DNA polymerases are divided into six families, A, B, C, D, X and Y based on sequence conservation. Replication is normally carried out by the A, B or C-family polymerases with high fidelity and high processivity. What differentiates the replicases in the A, B and C families from repair polymerases in the X- and Y-family is the proofreading mechanism and the structure and formation of the polymerase active site.

Family B DNA polymerases consist of five main structural domains: the N domain, the 3'-5' Exo (exonuclease) domain, the palm domain, the finger domain and the thumb domain. The most conserved region includes a conserved tetrapeptide with two aspartate residues. Its function is not yet known, however, it has been suggested that it may be involved in binding a magnesium ion. All sequences in the B family contain a characteristic DTDS motif, and possess many functional domains, including a 5'-3' elongabeta-barrel tion domain, a 3'-5' exonuclease domain, a DNA binding domain, and binding domains for both dNTP's and pyrophosphate.

The catalytic core of DNA polymerase is formed from the thumb, palm and finger domains. It has a typical right-hand DNA polymerase fold, with an active site formed by a palm holding the catalytic residues, a thumb that binds the primer:template DNA and fingers interacting with incoming nucleotide, and the N and Exo domains extend from the finger toward the thumb. Two 5' nucleotides (from the downstream template) are sandwiched by the N and Exo domains. This superfamily entry represents the beta-barrel in the N domain of DNA polymerases B. Members of this superfamily include: DNA Polymerase alpha, delta, epsilon, zeta, DNA polymerase II (Pol II) in E. coli, yeast and Archaea. The most widely spread B-family polymerases are E. coli DNA pol II and eukaryotic pol zeta and are involved in translesion and mutagenic DNA synthesis.

Structural and kinetic analyses reveal that an insertion in the N domain of Pol II alters enzyme-substrate interactions from a distance and ultimately results in reduced fidelity and TLS. The inserted beta-barrel loosens the N-palm linker, which leaves small cavities one and two base pairs upstream from the active site for looping out DNA lesions in the template. The inserted beta-barrel shifts the beta-hairpin loop in Pol II and alters substrate partitioning between polymerization and proofreading. Although Pol II is able to proofread, an increase of DNA residence time in the polymerase active site in the presence of a lesion can give Pol II the opportunity to sample downstream template and carry out TLS extension. These two features may also cause misincorporation and efficient extension of mismatched base pairs by Pol II when cells are under stresses.

Pfam family PFAM:PF00136, clan [PfamClan:CL0194], INTERPRO:IPR042087,PMID:20064374,PMID:25429975,PMID:19718023,PMID:10097083,PMID:23940661,PMID:23599895