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 ...
243-561
6.40e-137
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: 399.65 E-value: 6.40e-137
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed ...
40-124
7.02e-35
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: 126.07 E-value: 7.02e-35
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
243-561
6.40e-137
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: 399.65 E-value: 6.40e-137
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
374-483
2.29e-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: 158.11 E-value: 2.29e-46
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed ...
40-124
7.02e-35
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: 126.07 E-value: 7.02e-35
Nucleotidyltransferase (NT) domain of family X DNA Polymerases; X family polymerases fill in ...
243-561
6.40e-137
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: 399.65 E-value: 6.40e-137
DNA polymerase beta palm; The catalytic region of DNA polymerase beta is split into three ...
374-483
2.29e-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: 158.11 E-value: 2.29e-46
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed ...
40-124
7.02e-35
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: 126.07 E-value: 7.02e-35
DNA polymerase beta thumb; The catalytic region of DNA polymerase beta is split into three ...
490-562
5.73e-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: 100.52 E-value: 5.73e-26
Fingers domain of DNA polymerase lambda; DNA polymerases catalyze the addition of dNMPs onto ...
324-372
4.85e-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: 80.58 E-value: 4.85e-19
first BRCT domain of BRCA1-associated RING domain protein 1 (Bard1) and similar proteins; ...
47-124
7.75e-06
first BRCT domain of BRCA1-associated RING domain protein 1 (Bard1) and similar proteins; Bard1, also termed BARD-1, or RING-type E3 ubiquitin transferase BARD1, is a critical factor in BRCA1-mediated tumor suppression and may also serve as a target for tumorigenic lesions in some human cancers. It associates with BRCA1 (breast cancer-1) to form a heterodimeric BRCA1/BARD1 complex that is responsible for maintaining genomic stability through nuclear functions involving DNA damage signaling and repair, transcriptional regulation, and cell cycle control. The BRCA1/BARD1 complex catalyzes autoubiquitination of BRCA1 and trans ubiquitination of other protein substrates. Its E3 ligase activity is dramatically reduced in the presence of UBX domain protein 1 (UBXN1). BARD-1 contains an N-terminal C3HC4-type RING-HC finger that binds BRCA1, and a C-terminal region with three ankyrin repeats and tandem BRCT domains that bind CstF-50 (cleavage stimulation factor) to modulate mRNA processing and RNAP II stability in response to DNA damage. The family corresponds to the first BRCT domain.
Pssm-ID: 349366 Cd Length: 80 Bit Score: 44.13 E-value: 7.75e-06
first BRCT domain of breast cancer type 1 susceptibility protein (BRCA1) and similar proteins; ...
47-125
4.43e-05
first BRCT domain of breast cancer type 1 susceptibility protein (BRCA1) and similar proteins; BRCA1, also termed RING finger protein 53 (RNF53), is a RING finger protein encoded by BRCA1, a tumor suppressor gene that regulates all DNA double-strand break (DSB) repair pathways. BRCA1 is frequently mutated in patients with hereditary breast and ovarian cancer (HBOC). Its mutation is also associated with an increased risk of pancreatic, stomach, laryngeal, fallopian tube, and prostate cancer. It plays an important role in the DNA damage response signaling, and has been implicated in various cellular processes such as cell cycle regulation, transcriptional regulation, chromatin remodeling, DNA DSBs, and apoptosis. BRCA1 contains an N-terminal C3HC4-type RING-HC finger, and two BRCT (BRCA1 C-terminus domain) repeats at the C-terminus. The family corresponds to the first BRCT domain.
Pssm-ID: 349367 Cd Length: 97 Bit Score: 42.33 E-value: 4.43e-05
first (N-terminal) BRCT domain of Schizosaccharomyces pombe BRCT-containing protein 1 (BRC1) ...
61-129
1.12e-03
first (N-terminal) BRCT domain of Schizosaccharomyces pombe BRCT-containing protein 1 (BRC1) and similar proteins; Schizosaccharomyces pombe BRC1 is required for mitotic fidelity, specifically in the G2 phase of the cell cycle. It plays a role in chromatin organization. Members in this family contains six BRCT domains. This family corresponds to the fourth repeat.
Pssm-ID: 349388 Cd Length: 107 Bit Score: 38.85 E-value: 1.12e-03
first BRCT domain of DNA ligase 4 (LIG4) and similar proteins; LIG4 (EC 6.5.1.1), also termed ...
56-124
1.66e-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: 37.66 E-value: 1.66e-03
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
47-117
1.74e-03
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.
Pssm-ID: 349339 [Multi-domain] Cd Length: 68 Bit Score: 36.96 E-value: 1.74e-03
third BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins; PAXIP1, also ...
61-125
1.93e-03
third BRCT domain of PAX-interacting protein 1 (PAXIP1) and similar proteins; PAXIP1, also termed PAX transactivation activation domain-interacting protein (PTIP), is involved in DNA damage response and in transcriptional regulation through histone methyltransferase (HMT) complexes. It also facilitates ATM-mediated activation of p53 and promotes cellular resistance to ionizing radiation. PAXIP1 contains six BRCT repeats. This family corresponds to the third BRCT domain.
Pssm-ID: 349343 Cd Length: 81 Bit Score: 37.24 E-value: 1.93e-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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