The ubiquitin-activating enzyme exists as two isoforms: E1a, localized predominantly in the nucleus, and E1b, localized in the cytoplasm. Previously we generated hemagglutinin (HA) epitope-tagged cDNA constructs, HA1-E1 (epitope tag placed after the first methionine) and HA2-E1 (epitope tag placed after the second methionine) (Handley-Gearhart, P. M., Stephen, A. G., Trausch-Azar, J. S., Ciechanover, A., and Schwartz, A. L. (1994) J. Biol. Chem. 269, 33171-33178), which represent the native isoforms. HA1-E1 is exclusively nuclear, whereas HA2-E1 is found predominantly in the cytoplasm. Using high resolution isoelectric focusing and SDS-polyacrylamide gel electrophoresis, we confirm that these epitope-tagged constructs HA1-E1 and HA2-E1 represent the two isoforms E1a and E1b. HA1-E1/E1a exists as one non-phosphorylated and four phosphorylated forms, and HA2-E1/E1b exists as one predominant non-phosphorylated form and two minor phosphorylated forms. We demonstrate that the first 11 amino acids are essential for phosphorylation and exclusive nuclear localization of HA1-E1. Within this region are four serine residues and a putative nuclear localization sequence (NLS; 5 PLSKKRR). Removal of these four serine residues reduced phosphorylation levels by 60% but had no effect on nuclear localization of HA1-E1. Each serine residue was independently mutated to an alanine and analyzed by two-dimensional electrophoresis; only serine 4 was phosphorylated. Disruption of the basic amino acids within the NLS resulted in loss of exclusive nuclear localization and a 90 -95% decrease in the phosphorylation of HA1-E1. This putative NLS was able to confer nuclear import on a nonnuclear protein in digitonin-permeabilized cells in a temperature-and ATP-dependent manner. Thus the predominant requirement for efficient phosphorylation of HA1-E1/E1a is a functional NLS, suggesting that E1a may be phosphorylated within the nucleus.The ubiquitin-activating enzyme (E1) 1 catalyzes the first reaction in the ubiquitin (Ub) conjugation pathway. Activation of Ub occurs by the formation of a high energy thiol-ester bond between E1 and the C-terminal glycine of Ub and the production of AMP and PP i . Activated Ub is then transferred to a ubiquitin-conjugating enzyme (ubiquitin-carrier enzyme, E2 (5), yeast ␣ mating receptor (6), and growth hormone receptor (7) triggers their endocytosis and degradation within the lysosome. Because Ub requires activation prior to participation in any subsequent reactions, E1 plays a key role in the Ub-conjugating pathway. E1 is localized in both the nucleus and the cytoplasm (8, 9) and exists as two isoforms E1a (117 kDa) and E1b (110 kDa) (10, 11). To investigate the nature of these isoforms, epitope-tagged cDNA constructs of E1 were generated where the hemagglutinin (HA) epitope tag was placed after the first methionine (amino acid 1; HA1-E1) or after the second methionine (amino acid 40; HA2-E1) (11). HA1-E1 localized exclusively to the nucleus and displayed the same molecular weight as E1a, whereas HA2-E1 local...