Ferredoxin hydrogenase has an active metallocluster site referred to as an "H-cluster" or "H domain" that is involved in the inter-conversion of protons and electrons with hydrogen gas.

This broad category of metalloenzymes can be divided into [NiFe], [FeFe], and [Fe] variants based on the transition metals found in their active sites.

Ferredoxin hydrogenase found in the green algae Chlamydomonas reinhardtii use supplied electrons from photosystem I to reduce protons into hydrogen gas.

[5][6] The inter-conversion of protons and electrons with hydrogen gas allow organisms to modulate energy input and output, adjust organelle redox potential, and transduce chemical signals.

[9] In addition, ferredoxin hydrogenase is sensitive to oxygen; the typical half life for the enzyme under aerobic conditions is on the scale of seconds, rendering it difficult to cultivate and manage commercially.