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' elongation 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. This superfamily entry represents the helical finger 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.

The overall structures of Pol II, replicative phi29 and RB69 polymerases gp43 are highly similar. They share the conserved metal-ion ligands, the basic residues and steric gate (Y424) that interact with the triphosphate and deoxyribose of the incoming dNTP, respectively. They also share the conserved sequence motif that hugs the minor groove of the replicating base pair. Furthermore, after superposition of the palm domains of Pol II and gp43, the DNAs of the two ternary complexes have nearly identical structures. The Pol II finger domain is 60 residues shorter and undergoes a much smaller conformational change upon binding dNTP than that of gp43. But the finger domain of phi29 polymerase is as short and undergoes as limited conformational changes as Pol II. Therefore the finger domain alone is unlikely to explain TLS by Pol II.

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