Diverse aerobic bacteria use atmospheric H2 as an energy source to enhance growth and survival. This globally significant process controls the composition of the atmosphere, enhances soil biodiversity, and drives primary production in certain extreme environments. Several high-affinity lineages of [NiFe]-hydrogenases have been shown to mediate atmospheric H2 oxidation, though they remain to be biochemically or structurally characterized. As a result, it is unclear how these enzymes function under ambient conditions or interact with the respiratory chain. Here we show that structural adaptations enable the purified mycobacterial [NiFe]-hydrogenase Huc to directly couple atmospheric H2 oxidation to respiratory menaquinone reduction under ambient conditions. Based on a 1.57 Å resolution CryoEM structure, Huc oxidises atmospheric H2 via the [NiFe] active site of the large subunit and directly transfers electrons through three 3Fe-4S clusters to menaquinone at the small subunit. A narrow hydrophobic gas channel facilitates high-affinity H2 binding and sterically hinders O2, while the 3Fe-4S clusters and their ligation by an unusual D-histidine modulate the electrochemical properties of the enzyme such that atmospheric H2 oxidation is thermodynamically favourable. The Huc large and small subunits form an octamer around a unique membrane-associated central stalk, which extracts and transports menaquinone a remarkable 94 Å from the membrane for reduction. These structural inferences are supported by enzyme kinetics, protein film electrochemistry, spectroscopy, mass spectrometry, and molecular dynamics simulations. These findings provide a mechanistic basis for the biogeochemically and ecologically important process of atmospheric H2 oxidation and uncover a novel mode of energy coupling dependent on long-range quinone transport. As the first structural characterisation of a group 2 [NiFe]-hydrogenase, this study also paves way for development of biocatalysts that oxidize H2 in ambient air.