7-Hydroxymethyl chlorophyll a reductase (HCAR) catalyzes the second half-reaction in chlorophyll b to chlorophyll a conversion. HCAR is required for the degradation of light-harvesting complexes and is necessary for efficient photosynthesis by balancing the chlorophyll a/b ratio. Reduction of the hydroxymethyl group uses redox cofactors [4Fe-4S] cluster and FAD to transfer electrons and is difficult because of the strong carbonoxygen bond. Here, we report the crystal structure of Arabidopsis HCAR at 2.7-Å resolution and reveal that two [4Fe-4S] clusters and one FAD within a very short distance form a consecutive electron pathway to the substrate pocket. In vitro kinetic analysis confirms the ferredoxin-dependent electron transport chain, thus supporting a proton-activated electron transfer mechanism. HCAR resembles a partial reconstruction of an archaeal F 420 -reducing [NiFe] hydrogenase, which suggests a common mode of efficient proton-coupled electron transfer through conserved cofactor arrangements. Furthermore, the trimeric form of HCAR provides a biological clue of its interaction with light-harvesting complex II.The balance of chlorophyll metabolism is vital for plants to ensure an efficient photosynthesis and to support various biological processes (1). To this end, chlorophyll biosynthesis and degradation need to cooperate with the chlorophyll cycle, a process of interconversion between chlorophyll a and chlorophyll b (2-5). The chlorophyll a/b ratio is important for stabilization of the light-harvesting complexes (LHCs).2 In general, an increase of the chlorophyll b level correlates with accumulation of LHCs and thus improvement of light usage efficiency in normal condition; excessive chlorophyll b, however, could impair the energy transfer pathway by replacing chlorophyll a in LHCs (6). In the chlorophyll cycle, both the forward (from chlorophyll a to chlorophyll b) and the backward conversions use 7-hydroxymethyl chlorophyll a (HMChl) as the intermediate (see Fig. 1A). Chlorophyll a oxygenase catalyzes two sequential oxidation reactions from the 7-methyl to the 7-formyl group (7, 8); chlorophyll b reductase and HMChl reductase (HCAR) catalyze the reverse two sequential reduction reactions (9, 10). In addition, the reverse reduction reactions are essential for LHC-II turnover because chlorophyll degradation precedes degradation of the LHC-II apoprotein, and the chlorophyll catabolic process starts from chlorophyll a (11-13). Direct interaction between HCAR and LHC-II has been observed in senescing chloroplasts (14).HCAR is the last identified enzyme of the chlorophyll cycle (10). Bioinformatic studies have discovered that the HCAR homologues range from archaea to plants (15). They perform different roles, such as the Here, the crystal structure of Arabidopsis HCAR reveals the ligating cysteines of the two [4Fe-4S] clusters, residues involved in FAD binding, and a deep substrate pocket adjacent to the flavin ring. We established a quantitative in vitro assay, confirmed the reduced ferredoxin (Fd red )-...