In an attempt to clarify the regulatory mechanism that accounts for the shift ofprotein A24 in the mitotic cycle, we demonstrated the existence ofan enzyme, provisionally termed isopeptidase, that cleaves A24 stoichiometrically into histone H2A and ubiquitin. Properties of this enzyme are (i) most eukaryotes, including mammals, amphibia, chicken, and yeast, contain isopeptidase in the cytoplasm; (ii) a significant increase in enzyme binding to chromatin occurs when cells enter mitosis; (iii) Escherichia coli does not contain isopeptidase; (iv) isopeptidase has a molecular weight of 38,000; (v) at an ionic strength that induces globular conformation of H2A, isopeptidase activity is repressed; (vi) a SH group is an essential cofactor; and (vii) most divalent cations (except Mg2+ and Ca2+) are inhibitory. In view of the stoichiometric conversion of A24 into H2A and ubiquitin by isopeptidase in vitro, A24 probably contains a Gly-Gly dipeptide in isopeptide linkage but no other intervening polypeptides. Since ubiquitin in various eukaryotes binds to proteins other than H2A, and is proteolytically released, isopeptidase probably acts on isopeptide bonds in general and not uniquely on those of A24. Inasmuch as isopeptidase is present throughout the cell cycle, the level of A24 in chromatin appears to be controlled by a balance between isopeptidase and an as yet unestablished H2A-ubiquitin ligase.Despite extensive advances in chromatin biochemistry (1-3), the molecular basis of the higher order organization of chromatin remains unknown. Histone phosphorylation has been implicated in chromatin condensation in mitosis (4-9); however, this idea has been questioned recently (10,11). In attempts to seek feasible mechanisms, we found another mitosis-specific event that involves a reversible stoichiometric shift in one ofthe structural chromatin proteins, A24 (12-14), a conjugate of histone H2A and the nonhistone protein ubiquitin (15-17). A24 virtually disappears as a structural component of chromatin in mitosis (12)(13)(14)18) and, at the same time, a 10% increase in the H2A/DNA mass ratio occurs (12, 13). When cells revert to the G, phase from mitosis and the chromatin becomes decondensed, A24 is reformed by conjugation ofthe core histone H2A and preformed ubiquitin, apparently without new protein synthesis (13).In view of the reversible stoichiometric shift of A24 in the mitotic cycle of chromatin organization, we predicted the presence of novel enzymes that catalyze the interaction of H2A and ubiquitin (13,19). In this article, we present evidence that eukaryotes, but not prokaryotes such as Escherichia coli, contain a cytoplasmic enzyme, termed isopeptidase, that cleaves A24 into H2A and ubiquitin stoichiometrically in vitro. (13,21,22). '25I Labeling ofA24 was carried out by the chloramin T method (23). To protect A24 molecules from radiation-caused disintegration, the iodinated sample was immediately adjusted to a concentration of 18.7 nmol of A24/ml and A24-free calf thymus histone at 1 mg/ml was added as ...