A 16 kDa protein from an enriched gap junction preparation was isolated from bovine brain tissues. N-terminal amino acid microsequencing of the first 20 amino acids showed a complete homology with a recently published sequence of a proteolipid from a vacuolar H ÷-ATPase from chromaffin granules. Incubation of the brain gap junction preparation with 14C-N,N'-dicyclohexylcarbodiimide showed a significant binding of this compound to the 16 kDa protein, indicating that a proton binding site also occurs within that particular protein. The data suggest that this 16 kDa protein, which has also been described in gap junction preparations from various other tissues, belongs to the proton transporting ATPase.