DNA polymerase κ (Polκ) is the only known Y-family DNA polymerase that bypasses the 10S (+)-trans-anti-benzo[a]pyrene diol epoxide (BPDE)-N 2 -deoxyguanine adducts efficiently and accurately. The unique features of Polκ, a large structure gap between the catalytic core and little finger domain and a 90-residue addition at the N terminus known as the N-clasp, may give rise to its special translesion capability. We designed and constructed two mouse Polκ variants, which have reduced gap size on both sides [Polκ Gap Mutant (PGM) 1] or one side flanking the template base (PGM2). These Polκ variants are nearly as efficient as WT in normal DNA synthesis, albeit with reduced accuracy. However, PGM1 is strongly blocked by the 10S (+)-trans-anti-BPDE-N 2 -dG lesion. Steady-state kinetic measurements reveal a significant reduction in efficiency of dCTP incorporation opposite the lesion by PGM1 and a moderate reduction by PGM2. Consistently, Polκ-deficient cells stably complemented with PGM1 GFP-Polκ remained hypersensitive to BPDE treatment, and complementation with WT or PGM2 GFP-Polκ restored BPDE resistance. Furthermore, deletion of the first 51 residues of the N-clasp in mouse Polκ (mPolκ 52-516 ) leads to reduced polymerization activity, and the mutant PGM2 52-516 but not PGM1 52-516 can partially compensate the N-terminal deletion and restore the catalytic activity on normal DNA. However, neither WT nor PGM2 mPolκ 52-516 retains BPDE bypass activity. We conclude that the structural gap physically accommodates the bulky aromatic adduct and the N-clasp is essential for the structural integrity and flexibility of Polκ during translesion synthesis.translesion DNA synthesis | polycyclic aromatic hydrocarbons B enzo[a]pyrene (BP) is one of the best characterized polycyclic aromatic hydrocarbons generated during incomplete fuel combustion, in tobacco smoke, and in cooked food. The most mutagenic and tumorigenic metabolite of BP in vivo is the (+)-7R,8S,9S,10R-BP dihydrodiol epoxide [(+)-anti-BPDE] (1), which reacts readily with the exocyclic amino groups of guanine residues in DNA to form the major 10S (+)-trans-anti-BPDE-N 2 -dG adduct (2) (abbreviated as BPDE-dG hereafter). This adduct typically impedes normal DNA replication. Translesion DNA synthesis (TLS), which provides one mode of DNA damage tolerance, uses specialized bypass polymerases to synthesize DNA opposite and beyond a variety of replication-blocking lesions, thus avoiding replication fork collapse (3). The Y-family DNA polymerases are specialized for TLS. To date, four of them, namely DNA polymerase (Pol) η, Polι, Polκ, and REV1, have been identified in mammals (4-6). Polκ is the only one with homologs in bacteria (DinB; also known as Pol IV in Escherichia coli), archaea [DNA polymerase IV (Dpo4) in Sulfolobus solfataricus and DinB homologue (Dbh) in Sulfolobus acidocaldarius] and all eukaryotes. The mouse and human POLK gene are expressed ubiquitously, with highest levels in testis (7).Human Polκ can accurately incorporate dCMP opposite the BPDE-dG adduct ...