Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon ...
440-839
0e+00
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon catalytic subunit of DNA polymerase. It is found C terminal to pfam03104 and pfam00136.
:
Pssm-ID: 462493 Cd Length: 400 Bit Score: 584.12 E-value: 0e+00
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by ...
1-68
2.06e-37
DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is made up of distinct domains and sub-domains. The polymerase domain of DNA polymerase type B (Pol domain) is responsible for the template-directed polymerization of dNTPs onto the growing primer strand of duplex DNA that is usually magnesium dependent. In general, the architecture of the Pol domain has been likened to a right hand with fingers, thumb, and palm sub-domains with a deep groove to accommodate the nucleic acid substrate. There are a few conserved motifs in the Pol domain of family B DNA polymerases. The conserved aspartic acid residues in the DTDS motifs of the palm sub-domain is crucial for binding to divalent metal ion and is suggested to be important for polymerase catalysis.
The actual alignment was detected with superfamily member cd05535:
Pssm-ID: 353046 Cd Length: 621 Bit Score: 150.13 E-value: 2.06e-37
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon ...
440-839
0e+00
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon catalytic subunit of DNA polymerase. It is found C terminal to pfam03104 and pfam00136.
Pssm-ID: 462493 Cd Length: 400 Bit Score: 584.12 E-value: 0e+00
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
1-68
2.06e-37
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Pssm-ID: 99918 Cd Length: 621 Bit Score: 150.13 E-value: 2.06e-37
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon ...
440-839
0e+00
Domain of unknown function (DUF1744); This domain is found at the C-terminal of the epsilon catalytic subunit of DNA polymerase. It is found C terminal to pfam03104 and pfam00136.
Pssm-ID: 462493 Cd Length: 400 Bit Score: 584.12 E-value: 0e+00
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases ...
1-68
2.06e-37
DNA polymerase type-B epsilon subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase (Pol) epsilon has been proposed to play a role in elongation of the leading strand during DNA replication. Pol epsilon might also have a role in DNA repair. The structure of pol epsilon is characteristic of this family with the exception that it contains a large c-terminal domain with an unclear function. Phylogenetic analyses indicate that Pol epsilon is the ortholog to the archaeal Pol B3 rather than to Pol alpha, delta, or zeta. This might be because pol epsilon is ancestral to both archaea and eukaryotes DNA polymerases type B.
Pssm-ID: 99918 Cd Length: 621 Bit Score: 150.13 E-value: 2.06e-37
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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