nucleotidyltransferase domain-containing protein of family X DNA polymerases which includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT).
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
188-474
3.70e-123
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.
:
Pssm-ID: 143386 [Multi-domain] Cd Length: 307 Bit Score: 361.51 E-value: 3.70e-123
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed ...
41-125
9.56e-30
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed Pol Lambda, or DNA polymerase beta-2 (Pol beta2), or DNA polymerase kappa, is involved in base excision repair (BER) and is responsible for repair of lesions that give rise to abasic (AP) sites in DNA. It also contributes to DNA double-strand break repair by non-homologous end joining and homologous recombination. DNA polymerase lambda has both template-dependent and template-independent (terminal transferase) DNA polymerase activities, as well as a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity. DNA polymerase lambda contains one BRCT domain.
:
Pssm-ID: 349347 Cd Length: 80 Bit Score: 111.04 E-value: 9.56e-30
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
188-474
3.70e-123
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.
Pssm-ID: 143386 [Multi-domain] Cd Length: 307 Bit Score: 361.51 E-value: 3.70e-123
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
280-396
1.59e-46
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.
Pssm-ID: 464318 Cd Length: 110 Bit Score: 156.96 E-value: 1.59e-46
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed ...
41-125
9.56e-30
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed Pol Lambda, or DNA polymerase beta-2 (Pol beta2), or DNA polymerase kappa, is involved in base excision repair (BER) and is responsible for repair of lesions that give rise to abasic (AP) sites in DNA. It also contributes to DNA double-strand break repair by non-homologous end joining and homologous recombination. DNA polymerase lambda has both template-dependent and template-independent (terminal transferase) DNA polymerase activities, as well as a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity. DNA polymerase lambda contains one BRCT domain.
Pssm-ID: 349347 Cd Length: 80 Bit Score: 111.04 E-value: 9.56e-30
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
188-474
3.70e-123
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this family.
Pssm-ID: 143386 [Multi-domain] Cd Length: 307 Bit Score: 361.51 E-value: 3.70e-123
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
280-396
1.59e-46
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain.
Pssm-ID: 464318 Cd Length: 110 Bit Score: 156.96 E-value: 1.59e-46
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed ...
41-125
9.56e-30
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed Pol Lambda, or DNA polymerase beta-2 (Pol beta2), or DNA polymerase kappa, is involved in base excision repair (BER) and is responsible for repair of lesions that give rise to abasic (AP) sites in DNA. It also contributes to DNA double-strand break repair by non-homologous end joining and homologous recombination. DNA polymerase lambda has both template-dependent and template-independent (terminal transferase) DNA polymerase activities, as well as a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity. DNA polymerase lambda contains one BRCT domain.
Pssm-ID: 349347 Cd Length: 80 Bit Score: 111.04 E-value: 9.56e-30
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
403-475
5.39e-26
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the thumb domain.
Pssm-ID: 464317 [Multi-domain] Cd Length: 63 Bit Score: 100.14 E-value: 5.39e-26
Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto ...
230-278
1.85e-19
Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone.
Pssm-ID: 463069 [Multi-domain] Cd Length: 51 Bit Score: 81.73 E-value: 1.85e-19
first BRCT domain of DNA ligase 4 (LIG4) and similar proteins; LIG4 (EC 6.5.1.1), also termed ...
57-125
9.04e-03
first BRCT domain of DNA ligase 4 (LIG4) and similar proteins; LIG4 (EC 6.5.1.1), also termed DNA ligase IV, or polydeoxyribonucleotide synthase [ATP] 4, is involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination. It is a component of the LIG4-XRCC4 complex that is responsible for the NHEJ ligation step. LIG4 contains two BRCT domains. The family corresponds to the first one.
Pssm-ID: 349354 [Multi-domain] Cd Length: 90 Bit Score: 35.35 E-value: 9.04e-03
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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