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:

Palm domain of DNA polymerase

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, palm 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 palm 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 structure of Pol alpha bound to RNA primer/DNA template shows that, although the palm domain makes a canonical set of interactions with the first 3 bp of the primer-template helix, the thumb domain engages almost exclusively with the RNA primer strand. The interactions between the thumb domain and the RNA primer are concentrated in a contiguous region of five nucleotides, from position two to six of the RNA primer and involve solely the ribose and phosphate moieties of the RNA backbone. Two sequence motifs, residues 1074-1077 in the long segment of the L-shaped thumb, and residues 1130-1150 in the tip of the thumb, form a continuous protein interface that tracks the position of the phosphodiester backbone of the RNA primer. Pol alpha exploits the wide, shallow nature of the minor groove of the RNA/DNA helix with a series of hydrophobic contacts involving the side chains of Met1131, Leu1133, Tyr1140, Pro1141, Met1146, which recognise the C3'-endo conformation of the ribose moieties of RNA nucleotides in position four to six.

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
126 Unique GO terms

EC Diversity

Unique EC annotations
3 Unique EC terms

Species Diversity

Unique species annotations
5504 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: 251
Domain clusters (>95% seq id): 15
Domain clusters (>35% seq id): 9
Unique PDBs: 180
Structural Clusters (5A): 3
Structural Clusters (9A): 3
FunFam Clusters: 76
Unique EC: 3
Unique GO: 126
Unique Species: 5504