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A quarter of prokaryotic Family II inorganic pyrophosphatases (PPases) contain a regulatory insert comprised of two cystathionine β-synthase (CBS) domains and one DRTGG domain in addition to the two catalytic domains that form canonical Family II PPases. The CBS domain-containing PPases (CBS-PPases) are allosterically activated or inhibited by adenine mono- and dinucleotides that cooperatively bind to the CBS domains with a nanomolar to micromolar affinity. Here we use chemical cross-linking and analytical ultracentrifugation to show that CBS-PPases from Desulfitobacterium hafniense and four other bacterial species are active as 200–250-kDa homotetramers. Most other reported PPases are homohexamers of approximately 20-kDa subunits (prokaryotic Family I), homodimers of 32–70-kDa subunits (eukaryotic Family I, prokaryotic canonical Family II, and cation-transporting membrane PPases), or monomers (Family III). CBS-PPase is thus unique among different PPases by the type of its oligomeric structure. The deletion variants of the CBS-PPases from D. hafniense and Clostridium perfringens containing only catalytic or regulatory (CBS and DTRGG) domains are dimeric. Co2+ depletion by incubation with EDTA converts CBS-PPase into inactive tetrameric and dimeric forms. Adenine nucleotides stabilize the tetrameric form of CBS-PPase. Canonical Family II PPase from Streptococcus gordonii, which has only catalytic domains in its structure, is homodimeric but dissociates to monomers in the presence of EDTA or 2-propanol. The structure of CBS-PPase tetramer was modelled from the structures of dimeric catalytic and regulatory parts. These findings signify the role of the unique oligomeric structure of CBS-PPase in its multifaced regulation