ATP-dependent DNA helicase 2 subunit KU80 is part of a single-stranded DNA-dependent, ATP-dependent helicase involved in non-homologous end joining (NHEJ) DNA double strand break repair
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
281-579
2.07e-125
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
:
Pssm-ID: 238445 [Multi-domain] Cd Length: 300 Bit Score: 376.63 E-value: 2.07e-125
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation ...
47-280
4.74e-42
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.
The actual alignment was detected with superfamily member pfam03731:
Pssm-ID: 469594 Cd Length: 220 Bit Score: 152.51 E-value: 4.74e-42
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by ...
630-743
8.43e-38
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs.
:
Pssm-ID: 462604 Cd Length: 117 Bit Score: 136.95 E-value: 8.43e-38
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
281-579
2.07e-125
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
Pssm-ID: 238445 [Multi-domain] Cd Length: 300 Bit Score: 376.63 E-value: 2.07e-125
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
290-490
2.93e-60
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 and Ku80 proteins that form a DNA binding heterodimer.
Pssm-ID: 460669 Cd Length: 197 Bit Score: 201.70 E-value: 2.93e-60
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single ...
339-478
5.12e-43
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single stranded DNA- and ATP-depedent helicase that has a role in chromosome translocation. This is a domain of unknown function C-terminal to its von Willebrand factor A domain, that also occurs in bacterial hypothetical proteins.
Pssm-ID: 128831 [Multi-domain] Cd Length: 140 Bit Score: 152.45 E-value: 5.12e-43
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
47-280
4.74e-42
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold.
Pssm-ID: 427470 Cd Length: 220 Bit Score: 152.51 E-value: 4.74e-42
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to ...
45-209
7.90e-40
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Pssm-ID: 238735 Cd Length: 218 Bit Score: 146.35 E-value: 7.90e-40
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by ...
630-743
8.43e-38
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs.
Pssm-ID: 462604 Cd Length: 117 Bit Score: 136.95 E-value: 8.43e-38
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in ...
44-612
1.20e-10
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273151 [Multi-domain] Cd Length: 586 Bit Score: 64.91 E-value: 1.20e-10
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
48-202
1.03e-07
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
Pssm-ID: 214621 [Multi-domain] Cd Length: 175 Bit Score: 52.46 E-value: 1.03e-07
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
281-579
2.07e-125
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
Pssm-ID: 238445 [Multi-domain] Cd Length: 300 Bit Score: 376.63 E-value: 2.07e-125
Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the ...
282-574
1.77e-80
Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the C-terminal arm of Ku proteins. The Ku protein consists of two tightly associated homologous subunits, Ku70 and Ku80, and was originally identified as an autoantigen recognized by the sera of patients with an autoimmunity disease. In eukaryotes, the Ku heterodimer contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by non-homologous end-joining. The bacterial Ku homologs does not contain the conserved N-terminal extension that is present in the eukaryotic Ku protein.
Pssm-ID: 238334 [Multi-domain] Cd Length: 272 Bit Score: 258.74 E-value: 1.77e-80
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
290-490
2.93e-60
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the central DNA-binding beta-barrel domain. This domain is found in both the Ku70 and Ku80 proteins that form a DNA binding heterodimer.
Pssm-ID: 460669 Cd Length: 197 Bit Score: 201.70 E-value: 2.93e-60
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single ...
339-478
5.12e-43
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single stranded DNA- and ATP-depedent helicase that has a role in chromosome translocation. This is a domain of unknown function C-terminal to its von Willebrand factor A domain, that also occurs in bacterial hypothetical proteins.
Pssm-ID: 128831 [Multi-domain] Cd Length: 140 Bit Score: 152.45 E-value: 5.12e-43
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
47-280
4.74e-42
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the amino terminal alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six stranded beta sheet of the Rossman fold.
Pssm-ID: 427470 Cd Length: 220 Bit Score: 152.51 E-value: 4.74e-42
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to ...
45-209
7.90e-40
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Pssm-ID: 238735 Cd Length: 218 Bit Score: 146.35 E-value: 7.90e-40
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by ...
630-743
8.43e-38
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by which double stranded breaks in chromosomal DNA are repaired. Ku is a component of a multi-protein complex that is involved in the NHEJ. Ku has affinity for DNA ends and recruits the DNA-dependent protein kinase catalytic subunit (DNA-PKcs). This domain is found at the C terminal of Ku which binds to DNA-PKcs.
Pssm-ID: 462604 Cd Length: 117 Bit Score: 136.95 E-value: 8.43e-38
Ku70/Ku80 C-terminal arm; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
513-606
3.86e-21
Ku70/Ku80 C-terminal arm; The Ku heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks and facilitate repair by the non-homologous end-joining pathway. This is the C terminal arm. This alpha helical region embraces the beta-barrel domain pfam02735 of the opposite subunit.
Pssm-ID: 461029 Cd Length: 79 Bit Score: 88.10 E-value: 3.86e-21
Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in ...
285-536
6.32e-20
Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in multiple nuclear processes such as DNA repair, chromosome maintenance, transcription regulation, and V(D)J recombination. The mechanism underlying the regulation of all the diverse functions of Ku is still unclear, although it seems that Ku is a multifunctional protein that works in the nuclei. In mammalian cells, the Ku heterodimer recruits the catalytic subunit of DNA-dependent protein kinase (DNA-PK), which is dependent on its association with the Ku70/80 heterodimer bound to DNA for its protein kinase activity.
Pssm-ID: 238407 [Multi-domain] Cd Length: 287 Bit Score: 90.80 E-value: 6.32e-20
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in ...
44-612
1.20e-10
ATP-dependent DNA helicase II, 70 kDa subunit (ku70); Proteins in this family are involved in non-homologous end joining, a process used for the repair of double stranded DNA breaks. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Cutoff does not detect the putative ku70 homologs in yeast. [DNA metabolism, DNA replication, recombination, and repair]
Pssm-ID: 273151 [Multi-domain] Cd Length: 586 Bit Score: 64.91 E-value: 1.20e-10
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation ...
48-199
5.62e-09
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of most, if not all A domains.
Pssm-ID: 238119 [Multi-domain] Cd Length: 161 Bit Score: 55.65 E-value: 5.62e-09
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
48-202
1.03e-07
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins mediate adhesion via metal ion-dependent adhesion sites (MIDAS). Intracellular VWA domains and homologues in prokaryotes have recently been identified. The proposed VWA domains in integrin beta subunits have recently been substantiated using sequence-based methods.
Pssm-ID: 214621 [Multi-domain] Cd Length: 175 Bit Score: 52.46 E-value: 1.03e-07
Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA ...
282-515
4.02e-03
Ku-core domain, Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. The alignment includes the core domain shared by the prokaryotic YkoV-like proteins and the eukaryotic Ku70 and Ku80. The prokaryotic Ku homologs are predicted to form homodimers. It is proposed that the Ku homologs are functionally associated with ATP-dependent DNA ligase and the eukaryotic-type primase, probably as components of a double-strand break repair system.
Pssm-ID: 238408 [Multi-domain] Cd Length: 256 Bit Score: 39.83 E-value: 4.02e-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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