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ATP synthase is a ubiquitous enzyme that is located in the inner membranes of mitochondria, thylakoid membranes of chloroplasts, or the plasma membranes of bacteria.
The thylakoid ATP synthase is a CF1FO-ATP synthase similar to the mitochondrial ATPase. It is integrated into the thylakoid membrane with the CF1-part sticking into stroma. Thus, ATP synthesis occurs on the stromal side of the thylakoids where the ATP is needed for the light-independent reactions of photosynthesis.hotosystem II is located mostly in the grana thylakoids, whereas photosystem I and ATP synthase are mostly located in the stroma thylakoids and the outer layers of grana. The cytochrome b6f complex is distributed evenly throughout thylakoid membranes.