102
that encloses DNA allowing for high processivity [20]. The third assembly is a
seven-subunit (τ2γδδ′χψ) clamp loader complex.
4.2.2.4 Family D
D family consists exclusively of archaea polymerases. The DNA polD enzyme is
a heterodimer composed of large DP2 and small DP1 subunits [21]. DP2 is the
catalytic subunit, while DP1 serves as an accessory factor. The interaction of the
two subunits has been reported to be necessary for the optimal DNA pol and 3′ → 5′
exonuclease activity [21]. Accordingly, DP1 has been shown to possess an intrinsic
proofreading activity [22]. The DP1 subunit shows homology to small, non-catalytic subunits of eukaryotic DNA pols α (p70 subunit), DNA pol δ (Cdc27p) and DNA
pol ε (p55 subunit). Similarly to archaeal DNA pol B, DNA pol D is also stimulated
by PCNA and RF-C. However, the DP1 subunit also directly interacts with RadB, a
homolog of the eukaryotic proteins Dmc1 and Rad51 in Pyrococcus furiosus, suggesting that DNA pol D may participate in recombination and/or repair in addition
to its role in replication [23].
4.2.2.5 Family X
Family X polymerases contain the well-known eukaryotic polymerase pol β—the
main reparative polymerase of eukaryotes, as well as other eukaryotic polymerases such as pol σ, pol λ, pol μ, and terminal deoxynucleotidyl transferase (TdT)
[24]. Family X polymerases are mainly found in vertebrates and a few are found
in plants and fungi. These polymerases have highly conserved regions that include
two helix–hairpin–helix motifs that are imperative in the DNA–polymerase interactions. One motif is located in the N-terminal lyase domain (8 kDa domain) that
interacts with the downstream DNA and one motif is located in the thumb domain
that interacts with the primer strand. Pol β, encoded by polB gene, is required for
short-patch base excision repair, a DNA repair pathway that is essential for repairing alkylated or oxidized bases as well as abasic sites. Pol λ and pol μ, encoded by
the polL and polM genes respectively, are involved in non-homologous end-joining,
a mechanism for rejoining DNA double-strand breaks due to the influence of the
hydrogen peroxide and ionizing radiation, respectively. TdT is expressed only in
lymphoid tissue, and adds “n nucleotides” to double-strand breaks formed during
V(D)J recombination to promote immunological diversity [24].
4.2.2.6 Family Y
In E. coli, DNA polymerase IV (pol 4) is an error-prone DNA polymerase involved
in non-targeted mutagenesis [25]. Pol IV is a family Y polymerase expressed by
the dinB gene that is switched on via SOS induction caused by stalled polymerases
A. Yu. Nyporko
that encloses DNA allowing for high processivity [20]. The third assembly is a
seven-subunit (τ2γδδ′χψ) clamp loader complex.
4.2.2.4 Family D
D family consists exclusively of archaea polymerases. The DNA polD enzyme is
a heterodimer composed of large DP2 and small DP1 subunits [21]. DP2 is the
catalytic subunit, while DP1 serves as an accessory factor. The interaction of the
two subunits has been reported to be necessary for the optimal DNA pol and 3′ → 5′
exonuclease activity [21]. Accordingly, DP1 has been shown to possess an intrinsic
proofreading activity [22]. The DP1 subunit shows homology to small, non-catalytic subunits of eukaryotic DNA pols α (p70 subunit), DNA pol δ (Cdc27p) and DNA
pol ε (p55 subunit). Similarly to archaeal DNA pol B, DNA pol D is also stimulated
by PCNA and RF-C. However, the DP1 subunit also directly interacts with RadB, a
homolog of the eukaryotic proteins Dmc1 and Rad51 in Pyrococcus furiosus, suggesting that DNA pol D may participate in recombination and/or repair in addition
to its role in replication [23].
4.2.2.5 Family X
Family X polymerases contain the well-known eukaryotic polymerase pol β—the
main reparative polymerase of eukaryotes, as well as other eukaryotic polymerases such as pol σ, pol λ, pol μ, and terminal deoxynucleotidyl transferase (TdT)
[24]. Family X polymerases are mainly found in vertebrates and a few are found
in plants and fungi. These polymerases have highly conserved regions that include
two helix–hairpin–helix motifs that are imperative in the DNA–polymerase interactions. One motif is located in the N-terminal lyase domain (8 kDa domain) that
interacts with the downstream DNA and one motif is located in the thumb domain
that interacts with the primer strand. Pol β, encoded by polB gene, is required for
short-patch base excision repair, a DNA repair pathway that is essential for repairing alkylated or oxidized bases as well as abasic sites. Pol λ and pol μ, encoded by
the polL and polM genes respectively, are involved in non-homologous end-joining,
a mechanism for rejoining DNA double-strand breaks due to the influence of the
hydrogen peroxide and ionizing radiation, respectively. TdT is expressed only in
lymphoid tissue, and adds “n nucleotides” to double-strand breaks formed during
V(D)J recombination to promote immunological diversity [24].
4.2.2.6 Family Y
In E. coli, DNA polymerase IV (pol 4) is an error-prone DNA polymerase involved
in non-targeted mutagenesis [25]. Pol IV is a family Y polymerase expressed by
the dinB gene that is switched on via SOS induction caused by stalled polymerases
A. Yu. Nyporko