id: A4GYR4
gene_symbol: ndhK
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:3694
  label: Populus trichocarpa
description: Chloroplast NDH complex subunit K, a 4Fe-4S protein in the plastid NAD(P)H-plastoquinone
  oxidoreductase system that couples photosynthetic electron transport to proton translocation.
existing_annotations:
- term:
    id: GO:0009060
    label: aerobic respiration
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: The respiratory-chain/aerobic-respiration propagation is not appropriate for chloroplast
      ndhK.
    action: REMOVE
    reason: Poplar ndhK is a chloroplast NDH subunit in photosynthetic electron transport, not a mitochondrial
      respiratory complex I subunit.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane.'
- term:
    id: GO:0045271
    label: respiratory chain complex I
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Respiratory chain complex I is a misleading cellular-component assignment for a plastid NDH
      subunit.
    action: REMOVE
    reason: The chloroplast NDH complex is complex-I-like but is not respiratory chain complex I.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'FUNCTION: NDH shuttles electrons from NAD(P)H:plastoquinone to quinones in the
        photosynthetic chain.'
- term:
    id: GO:0008137
    label: NADH dehydrogenase (ubiquinone) activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: NADH dehydrogenase (ubiquinone) activity is too mitochondrial/bacterial for the chloroplast
      NDH reaction.
    action: MODIFY
    reason: The UniProt-curated reaction uses plastoquinone and NAD(P)H, so the broader quinone-acceptor
      oxidoreductase term is safer.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'CATALYTIC ACTIVITY: a plastoquinone + NADH/NADPH + protons = 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 a core process for chloroplast NDH.
    action: ACCEPT
    reason: The NDH reaction conserves redox energy as a proton gradient.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: Couples the redox reaction to proton translocation, and thus conserves the redox
        energy in a proton gradient.
- term:
    id: GO:0005506
    label: iron ion binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  review:
    summary: Generic iron ion binding is less informative than the specific 4Fe-4S cluster binding annotation.
    action: MODIFY
    reason: The relevant iron is in the 4Fe-4S cluster bound by ndhK.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'COFACTOR: Binds 1 [4Fe-4S] cluster.'
    proposed_replacement_terms:
    - id: GO:0051539
      label: 4 iron, 4 sulfur cluster 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 mitochondrial/bacterial for the chloroplast
      NDH reaction.
    action: MODIFY
    reason: The UniProt-curated reaction uses plastoquinone and NAD(P)H, so the broader quinone-acceptor
      oxidoreductase term is safer.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'CATALYTIC ACTIVITY: a plastoquinone + NADH/NADPH + protons = 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 ndhK.
    action: ACCEPT
    reason: The UniProt entry places the protein on the chloroplast thylakoid membrane.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane.'
- term:
    id: GO:0009536
    label: plastid
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: Plastid is correct but too broad for this thylakoid membrane NDH subunit.
    action: MODIFY
    reason: Use the more specific chloroplast thylakoid membrane term.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane.'
    proposed_replacement_terms:
    - id: GO:0009535
      label: 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:0000104
  review:
    summary: This oxidoreductase term matches the chloroplast NAD(P)H-plastoquinone NDH reaction.
    action: ACCEPT
    reason: It avoids the incorrect ubiquinone-specific wording while preserving the quinone-acceptor
      reaction.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'FUNCTION: NDH shuttles electrons from NAD(P)H:plastoquinone to quinones in the
        photosynthetic chain.'
- term:
    id: GO:0019684
    label: photosynthesis, light reaction
  evidence_type: IEA
  original_reference_id: GO_REF:0000104
  review:
    summary: Photosynthesis light reaction is the appropriate biological-process context for the chloroplast
      NDH reaction.
    action: ACCEPT
    reason: The protein acts in the photosynthetic electron transport chain.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'FUNCTION: NDH shuttles electrons to quinones in the photosynthetic chain.'
- term:
    id: GO:0048038
    label: quinone binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Quinone binding is consistent with the plastoquinone electron acceptor in the NDH reaction.
    action: ACCEPT
    reason: The catalytic reaction uses plastoquinone/plastoquinol.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'CATALYTIC ACTIVITY: a plastoquinone is reduced to a plastoquinol.'
- term:
    id: GO:0051536
    label: iron-sulfur cluster binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Iron-sulfur cluster binding is correct but less specific than the curated 4Fe-4S cluster
      binding.
    action: MODIFY
    reason: The UniProt cofactor annotation specifies a single 4Fe-4S cluster.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'COFACTOR: Binds 1 [4Fe-4S] cluster.'
    proposed_replacement_terms:
    - id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
- term:
    id: GO:0051539
    label: 4 iron, 4 sulfur cluster binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: The specific 4Fe-4S cluster binding annotation is supported by the HAMAP-curated UniProt
      entry.
    action: ACCEPT
    reason: This is a real cofactor-binding role for the ndhK subunit.
    supported_by:
    - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
      supporting_text: 'COFACTOR: Binds 1 [4Fe-4S] cluster.'
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:0000104
  title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related
    proteins based on shared sequence features
  findings:
  - statement: GO_REF:0000104 supplied one or more source GOA annotations reviewed in this file.
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings:
  - statement: GO_REF:0000117 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/ndhK/ndhK-uniprot.txt
  title: UniProtKB reviewed entry for ndhK
  findings:
  - statement: UniProt identifies ndhK as chloroplast NAD(P)H-quinone oxidoreductase subunit K, with a
      4Fe-4S cluster, plastoquinone-linked oxidoreductase activity, and thylakoid membrane localization.
core_functions:
- description: Contributes a 4Fe-4S-containing subunit to chloroplast NDH, supporting NAD(P)H-plastoquinone
    oxidoreductase electron transfer and proton translocation during the light reaction.
  molecular_function:
    id: GO:0051539
    label: 4 iron, 4 sulfur cluster binding
  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
  - id: GO:0019684
    label: photosynthesis, light reaction
  locations:
  - id: GO:0009535
    label: chloroplast thylakoid membrane
  supported_by:
  - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
    supporting_text: 'FUNCTION: NDH shuttles electrons from NAD(P)H:plastoquinone, via FMN and iron-sulfur
      centers, to quinones in the photosynthetic chain.'
  - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
    supporting_text: 'COFACTOR: Binds 1 [4Fe-4S] cluster.'
  - reference_id: file:POPTR/ndhK/ndhK-uniprot.txt
    supporting_text: 'SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane.'
proposed_new_terms: []
suggested_questions:
- question: Does Populus ndhK loss specifically affect cyclic electron flow or chlororespiratory NDH activity
    under stress?
suggested_experiments:
- description: Measure chlorophyll fluorescence and P700 redox kinetics in ndhK perturbation lines under
    fluctuating light.
  experiment_type: targeted functional assay