Background: Cyanobacterial uptake hydrogenases perform hydrogen oxidation in nitrogen-fixing cyanobacteria, but their biophysical properties are unknown. Results: The small subunit, HupS, from the Nostoc punctiforme uptake hydrogenase was heterologously expressed and spectroscopically characterized in different redox conditions. Conclusion: Recombinant HupS incorporates three iron-sulfur clusters with unusual iron coordination. Significance: We provide the foundation for engineering of cyanobacterial uptake hydrogenases.