Hydrogen sulfide engages catalytic zinc in HDAC6 to modulate an alternative deacetylation pathway.

Hydrogen sulfide (H₂S) is a gasotransmitter whose non-covalent effects on protein function remain incompletely understood. Here we show that H₂S-derived sulfur species engage the catalytic Zn²⁺ center of histone deacetylase 6 (HDAC6) and enhance deacetylase activity under defined conditions. Molecular dynamics simulations support access of HS⁻ to the CD2 active-site tunnel, whereas surface plasmon resonance and zinc-depletion experiments support reversible, zinc-dependent engagement. Quantum chemical calculations support a chemically feasible sulfur-associated deacetylation pathway that generates thioacetic acid, which we detect in cell-free reactions, cultured cells, mouse tissues and human serum. Cryo-electron microscopy defines the tandem organization of human HDAC6 catalytic domains and reveals distinct CD1 and CD2 tunnel architectures. HDAC6 loss blunts H₂S-induced endothelial migration and angiogenesis, and CD2 is required for these responses. These findings support HDAC6 as an H₂S-responsive Zn²⁺-dependent deacetylase and link zinc-sulfur coordination to altered deacetylation chemistry.