id: A4GYW6
gene_symbol: ndhD
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:3694
  label: Populus trichocarpa
description: Chloroplast NDH chain 4 membrane subunit that contributes to plastid NAD(P)H-plastoquinone
  oxidoreductase activity and proton translocation in photosynthetic electron transport.
existing_annotations:
- term:
    id: GO:0009060
    label: aerobic respiration
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Aerobic respiration is a misleading over-propagation for chloroplast ndhD.
    action: REMOVE
    reason: The protein is a plastid NDH subunit in photosynthetic electron transport, not a mitochondrial
      respiratory-chain component.
    supported_by:
    - reference_id: file:POPTR/ndhD/ndhD-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane.'
- term:
    id: GO:0003954
    label: NADH dehydrogenase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: contributes_to
  review:
    summary: Generic NADH dehydrogenase activity is directionally correct but misses the chloroplast quinone
      acceptor context.
    action: MODIFY
    reason: Use the quinone-acceptor oxidoreductase term and keep the contributes_to relationship for
      the NDH complex.
    supported_by:
    - reference_id: file:POPTR/ndhD/ndhD-uniprot.txt
      supporting_text: Reaction=a plastoquinone + NADH/NADPH = a plastoquinol + NAD/NADP.
    proposed_replacement_terms:
    - id: GO:0016655
      label: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
- term:
    id: GO:0015990
    label: electron transport coupled proton transport
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Electron transport coupled proton transport is the core process for chloroplast NDH.
    action: ACCEPT
    reason: The NDH reaction is coupled to proton translocation across the thylakoid membrane.
    supported_by:
    - reference_id: file:POPTR/ndhD/ndhD-uniprot.txt
      supporting_text: Reaction=a plastoquinone + NADH + (n+1) H(+)(in) = a plastoquinol + NAD(+) + n
        H(+)(out).
- term:
    id: GO:0048039
    label: ubiquinone binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Ubiquinone binding is not the right quinone specificity for chloroplast NDH.
    action: MODIFY
    reason: The UniProt-curated reaction uses plastoquinone; a generic quinone-binding term is preferable
      to ubiquinone binding.
    supported_by:
    - reference_id: file:POPTR/ndhD/ndhD-uniprot.txt
      supporting_text: Reaction=a plastoquinone + NADH/NADPH = a plastoquinol + NAD/NADP.
    proposed_replacement_terms:
    - id: GO:0048038
      label: quinone binding
- term:
    id: GO:0008137
    label: NADH dehydrogenase (ubiquinone) activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: NADH dehydrogenase (ubiquinone) activity is too respiratory-chain specific for a chloroplast
      NDH subunit.
    action: MODIFY
    reason: The chloroplast reaction uses plastoquinone and NAD(P)H, so the broader quinone-acceptor oxidoreductase
      term is safer.
    supported_by:
    - reference_id: file:POPTR/ndhD/ndhD-uniprot.txt
      supporting_text: Reaction=a plastoquinone + NADH/NADPH = a plastoquinol + NAD/NADP.
    proposed_replacement_terms:
    - id: GO:0016655
      label: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
- term:
    id: GO:0009535
    label: chloroplast thylakoid membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Chloroplast thylakoid membrane is the correct localization for this plastid NDH subunit.
    action: ACCEPT
    reason: The reviewed UniProt entry places this multi-pass NDH subunit in the chloroplast thylakoid
      membrane.
    supported_by:
    - reference_id: file:POPTR/ndhD/ndhD-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane.'
- term:
    id: GO:0016655
    label: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: This term matches the chloroplast NAD(P)H-plastoquinone NDH reaction.
    action: ACCEPT
    reason: It captures the redox chemistry without imposing an incorrect ubiquinone acceptor.
    supported_by:
    - reference_id: file:POPTR/ndhD/ndhD-uniprot.txt
      supporting_text: Reaction=a plastoquinone + NADH/NADPH = a plastoquinol + NAD/NADP.
- term:
    id: GO:0042773
    label: ATP synthesis coupled electron transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: ATP synthesis coupled electron transport is plausible as a downstream consequence of the
      proton gradient but is broader than the direct NDH function.
    action: KEEP_AS_NON_CORE
    reason: Keep as non-core; the direct process is electron transport coupled proton transport.
    supported_by:
    - reference_id: file:POPTR/ndhD/ndhD-uniprot.txt
      supporting_text: Reaction=a plastoquinone + NADH + (n+1) H(+)(in) = a plastoquinol + NAD(+) + n
        H(+)(out).
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings:
  - statement: GO_REF:0000002 supplied one or more source GOA annotations reviewed in this file.
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings:
  - statement: GO_REF:0000033 supplied one or more source GOA annotations reviewed in this file.
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings:
  - statement: GO_REF:0000120 supplied one or more source GOA annotations reviewed in this file.
- id: file:POPTR/ndhD/ndhD-uniprot.txt
  title: UniProtKB reviewed entry for ndhD
  findings:
  - statement: UniProt identifies ndhD as chloroplast NAD(P)H-quinone oxidoreductase chain 4, a thylakoid
      membrane NDH subunit using plastoquinone rather than ubiquinone.
- id: file:POPTR/ndhD/ndhD-goa.tsv
  title: QuickGO GOA annotations for ndhD
  findings:
  - statement: GOA rows supplied the existing_annotations reviewed in this file.
core_functions:
- description: Contributes a membrane subunit to chloroplast NDH, supporting NAD(P)H-plastoquinone electron
    transfer coupled to proton translocation.
  contributes_to_molecular_function:
    id: GO:0016655
    label: oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor
  directly_involved_in:
  - id: GO:0015990
    label: electron transport coupled proton transport
  locations:
  - id: GO:0009535
    label: chloroplast thylakoid membrane
  supported_by:
  - reference_id: file:POPTR/ndhD/ndhD-uniprot.txt
    supporting_text: Reaction=a plastoquinone + NADH/NADPH = a plastoquinol + NAD/NADP.
  - reference_id: file:POPTR/ndhD/ndhD-uniprot.txt
    supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane.'
proposed_new_terms: []
suggested_questions:
- question: Which stress conditions most require Populus chloroplast NDH chain 4 for cyclic electron flow
    or chlororespiration?
suggested_experiments:
- description: Measure chlorophyll fluorescence and P700 redox kinetics in ndhD perturbation lines under
    fluctuating light.
  experiment_type: targeted functional assay