The name of this superfamily has been modified since the most recent official CATH+ release (v4_3_0). At the point of the last release, this superfamily was named:

Helix hairpin bin

Functional Families

Overview of the Structural Clusters (SC) and Functional Families within this CATH Superfamily. Clusters with a representative structure are represented by a filled circle.

Superfamily: B family DNA polymerase, finger domain

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

GO Diversity

Unique GO annotations
109 Unique GO terms

EC Diversity

Unique EC annotations
2 Unique EC terms

Species Diversity

Unique species annotations
3888 Unique species

Sequence/Structure Diversity

Overview of the sequence / structure diversity of this superfamily compared to other superfamilies in CATH. Click on the chart to view the data in more detail.

Superfamily Summary

A general summary of information for this superfamily.
Domains: 247
Domain clusters (>95% seq id): 18
Domain clusters (>35% seq id): 9
Unique PDBs: 180
Structural Clusters (5A): 1
Structural Clusters (9A): 1
FunFam Clusters: 31
Unique EC: 2
Unique GO: 109
Unique Species: 3888