ndhD

Summary: Plastid NDH contributes to cyclic electron flow and chlororespiration, not mitochondrial-style aerobic respiration.

Reason: The focused report checked the term scope and separated NDH-mediated plastoquinone reduction from the separate PTOX oxygen-consuming step of chlororespiration. Higher-plant NDH transfers electrons from ferredoxin to plastoquinone and pumps protons in the thylakoid during cyclic electron flow; it does not perform an aerobic-respiration process with oxygen as the terminal electron acceptor. Remove this mitochondrial/bacterial process propagation while retaining the accepted electron transport coupled proton transport row.

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: Ubiquinone binding is wrong for the NdhD antiporter-like membrane subunit.

Reason: The spinach plastid NDH structure places the plastoquinone pocket in the NdhA/NdhH/NdhK module. NdhD is the ND4/NuoM antiporter-like subunit in the membrane arm, not the quinone-binding subunit, and the chloroplast complex reduces plastoquinone rather than ubiquinone. Remove the subunit-level ligand overpropagation instead of retargeting NdhD to generic quinone binding.

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.

Summary: Add cyclic photosynthetic phosphorylation as the specific photosynthesis process for chloroplast NdhD.

Reason: Higher-plant NDH pumps protons during ferredoxin-to-plastoquinone electron transfer and thereby increases ATP production by cyclic electron flow around photosystem I. As an antiporter-like membrane subunit of this thylakoid complex, NdhD participates directly in the same energy-conserving process as the sibling Populus plastid NDH subunits that already carry photosynthesis/light-reaction annotations with cyclic-photosynthetic-phosphorylation replacements.