ndhD

Summary: Chlororespiration prevents categorical rejection from chloroplast localization alone.

Reason: The GO definition does not restrict this process to mitochondria. Tobacco ndhJK/ndhCJK mutants and PTOX inhibition support NDH participation in chlororespiratory electron flow, while independent work demonstrates energy-conserving proton pumping. Whether the full GO process is sufficiently supported for this inherited Populus assertion, including oxygen-coupled energy conservation where required, is under shared adjudication. Current target descent from the positive ancestral node is verified; photosynthetic specialization alone is not evidence of loss.

Summary: Replace NAD(P)H-donor activity with contribution to ferredoxin-dependent oxidoreduction.

Reason: Modern chloroplast NDH biochemistry identifies reduced ferredoxin as the immediate electron donor and plastoquinone as acceptor; the complex lacks the NADH-oxidizing module. GO:0016655 still explicitly requires NAD(P)H, so the previous broader replacement does not correct the donor mismatch. GO:0016730 accommodates an iron-sulfur protein donor. Apply the replacement with contributes_to for this subunit of the enzyme; original source qualifiers are preserved here.

Proposed replacements: oxidoreductase activity, acting on iron-sulfur proteins as donors

Summary: Coupled electron transfer and proton transport are core NDH functions.

Reason: Higher-plant NDH conserves ferredoxin-to-plastoquinone redox energy by proton pumping. This subunit contributes to the electron-transfer/proton-pumping complex and therefore directly participates in the process.

Summary: Direct quinone binding by NdhD cannot be inferred from the substrate of the whole complex.

Reason: The spinach structure places the plastoquinone pocket in NdhA/H/K; NdhD is an antiporter-like subunit elsewhere in the membrane arm. This warrants examination of the ancestral binding assertion, but the present structure alone does not test all possible NdhD binding. Withdraw the unsubstantiated generic quinone-binding replacement and seek subunit-specific adjudication.

Summary: Replace NAD(P)H-donor activity with contribution to ferredoxin-dependent oxidoreduction.

Reason: Modern chloroplast NDH biochemistry identifies reduced ferredoxin as the immediate electron donor and plastoquinone as acceptor; the complex lacks the NADH-oxidizing module. GO:0016655 still explicitly requires NAD(P)H, so the previous broader replacement does not correct the donor mismatch. GO:0016730 accommodates an iron-sulfur protein donor. Apply the replacement with contributes_to for this subunit of the enzyme; original source qualifiers are preserved here.

Proposed replacements: oxidoreductase activity, acting on iron-sulfur proteins as donors

Summary: Chloroplast thylakoid membrane is the correct localization for this plastid NDH subunit.

Reason: The reviewed UniProt entry places this multi-pass NDH subunit in the chloroplast thylakoid membrane.

Summary: Replace NAD(P)H-donor activity with contribution to ferredoxin-dependent oxidoreduction.

Reason: Modern chloroplast NDH biochemistry identifies reduced ferredoxin as the immediate electron donor and plastoquinone as acceptor; the complex lacks the NADH-oxidizing module. GO:0016655 still explicitly requires NAD(P)H, so the previous broader replacement does not correct the donor mismatch. GO:0016730 accommodates an iron-sulfur protein donor. Apply the replacement with contributes_to for this subunit of the enzyme; original source qualifiers are preserved here.

Proposed replacements: oxidoreductase activity, acting on iron-sulfur proteins as donors

Summary: NDH directly performs ATP-synthesis-coupled electron transport.

Reason: The term covers electron transfer that conserves energy ultimately used for ATP synthesis. NDH transfers electrons and pumps protons; these are actual steps of that process, not a remote perturbation effect. Higher-plant NDH proton pumping directly increases the ATP yield of cyclic electron flow.