported_by:
        - reference_id: PMID:34800366
          supporting_text: We classified >8,000 proteins in mitochondrial preparations
            of human cells and defined a mitochondrial high-confidence proteome of
            >1,100 proteins (MitoCoP)
  - term:
      id: GO:0045273
      label: respiratory chain complex II (succinate dehydrogenase)
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation for Complex II membership transferred from ortholog
        (UniProtKB:A5GZW8, A. suum SDHD). Consistent with IBA, IDA, TAS, and IEA annotations
        for the same term.
      action: ACCEPT
      reason: Correct. Consistent with multiple other evidence lines. Complex II membership
        is the core component annotation for SDHD.
  - term:
      id: GO:0045273
      label: respiratory chain complex II (succinate dehydrogenase)
    evidence_type: IDA
    original_reference_id: PMID:37098072
    review:
      summary: IDA annotation for Complex II membership based on the cryo-EM structure
        of human Complex II (Du et al., 2023). The structure was determined at 2.86
        angstrom resolution by cryo-EM showing all four subunits (SDHA, SDHB, SDHC,
        SDHD) in a monomeric assembly. SDHD was identified by mass spectrometry and
        its structure was resolved in the complex showing three transmembrane helices.
      action: ACCEPT
      reason: Strong experimental evidence from the definitive human Complex II structure.
        This is the highest-quality direct evidence for SDHD as a Complex II subunit.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: All the four subunits (SDHA, SDHB, SDHC, and SDHD) were
            detected by SDS-PAGE (SI Appendix, Fig. S1D) and mass spectrometry (MS)
        - reference_id: PMID:37098072
          supporting_text: The two membrane-anchored proteins (SDHC and SDHD) in human
            CII, each with three transmembrane helices, contain only one heme b group
  - term:
      id: GO:0045273
      label: respiratory chain complex II (succinate dehydrogenase)
    evidence_type: TAS
    original_reference_id: PMID:9533030
    review:
      summary: TAS annotation for Complex II membership based on the original cDNA
        cloning study by Hirawake et al. (1997). This study cloned the cDNA for the
        small (cybS/SDHD) subunit of cytochrome b in human liver Complex II and mapped
        the gene to chromosome 11q23.
      action: ACCEPT
      reason: Correct. The original cloning study establishing SDHD as a Complex II
        subunit. Consistent with all subsequent structural and biochemical evidence.
      supported_by:
        - reference_id: PMID:9533030
          supporting_text: the amino acid sequences of the large (cybL) and small
            (cybS) subunits of cytochrome b in human liver complex II were deduced
            from cDNAs
  - term:
      id: GO:0005743
      label: mitochondrial inner membrane
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-70994
    review:
      summary: TAS annotation from Reactome pathway R-HSA-70994 (SDH complex dehydrogenates
        succinate). SDHD is placed in the inner mitochondrial membrane as part of
        the SDH complex in this Reactome reaction.
      action: ACCEPT
      reason: Correct localization. Consistent with all other evidence for SDHD in
        the inner mitochondrial membrane.
  - term:
      id: GO:0005743
      label: mitochondrial inner membrane
    evidence_type: TAS
    original_reference_id: Reactome:R-HSA-9855252
    review:
      summary: TAS annotation from Reactome pathway R-HSA-9855252 (SDHA:SDHB binds
        to SDHC:SDHD). This Reactome reaction describes the assembly of the SDHA/SDHB
        catalytic dimer with the SDHC/SDHD membrane anchor in the inner mitochondrial
        membrane.
      action: ACCEPT
      reason: Correct localization. The assembly of SDHC:SDHD with SDHA:SDHB occurs
        at the inner mitochondrial membrane. Consistent with all other evidence.
  - term:
      id: GO:0005743
      label: mitochondrial inner membrane
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation for inner mitochondrial membrane localization transferred
        from ortholog (UniProtKB:A5GZW8, A. suum SDHD). Consistent with IDA, NAS,
        TAS, and IEA annotations for the same term.
      action: ACCEPT
      reason: Correct. Consistent with multiple other evidence lines for inner mitochondrial
        membrane localization.
  - term:
      id: GO:0020037
      label: heme binding
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation for heme binding transferred from ortholog (UniProtKB:A5GZW8,
        A. suum SDHD). Consistent with the IBA annotation for the same term. SDHD
        coordinates heme b via His102 as an axial ligand, confirmed by the human cryo-EM
        structure (PMID:37098072).
      action: ACCEPT
      reason: Correct. Heme binding is a core molecular function of SDHD. The ISS
        transfer is validated by the human cryo-EM structure showing heme b coordination.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: Electron paramagnetic resonance (EPR) spectra revealed
            the presence of redox centers
  - term:
      id: GO:0048039
      label: ubiquinone binding
    evidence_type: ISS
    original_reference_id: GO_REF:0000024
    review:
      summary: ISS annotation for ubiquinone binding transferred from ortholog (UniProtKB:A5GZW8,
        A. suum SDHD). Consistent with the IBA annotation for the same term. SDHD
        Tyr114 directly contacts ubiquinone in the binding pocket as shown by the
        cryo-EM structure (PMID:37098072).
      action: ACCEPT
      reason: Correct. Ubiquinone binding is a core molecular function of SDHD. The
        ISS transfer is validated by the human cryo-EM structure.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: UQ is also observed to bind at the entrance of the pocket
            formed by the transmembrane helix I of SDHC, transmembrane helix II of
            SDHD, and the C-terminal segment of SDHB. It interacts with Pro-SDHB197,
            Trp-SDHB201, Ile-SDHB246, Ile-SDHC56, Trp-SDHC61, Met-SDHC65, Ile-SDHC69,
            and Tyr-SDHD114
  - term:
      id: GO:0009055
      label: electron transfer activity
    evidence_type: TAS
    original_reference_id: PMID:9533030
    review:
      summary: TAS annotation for electron transfer activity based on the original
        cloning study (Hirawake et al., 1997). SDHD contributes to electron transfer
        by coordinating heme b (electron sink) and forming the ubiquinone-binding
        site where the terminal electron transfer step occurs. However, SDHD itself
        does not harbor iron-sulfur clusters or FAD; the primary electron transfer
        function resides in SDHB. The heme b coordinated by SDHD/SDHC serves as an
        electron sink that stabilizes semiquinone intermediates rather than being
        a primary electron carrier.
      action: ACCEPT
      reason: SDHD contributes to electron transfer through heme b coordination and
        ubiquinone binding. While SDHB is the primary electron relay subunit, SDHD
        provides essential structural elements for the terminal electron transfer
        step. The heme b acts as an electron sink with edge-to-edge distances of about
        6.6 angstroms to both ubiquinone and the [3Fe-4S] cluster, within efficient
        electron transfer range.
      supported_by:
        - reference_id: PMID:37098072
          supporting_text: The edge-to-edge distance between these redox-active prosthetic
            groups is less than 14 Å (Fig. 3), a distance range that can efficiently
            support the delivery of electrons between these redox centers (22)
  - term:
      id: GO:0005743
      label: mitochondrial inner membrane
    evidence_type: IDA
    original_reference_id: PMID:9533030
    review:
      summary: IDA annotation for inner mitochondrial membrane localization based
        on the original cloning study (Hirawake et al., 1997). The study characterized
        SDHD as a hydrophobic membrane anchor subunit of Complex II with three predicted
        transmembrane segments, indicating its location in the inner mitochondrial
        membrane. UniProt annotates this as confirmed experimental localization.
      action: ACCEPT
      reason: Strong experimental evidence from the original cloning and characterization
        study. SDHD is an integral multi-pass protein of the inner mitochondrial membrane.
      supported_by:
        - reference_id: PMID:9533030
          supporting_text: From hydrophobicity analysis, both cybL and cybS appear
            to have three transmembrane segments, indicating their role as membrane-anchors
            for the enzyme complex
  - term:
      id: GO:0006099
      label: tricarboxylic acid cycle
    evidence_type: IDA
    original_reference_id: PMID:9533030
    review:
      summary: IDA annotation for TCA cycle involvement based on the original cloning
        study. The study established SDHD as a subunit of Complex II (succinate-ubiquinone
        oxidoreductase), which is an important enzyme of the tricarboxylic acid cycle.
      action: ACCEPT
      reason: Correct. The original study directly states the role of Complex II in
        the TCA cycle, and SDHD was identified as a core subunit of this complex.
      supported_by:
        - reference_id: PMID:9533030
          supporting_text: Complex II (succinate-ubiquinone oxidoreductase) is an
            important enzyme complex in both the tricarboxylic acid cycle and the
            aerobic respiratory chains of mitochondria in eukaryotic cells and prokaryotic
            organisms
  - term:
      id: GO:0005739
      label: mitochondrion
    evidence_type: TAS
    original_reference_id: PMID:2302193
    review:
      summary: TAS annotation for mitochondrion localization citing Kita et al. (1990),
        which cloned the iron-sulfur subunit (SDHB/Ip) of human liver mitochondrial
        Complex II. While this paper primarily concerns SDHB, it establishes the mitochondrial
        localization of Complex II. SDHD is a subunit of the same complex.
      action: ACCEPT
      reason: Correct localization. SDHD is a mitochondrial protein as part of Complex
        II. The reference is to a Complex II study that established its mitochondrial
        context.
      supported_by:
        - reference_id: PMID:2302193
          supporting_text: Complex II (succinate-ubiquinone oxidoreductase) is an
            important enzyme complex of both the tricarboxylic acid cycle and of the
            aerobic respiratory chains of mitochondria in eukaryotic cell and prokaryotic
            organisms
  - term:
      id: GO:0005740
      label: mitochondrial envelope
    evidence_type: TAS
    original_reference_id: PMID:9533030
    review:
      summary: TAS annotation for mitochondrial envelope localization from the original
        SDHD cloning study (Hirawake et al., 1997). SDHD is a membrane-spanning subunit
        of Complex II in the inner mitochondrial membrane. This is correct but less
        specific than GO:0005743 (mitochondrial inner membrane), which is also annotated.
      action: ACCEPT
      reason: Correct but less specific than GO:0005743. Acceptable to retain as the
        original study supports this localization.
      supported_by:
        - reference_id: PMID:9533030
          supporting_text: From hydrophobicity analysis, both cybL and cybS appear
            to have three transmembrane segments, indicating their role as membrane-anchors
            for the enzyme complex
core_functions:
  - molecular_function:
      id: GO:0020037
      label: heme binding
    contributes_to_molecular_function:
      id: GO:0008177
      label: succinate dehydrogenase (quinone) activity
    directly_involved_in:
      - id: GO:0006121
        label: mitochondrial electron transport, succinate to ubiquinone
      - id: GO:0006099
        label: tricarboxylic acid cycle
    locations:
      - id: GO:0005743
        label: mitochondrial inner membrane
    in_complex:
      id: GO:0045273
      label: respiratory chain complex II (succinate dehydrogenase)
    description: SDHD is the small cytochrome b-like membrane anchor subunit (cybS)
      of succinate dehydrogenase (Complex II). Together with SDHC, it forms the membrane
      anchor domain that attaches the catalytic SDHA:SDHB subcomplex to the inner
      mitochondrial membrane. SDHD provides the His102 axial ligand to the heme b
      (cytochrome b560) iron atom shared between SDHC and SDHD, making heme binding
      (GO:0020037) its primary subunit-specific molecular function. SDHD also contributes
      to ubiquinone binding at the Q-site (Tyr114 directly contacts ubiquinone at
      the entrance pocket formed by SDHC TM1, SDHD TM2, and SDHB C-terminus). SDHD
      has no independent catalytic activity but contributes to the overall succinate
      dehydrogenase (quinone) activity (GO:0008177) of the Complex II heterotetramer.
      The heme b coordinated by SDHD and SDHC serves as an electron sink stabilizing
      semiquinone intermediates during ubiquinone reduction. Through Complex II, SDHD
      participates in mitochondrial electron transport from succinate to ubiquinone
      (GO:0006121) and the tricarboxylic acid cycle (GO:0006099). Complex II is unique
      among OXPHOS complexes in that it does NOT pump protons across the inner membrane.
    supported_by:
      - reference_id: PMID:37098072
        supporting_text: The two membrane-anchored proteins (SDHC and SDHD) in human
          CII, each with three transmembrane helices, contain only one heme b group
      - reference_id: PMID:37098072
        supporting_text: UQ is also observed to bind at the entrance of the pocket
          formed by the transmembrane helix I of SDHC, transmembrane helix II of SDHD,
          and the C-terminal segment of SDHB. It interacts with Pro-SDHB197, Trp-SDHB201,
          Ile-SDHB246, Ile-SDHC56, Trp-SDHC61, Met-SDHC65, Ile-SDHC69, and Tyr-SDHD114
      - reference_id: PMID:9533030
        supporting_text: Histidine residues, which are possible heme axial ligands
          in cytochrome b of complex II, were found in the second transmembrane segment
          of each subunit
references:
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with GO
      terms
    findings:
      - statement: InterPro2GO mapping (SDH cytochrome b-small / CybS / SQR_TypeC_SdhD
          domains) propagates Complex II / electron-transport annotations to SDHD.
  - id: GO_REF:0000024
    title: Manual transfer of experimentally-verified manual GO annotation data to
      orthologs by curator judgment of sequence similarity
    findings:
      - statement: ISS curator transfer from a well-characterized mammalian SDHD ortholog
          propagates inner mitochondrial membrane localization and Complex II membership
          to human SDHD.
  - id: GO_REF:0000033
    title: Annotation inferences using phylogenetic trees
    findings:
      - statement: PAINT/IBA phylogenetic propagation supports Complex II membership,
          TCA cycle involvement, mitochondrial inner-membrane localization, and the
          succinate-to-ubiquinone electron transport process for SDHD across SDHD/CybS
          orthologs.
  - id: GO_REF:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
    findings:
      - statement: UniProt keyword mapping (Electron transport, Mitochondrion, Membrane,
          Tricarboxylic acid cycle) propagates Complex II / OXPHOS process and localization
          annotations to SDHD.
  - 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:
      - statement: UniProt Subcellular Location vocabulary mapping propagates mitochondrial
          inner membrane localization to SDHD, consistent with its three transmembrane
          helices and role as a CII membrane anchor.
  - id: GO_REF:0000107
    title: Automatic transfer of experimentally verified manual GO annotation data
      to orthologs using Ensembl Compara
    findings:
      - statement: Ensembl Compara automatic ortholog transfer propagates mitochondrial
          inner membrane localization and Complex II / TCA cycle involvement to human
          SDHD.
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods
    findings:
      - statement: Combined automated IEA methods propagate inner mitochondrial membrane
          localization and Complex II / succinate-ubiquinone oxidoreductase activity
          annotations to SDHD.
  - id: file:human/SDHD/SDHD-deep-research-falcon.md
    title: Falcon deep research synthesis for human SDHD
    findings:
      - statement: SDHD encodes the small cytochrome b-like membrane subunit of
          mitochondrial Complex II, partnering with SDHC to anchor the catalytic
          SDHA/SDHB dimer, harbor heme b, and form the ubiquinone-binding entrance
          channel.
        supporting_text: The SDHD gene (chromosome 11q23.1) encodes the small cytochrome
          b-like membrane subunit of mitochondrial Complex II (succinate dehydrogenase;
          SQR), partnering with SDHC to anchor the catalytic SDHA/SDHB dimer, harbor
          heme b, and form the ubiquinone-binding/channel region
        reference_section_type: OTHER
  - id: PMID:2302193
    title: 'Human complex II (succinate-ubiquinone oxidoreductase): cDNA cloning of
      iron sulfur (Ip) subunit of liver mitochondria.'
    findings:
      - statement: Complex II is an important enzyme complex of both the TCA cycle
          and aerobic respiratory chains. The iron-sulfur subunit of human liver mitochondrial
          Complex II was cloned from cDNA.
        supporting_text: Complex II (succinate-ubiquinone oxidoreductase) is an important
          enzyme complex of both the tricarboxylic acid cycle and of the aerobic respiratory
          chains of mitochondria in eukaryotic cell and prokaryotic organisms
  - id: PMID:30030361
    title: Assembly of mammalian oxidative phosphorylation complexes I-V and supercomplexes.
    findings:
      - statement: Review of OXPHOS complex assembly including Complex II. Complex
          II assembly involves SDHAF assembly factors and proceeds via SDHA flavinylation
          and SDHB Fe-S maturation before SDHC/SDHD membrane integration.
        supporting_text: The assembly of the five oxidative phosphorylation system
          (OXPHOS) complexes in the inner mitochondrial membrane is an intricate process
  - id: PMID:32296183
    title: A reference map of the human binary protein interactome.
    findings:
      - statement: High-throughput Y2H screen detecting SDHD interaction with RHBDD2
          (Q6NTF9-3). This is a systematic proteome-wide binary interactome study.
        supporting_text: Here we present a human 'all-by-all' reference interactome
          map of human binary protein interactions, or 'HuRI'
  - id: PMID:34800366
    title: Quantitative high-confidence human mitochondrial proteome and its dynamics
      in cellular context.
    findings:
      - statement: SDHD detected in the high-confidence human mitochondrial proteome
          by quantitative mass spectrometry.
        supporting_text: We classified >8,000 proteins in mitochondrial preparations
          of human cells and defined a mitochondrial high-confidence proteome of >1,100
          proteins (MitoCoP)
  - id: PMID:37098072
    title: Structure of the human respiratory complex II.
    findings:
      - statement: Cryo-EM structure of human Complex II at 2.86 angstrom resolution
          showing all four subunits (SDHA, SDHB, SDHC, SDHD). SDHD has three transmembrane
          helices. Ubiquinone binds at the entrance pocket formed by SDHC TM1, SDHD
          TM2, and SDHB C-terminus. SDHD Tyr114 directly contacts ubiquinone. His102
          of SDHD coordinates heme b as axial ligand. Heme b serves as electron sink
          with 6.6 angstrom edge-to-edge distance to both ubiquinone and [3Fe-4S].
          Disease-relevant SDHD mutations (E69K, D92G) are mapped onto the structure.
        supporting_text: UQ is also observed to bind at the entrance of the pocket
          formed by the transmembrane helix I of SDHC, transmembrane helix II of SDHD,
          and the C-terminal segment of SDHB. It interacts with Pro-SDHB197, Trp-SDHB201,
          Ile-SDHB246, Ile-SDHC56, Trp-SDHC61, Met-SDHC65, Ile-SDHC69, and Tyr-SDHD114
  - id: PMID:9533030
    title: 'Cytochrome b in human complex II (succinate-ubiquinone oxidoreductase):
      cDNA cloning of the components in liver mitochondria and chromosome assignment
      of the genes for the large (SDHC) and small (SDHD) subunits to 1q21 and 11q23.'
    findings:
      - statement: Original cloning of SDHD (cybS) cDNA from human liver. SDHD encodes
          a 103 amino acid mature protein with three transmembrane segments serving
          as membrane anchor for Complex II. Histidine residues in the second transmembrane
          segment are potential heme axial ligands. SDHD gene mapped to chromosome
          11q23.
        supporting_text: The mature cybL and cybS contain 140 and 103 amino acids,
          respectively, and show little similarity to the amino acid sequences of
          the subunits from other species in contrast to the highly conserved features
          of the flavoprotein (Fp) subunit and iron-sulfur protein (Ip) subunit
  - id: Reactome:R-HSA-70994
    title: SDH complex dehydrogenates succinate
    findings:
      - statement: Reactome reaction for SDH-catalyzed succinate oxidation to fumarate
          with electron transfer to ubiquinone in the inner mitochondrial membrane.
        supporting_text: The succinate dehydrogenase complex (SDH, complex II), associated
          with the inner mitochondrial membrane, catalyzes the dehydrogenation of
          succinate to fumarate, reducing ubiquinone (Q10) to ubiquinol (Q10H2) on
          the membrane part of the enzyme
  - id: Reactome:R-HSA-9855252
    title: SDHA:SDHB binds to SDHC:SDHD
    findings:
      - statement: Reactome reaction describing assembly of the SDHA/SDHB catalytic
          dimer with the SDHC/SDHD membrane anchor dimer in the inner mitochondrial
          membrane.
        supporting_text: After translation in cytosol and translocation to the mitochondrial
          inner membrane SDH subunits C and D (SDHC, SDHD), together with the heme
          b cofactor, bind to the assembled cytosolic SDHA:SDHB construct to form
          the fully functional SDH complex
suggested_questions:
  - question: >-
      How do PPGL1-causing SDHD missense variants — particularly E69K and D92G mapped
      onto the cryo-EM structure (PMID:37098072) — disrupt heme b coordination
      (His102), ubiquinone binding (Tyr114), or the SDHC/SDHD membrane-anchor
      interface? Distinguishing these mechanisms would refine the annotation of which
      molecular function (succinate-ubiquinone oxidoreductase activity vs. heme
      binding) is most relevant for "contributes_to" capture at the SDHD level.
  - question: >-
      Why does heterozygous SDHD loss-of-function follow a maternal-imprinting
      pattern in PPGL1 (paragangliomas typically arise after paternal transmission of
      a mutant allele), and how does residual SDHD expression from the maternal
      allele in chromaffin tissues escape silencing? Resolving the tissue-specific
      epigenetic mechanism would underpin a more accurate process annotation around
      tumor suppression in chromaffin / paraganglion lineages.
  - question: >-
      How does succinate accumulation from biallelic SDHD-null tumors specifically
      inhibit α-ketoglutarate-dependent dioxygenases (TET, JmjC, PHDs) at
      pathophysiological intratumoral concentrations, and which of these substrates
      drive the pseudohypoxia/hypermethylation phenotype most directly? This would
      support adding more specific BP / regulation terms for the oncometabolite
      signalling axis.
suggested_experiments:
  - description: >-
      Cryo-EM and site-directed mutagenesis of human Complex II reconstituted with
      SDHD E69K, D92G, H102A, Y114A variants. Quantify succinate-dependent ubiquinone
      reduction, heme b spectroscopy (UV-vis, EPR), CII holoenzyme assembly by
      BN-PAGE, and intracellular succinate accumulation in matched HEK293 knock-in
      cell lines.
    hypothesis: >-
      E69K and D92G destabilize the SDHC/SDHD membrane-anchor interface and
      indirectly perturb heme b coordination, whereas H102A and Y114A directly
      uncouple succinate oxidation from ubiquinone reduction; only the latter two
      class of mutations should abolish electron transfer without affecting holoenzyme
      assembly.
    experiment_type: structural biology / enzyme kinetics
  - description: >-
      Allele-specific expression analysis of SDHD mRNA in chromaffin tissue and
      paraganglion-derived organoids from paternal vs. maternal SDHD-mutation
      carriers, combined with WGBS and ATAC-seq of the SDHD locus and surrounding
      imprinted control region. Validate parent-of-origin silencing with
      single-nucleus RNA-seq.
    hypothesis: >-
      Chromaffin and paraganglion cell lineages selectively silence the maternal
      SDHD allele through a tissue-restricted imprinting mechanism, leaving cells
      with only paternal SDHD expression and explaining the dependency on paternal
      transmission of mutations for PPGL1 manifestation.
    experiment_type: epigenetics / single-cell genomics
  - description: >-
      Targeted metabolomics measuring intratumoral succinate and α-KG concentrations
      in PPGL1 SDHD-deficient tumors vs. SDHB / SDHA / non-SDH counterparts, paired
      with biochemical inhibition assays of TET2, KDM6A, FIH-1, and PHD2 across the
      observed succinate ranges. Use isogenic HEK293 SDHD-KO lines complemented with
      WT vs. patient variants to confirm causality of specific dioxygenase inhibition.
    hypothesis: >-
      Intratumoral succinate in SDHD-deficient PPGL reaches concentrations sufficient
      to selectively inhibit PHD2 and TET2 over a broader panel of α-KG-dependent
      dioxygenases, driving the HIF-1α stabilization and DNA hypermethylation that
      define the cluster-1 PPGL phenotype.
    experiment_type: cancer metabolomics / biochemistry