Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
176-517
9.97e-110
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: 328.77 E-value: 9.97e-110
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
75-143
1.30e-20
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The BRCT (BRCA1 C-terminus) domain is found within many DNA damage repair and cell cycle checkpoint proteins. BRCT domains interact with each other forming homo/hetero BRCT multimers, but are also involved in BRCT-non-BRCT interactions and interactions within DNA strand breaks. BRCT tandem repeats bind to phosphopeptides; it has been shown that the repeats in human BRCA1 bind specifically to pS-X-X-F motifs, mediating the interaction between BRCA1 and the DNA helicase BACH1, or BRCA1 and CtIP, a transcriptional corepressor. It is assumed that BRCT repeats play similar roles in many signaling pathways associated with the response to DNA damage.
The actual alignment was detected with superfamily member cd18442:
Pssm-ID: 469589 Cd Length: 98 Bit Score: 86.44 E-value: 1.30e-20
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
176-517
9.97e-110
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: 328.77 E-value: 9.97e-110
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
455-518
1.35e-23
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: 93.59 E-value: 1.35e-23
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins; ...
75-143
1.30e-20
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins; Polymerase Mu (EC 2.7.7.7), also termed Pol mu, or terminal transferase, is a Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). It participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. Polymerase Mu contains a BRCT domain.
Pssm-ID: 349395 Cd Length: 98 Bit Score: 86.44 E-value: 1.30e-20
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
176-517
9.97e-110
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: 328.77 E-value: 9.97e-110
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
455-518
1.35e-23
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: 93.59 E-value: 1.35e-23
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins; ...
75-143
1.30e-20
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu) and similar proteins; Polymerase Mu (EC 2.7.7.7), also termed Pol mu, or terminal transferase, is a Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). It participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. Polymerase Mu contains a BRCT domain.
Pssm-ID: 349395 Cd Length: 98 Bit Score: 86.44 E-value: 1.30e-20
Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto ...
258-311
8.37e-17
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: 74.03 E-value: 8.37e-17
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu), DNA ...
75-135
1.07e-16
BRCT domain of DNA-directed DNA/RNA polymerase mu (polymerase mu), DNA nucleotidylexotransferase and similar proteins; The family includes DNA-directed DNA/RNA polymerase mu (polymerase mu) and DNA nucleotidylexotransferase. Polymerase mu (EC 2.7.7.7), also termed Pol mu, or terminal transferase, is a Gap-filling polymerase involved in repair of DNA double-strand breaks by non-homologous end joining (NHEJ). It participates in immunoglobulin (Ig) light chain gene rearrangement in V(D)J recombination. DNA nucleotidylexotransferase (EC 2.7.7.31), also termed terminal addition enzyme, or terminal deoxynucleotidyltransferase, or terminal transferase, is a template-independent DNA polymerase which catalyzes the random addition of deoxynucleoside 5'-triphosphate to the 3'-end of a DNA initiator. It is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells. All family members contains a BRCT domain.
Pssm-ID: 349345 Cd Length: 87 Bit Score: 75.12 E-value: 1.07e-16
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
316-384
9.08e-14
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: 67.59 E-value: 9.08e-14
BRCT domain of DNA nucleotidylexotransferase (DNTT) and similar proteins; DNTT (EC 2.7.7.31), ...
75-143
1.34e-13
BRCT domain of DNA nucleotidylexotransferase (DNTT) and similar proteins; DNTT (EC 2.7.7.31), also termed terminal addition enzyme, or terminal deoxynucleotidyltransferase, or terminal transferase, is a template-independent DNA polymerase which catalyzes the random addition of deoxynucleoside 5'-triphosphate to the 3'-end of a DNA initiator. It is the addition of nucleotides at the junction (N region) of rearranged Ig heavy chain and T-cell receptor gene segments during the maturation of B- and T-cells. DNA nucleotidylexotransferase contains a BRCT domain.
Pssm-ID: 349396 Cd Length: 95 Bit Score: 66.36 E-value: 1.34e-13
Nucleotidyltransferase domain; Members of this family belong to a large family of ...
329-371
7.63e-06
Nucleotidyltransferase domain; Members of this family belong to a large family of nucleotidyltransferases. This family includes kanamycin nucleotidyltransferase (KNTase) which is a plasmid-coded enzyme responsible for some types of bacterial resistance to aminoglycosides. KNTase in-activates antibiotics by catalysing the addition of a nucleotidyl group onto the drug.
Pssm-ID: 396474 Cd Length: 91 Bit Score: 44.33 E-value: 7.63e-06
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.
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