Two separable structural domains were identified in the Escherichia coli dnaB protein (Mr = 52,000) by partial proteolytic cleavage under nondenaturing conditions. The hydrolysis of dnaB protein by trypsin proceeded in two distinct stages in the presence of ATP or ADP. In the first stage, 14 amino acid residues at the NH2-terminal end were removed and dnaB protein was converted into a fragment with a molecular weight of 50,000 (Fragment I). Fragment I retained about 60% of the original activity in priming DNA replication and was fully active in DNA-dependent ATPase activity. In the second stage, Fragment I was further cleaved into two separable polypeptides with molecular weights of 33,000 (Fragment II) and 12,000 (Fragment III), respectively. Fragment II, as a hexamer, retained DNA-dependent ATPase activity comparable to the intact protein but was totally inactive in priming DNA replication. No known activity of dnaB protein was detected in Fragment III alone. NH2 termini of Fragments I and III and COOH termini of dnaB protein and Fragment II were identical indicating that Fragments III and II were located at the NH2 and COOH termini of Fragment I, respectively. These results indicate that dnaB protein is composed of at least two distinct domains. 1) Fragment III, the rigid domain, is essential for protein interaction, i.e. association with dnaC protein and primase in priming DNA replication in the primosome. 2) A 14-amino acid residue fragment, at the NH2-terminal end adjacent to Fragment III, probably required to stabilize the protein interaction involved in priming DNA replication. 3) Fragment II, the flexible COOH-terminal domain, contains the active sites for DNA binding, ATP binding, and protein oligomerization. Fragment II is cleaved by trypsin at many sites in the absence of ATP or ADP ligands. The rate of conversion of Fragment I into the yield of Fragments II and III was decreased approximately by 2 orders of magnitude by changing the ligand from ADP to the nonhydrolyzed ATP analog, adenosine 5'-O-(3-thiotriphosphate). These results indicate that the conformation of the COOH-terminal domain in the dnaB protein is stabilized by ATP or ADP. Such a nucleotide-induced conformational change was also demonstrated by circular dichroism spectroscopy. Moreover, the data suggest that the conformation of the dnaB protein complexed with adenosine 5'-O-(3-thiotriphosphate) is different from that complexed with ADP.(ABSTRACT TRUNCATED AT 400 WORDS)