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Conserved domains on  [gi|2222400198|gb|KAI2526849|]
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X-ray repair cross complementing 5 [Homo sapiens]

Protein Classification

ATP-dependent DNA helicase 2 subunit KU80( domain architecture ID 10509365)

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

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
KU80 cd00873
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
244-543 3.58e-126

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: 377.40  E-value: 3.58e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 244 SIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDA-KTLKK--EDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDI 320
Cdd:cd00873     1 VAAFKGQLTLGSPLSIAVELYKKTKEERPPKLKKVSDAeKTGEDafEDVKSERSYDVNDDDKTEVEKEDLIKGYRYGRDI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 321 VPFSKVDEEQMKYkSEGKCFSVLGFCKSSQVQRRFFMGnQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKR 400
Cdd:cd00873    81 VPLSEEDEEATKL-STSKGLDILGFIKASNVPRYYLMG-ESSYVVPQQDDEAAALAFSALVRALAELDKYAIARYVYKDN 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 401 ANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSK-KYAPTEAQLNAVDALIDSMSLAKKDEktDTLEDLFPT 479
Cdd:cd00873   159 SEPQLGVLFPRIKEDYECLVLVRLPFAEDVRQYRFPSLDKLKtPNLPTEEQLEAMDDLVDSMDLDDDEE--DDPEEALKP 236
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2222400198 480 TKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAK 543
Cdd:cd00873   237 DETPNPVLQRIYQALRHRALHPDEPLPPLLQVLLRYLEPPEEVLEKSKEALKKIKEKFPLKEVP 300
Ku_N pfam03731
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
9-244 3.33e-59

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: 199.51  E-value: 3.33e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198   9 AVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNplsgGDQYQNITVHRHLMLPDF 88
Cdd:pfam03731   1 AILFVIDVSPAMFESSKLLEAPFDMALKCIRELLKSKIISRDKDLIGVVLYGTDNSEN----SEGLPNITVLRDLDLPGA 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198  89 DLLEDIESKIQPG----------SQQADFLDALIVSMDVIQHetIGKKFEKRHIEIFTDLSSRF-SKSQLDIIIHSLKkc 157
Cdd:pfam03731  77 ELILELDQFVESFgrdvrgfsgdSSDGSLLSALWVCLELLQK--TGKKLSHKRIFLFTDLDDPFeDQDKLDIALQRLL-- 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 158 dislqfflpfslgKEDGSGDRGD-GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEdgldeiySFSESLRKLCV 236
Cdd:pfam03731 153 -------------AEDLRDTRGEfDLIHLPNADGFDPNLFYKDIIKLGSDEVLNVMLDLEGQ-------KLEDLLAKIRA 212

                  ....*...
gi 2222400198 237 FKKIERHS 244
Cdd:pfam03731 213 KKTAKRAH 220
Ku_PK_bind pfam08785
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by ...
593-706 3.62e-37

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: 135.02  E-value: 3.62e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 593 NPAENFRVLVKQKK--ASFEEASNQLINHIEQFLDTNETP-YFMKSIDCIRAFREEAIKFSEEQRFNNFLKALQEKVEIK 669
Cdd:pfam08785   1 NPVPDFKQLLARGDdvDAVEKAVKQMGNIIEDLVRDSFGDsNYDKALECLRALREECIEEEEPDLYNDFLRDLKKKLLEG 80
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2222400198 670 QLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLA 706
Cdd:pfam08785  81 DRREFWELVRKNKLGLITKDEAEDSDVTEEEAKEFLS 117
 
Name Accession Description Interval E-value
KU80 cd00873
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
244-543 3.58e-126

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: 377.40  E-value: 3.58e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 244 SIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDA-KTLKK--EDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDI 320
Cdd:cd00873     1 VAAFKGQLTLGSPLSIAVELYKKTKEERPPKLKKVSDAeKTGEDafEDVKSERSYDVNDDDKTEVEKEDLIKGYRYGRDI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 321 VPFSKVDEEQMKYkSEGKCFSVLGFCKSSQVQRRFFMGnQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKR 400
Cdd:cd00873    81 VPLSEEDEEATKL-STSKGLDILGFIKASNVPRYYLMG-ESSYVVPQQDDEAAALAFSALVRALAELDKYAIARYVYKDN 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 401 ANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSK-KYAPTEAQLNAVDALIDSMSLAKKDEktDTLEDLFPT 479
Cdd:cd00873   159 SEPQLGVLFPRIKEDYECLVLVRLPFAEDVRQYRFPSLDKLKtPNLPTEEQLEAMDDLVDSMDLDDDEE--DDPEEALKP 236
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2222400198 480 TKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAK 543
Cdd:cd00873   237 DETPNPVLQRIYQALRHRALHPDEPLPPLLQVLLRYLEPPEEVLEKSKEALKKIKEKFPLKEVP 300
Ku_N pfam03731
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
9-244 3.33e-59

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: 199.51  E-value: 3.33e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198   9 AVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNplsgGDQYQNITVHRHLMLPDF 88
Cdd:pfam03731   1 AILFVIDVSPAMFESSKLLEAPFDMALKCIRELLKSKIISRDKDLIGVVLYGTDNSEN----SEGLPNITVLRDLDLPGA 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198  89 DLLEDIESKIQPG----------SQQADFLDALIVSMDVIQHetIGKKFEKRHIEIFTDLSSRF-SKSQLDIIIHSLKkc 157
Cdd:pfam03731  77 ELILELDQFVESFgrdvrgfsgdSSDGSLLSALWVCLELLQK--TGKKLSHKRIFLFTDLDDPFeDQDKLDIALQRLL-- 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 158 dislqfflpfslgKEDGSGDRGD-GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEdgldeiySFSESLRKLCV 236
Cdd:pfam03731 153 -------------AEDLRDTRGEfDLIHLPNADGFDPNLFYKDIIKLGSDEVLNVMLDLEGQ-------KLEDLLAKIRA 212

                  ....*...
gi 2222400198 237 FKKIERHS 244
Cdd:pfam03731 213 KKTAKRAH 220
Ku pfam02735
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
253-453 1.80e-56

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: 191.30  E-value: 1.80e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 253 IGSNLSIRIAAYKSIlQERVKKTWTVVDAKTlkKEDIQKETVYClNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMK 332
Cdd:pfam02735   1 IGGLVSIPVKLYSAT-EEEKKPSFKKLDRET--NDGVRIKYKYV-CEDTGKEVEKEDIVKGYEYGGTYVPLSDEELEELK 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 333 YKSEgKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAV-ALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPH 411
Cdd:pfam02735  77 PEST-KGLDLLGFVPLDEIDPIYFMGDKSYFLYPDKGDIAGSTkAFSALREALLETDKVAIARFVLRRREHPRLVALRPQ 155
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2222400198 412 IKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNA 453
Cdd:pfam02735 156 EEEPDPGLVLITLPFADDVREEFFPIPSLLEKPKPTEEQLDL 197
Ku78 smart00559
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single ...
302-440 2.16e-47

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: 164.39  E-value: 2.16e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198  302 ETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEgKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLI 381
Cdd:smart00559   1 GKEVKPEDIVKGYEYGGRYVPLSDEELEQLKYKSE-PGLELLGFKPLSSLPPYYFLRPSYFLVPDDKSVIGSTKAFSALV 79
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198  382 HALDDLDMVAIVRYAYDKRANPQVGVAFPHI-KHNYECLVYVQLPFMEDLRQYMFSSLKN 440
Cdd:smart00559  80 EALLETDKIAIARYTLRTKSNPRLVALRPYDeEDDGEGLVLVQLPFADDVRKLDFPELNT 139
vWA_ku cd01458
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to ...
7-237 4.86e-47

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: 166.00  E-value: 4.86e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198   7 KAAVVLCMDVGFTMSNSIPGI-ESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPlsggDQYQNITVHRHLML 85
Cdd:cd01458     1 KESVVFLVDVSPSMFESKDGEyESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKNP----VGYENIYVLLDLDT 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198  86 PDFDLLEDIESKIQPG----------SQQADFLDALIVSMDVIQHetIGKKFEKRHIEIFTDL-----SSRFSKSQLDII 150
Cdd:cd01458    77 PGAERVEDLKELIEPGglsfagqvgdSGQVSLSDALWVCLDLFSK--GKKKKSHKRIFLFTNNddphgGDSIKDSQAAVK 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 151 IHSLKKCDISLQFFLPFSLGKedgsgdrgdgpfrlgghgpsfplkgiteqQKEGLEIVKMVMISLEG--EDGLDEIYSFS 228
Cdd:cd01458   155 AEDLKDKGIELELFPLSSPGK-----------------------------KFDVSKFYKDIIALVEDanEELLDEFTEPS 205
                         250
                  ....*....|...
gi 2222400198 229 ----ESLRKLCVF 237
Cdd:cd01458   206 kdleDLLKRLRAK 218
Ku_PK_bind pfam08785
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by ...
593-706 3.62e-37

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: 135.02  E-value: 3.62e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 593 NPAENFRVLVKQKK--ASFEEASNQLINHIEQFLDTNETP-YFMKSIDCIRAFREEAIKFSEEQRFNNFLKALQEKVEIK 669
Cdd:pfam08785   1 NPVPDFKQLLARGDdvDAVEKAVKQMGNIIEDLVRDSFGDsNYDKALECLRALREECIEEEEPDLYNDFLRDLKKKLLEG 80
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2222400198 670 QLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLA 706
Cdd:pfam08785  81 DRREFWELVRKNKLGLITKDEAEDSDVTEEEAKEFLS 117
VWA smart00327
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
10-156 2.67e-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: 51.30  E-value: 2.67e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198   10 VVLCMDVgftmSNSIpgIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDgtdnplsggdqyqnitVHRHLMLPDFD 89
Cdd:smart00327   2 VVFLLDG----SGSM--GGNRFELAKEFVLKLVEQLDIGPDGDRVGLVTFSDD----------------ARVLFPLNDSR 59
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2222400198   90 LLEDIESKIQ----PGSQQADFLDALIVSMDVIQHETIG-KKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKK 156
Cdd:smart00327  60 SKDALLEALAslsyKLGGGTNLGAALQYALENLFSKSAGsRRGAPKVVILITDGESNDGPKDLLKAAKELKR 131
 
Name Accession Description Interval E-value
KU80 cd00873
Ku-core domain, Ku80 subfamily; Ku80 is a subunit of the Ku protein, which plays a key role in ...
244-543 3.58e-126

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: 377.40  E-value: 3.58e-126
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 244 SIHWPCRLTIGSNLSIRIAAYKSILQERVKKTWTVVDA-KTLKK--EDIQKETVYCLNDDDETEVLKEDIIQGFRYGSDI 320
Cdd:cd00873     1 VAAFKGQLTLGSPLSIAVELYKKTKEERPPKLKKVSDAeKTGEDafEDVKSERSYDVNDDDKTEVEKEDLIKGYRYGRDI 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 321 VPFSKVDEEQMKYkSEGKCFSVLGFCKSSQVQRRFFMGnQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKR 400
Cdd:cd00873    81 VPLSEEDEEATKL-STSKGLDILGFIKASNVPRYYLMG-ESSYVVPQQDDEAAALAFSALVRALAELDKYAIARYVYKDN 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 401 ANPQVGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSK-KYAPTEAQLNAVDALIDSMSLAKKDEktDTLEDLFPT 479
Cdd:cd00873   159 SEPQLGVLFPRIKEDYECLVLVRLPFAEDVRQYRFPSLDKLKtPNLPTEEQLEAMDDLVDSMDLDDDEE--DDPEEALKP 236
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2222400198 480 TKIPNPRFQRLFQCLLHRALHPREPLPPIQQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAK 543
Cdd:cd00873   237 DETPNPVLQRIYQALRHRALHPDEPLPPLLQVLLRYLEPPEEVLEKSKEALKKIKEKFPLKEVP 300
KU cd00594
Ku-core domain; includes the central DNA-binding beta-barrels, polypeptide rings, and the ...
245-537 2.16e-74

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: 241.79  E-value: 2.16e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 245 IHWPCRLTIGSNLSIRIAAYKSILQERvKKTWTVVDAKTLKKEDIQKETVYClnddDETEVLKEDIIQGFRYGSDIVPFS 324
Cdd:cd00594     2 AIWKGALSLGLDVSIPVKLYSAATEEK-PPSFKQLDRKTGERVKVKRVCKYT----GGKEVEKEDIVKGYEYGGDYVPLT 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 325 KVDEEQMKYKSEgKCFSVLGFCKSSQVQRRFFMGnQVLKVFAARDDEAAAVALSSLIHALDDLDMVAIVRYAYDKRANPQ 404
Cdd:cd00594    77 EEELEQLKLETS-KGLDILGFVPASEIPPYYFDK-ESYYLVPDDSDKGSEKAFSALRRALLEKDKVAIARYVLRRNSRPR 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 405 VGVAFPHIKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKkdektdtledlFPTTKIPN 484
Cdd:cd00594   155 LVALRPQEEEDPEGLVLVTLPFADDVRSYPFPLLLDIKTEKPTDEELELAKQLIDSLDLDD-----------FDPEKFPN 223
                         250       260       270       280       290
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2222400198 485 PRFQRLFQCLLHRALHPREPLPPIQQhiwnMLNPPAEVTTKSQIPLSKIKTLF 537
Cdd:cd00594   224 PYLQRLYALLEAKALGEEIPEPPEDL----TLPPPEEIPKRVIDLLEALKKSL 272
Ku_N pfam03731
Ku70/Ku80 N-terminal alpha/beta domain; The Ku heterodimer (composed of Ku70 and Ku80) ...
9-244 3.33e-59

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: 199.51  E-value: 3.33e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198   9 AVVLCMDVGFTMSNSIPGIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNplsgGDQYQNITVHRHLMLPDF 88
Cdd:pfam03731   1 AILFVIDVSPAMFESSKLLEAPFDMALKCIRELLKSKIISRDKDLIGVVLYGTDNSEN----SEGLPNITVLRDLDLPGA 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198  89 DLLEDIESKIQPG----------SQQADFLDALIVSMDVIQHetIGKKFEKRHIEIFTDLSSRF-SKSQLDIIIHSLKkc 157
Cdd:pfam03731  77 ELILELDQFVESFgrdvrgfsgdSSDGSLLSALWVCLELLQK--TGKKLSHKRIFLFTDLDDPFeDQDKLDIALQRLL-- 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 158 dislqfflpfslgKEDGSGDRGD-GPFRLGGHGPSFPLKGITEQQKEGLEIVKMVMISLEGEdgldeiySFSESLRKLCV 236
Cdd:pfam03731 153 -------------AEDLRDTRGEfDLIHLPNADGFDPNLFYKDIIKLGSDEVLNVMLDLEGQ-------KLEDLLAKIRA 212

                  ....*...
gi 2222400198 237 FKKIERHS 244
Cdd:pfam03731 213 KKTAKRAH 220
Ku pfam02735
Ku70/Ku80 beta-barrel domain; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
253-453 1.80e-56

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: 191.30  E-value: 1.80e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 253 IGSNLSIRIAAYKSIlQERVKKTWTVVDAKTlkKEDIQKETVYClNDDDETEVLKEDIIQGFRYGSDIVPFSKVDEEQMK 332
Cdd:pfam02735   1 IGGLVSIPVKLYSAT-EEEKKPSFKKLDRET--NDGVRIKYKYV-CEDTGKEVEKEDIVKGYEYGGTYVPLSDEELEELK 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 333 YKSEgKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAV-ALSSLIHALDDLDMVAIVRYAYDKRANPQVGVAFPH 411
Cdd:pfam02735  77 PEST-KGLDLLGFVPLDEIDPIYFMGDKSYFLYPDKGDIAGSTkAFSALREALLETDKVAIARFVLRRREHPRLVALRPQ 155
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2222400198 412 IKHNYECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNA 453
Cdd:pfam02735 156 EEEPDPGLVLITLPFADDVREEFFPIPSLLEKPKPTEEQLDL 197
Ku78 smart00559
Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen; This is a single ...
302-440 2.16e-47

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: 164.39  E-value: 2.16e-47
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198  302 ETEVLKEDIIQGFRYGSDIVPFSKVDEEQMKYKSEgKCFSVLGFCKSSQVQRRFFMGNQVLKVFAARDDEAAAVALSSLI 381
Cdd:smart00559   1 GKEVKPEDIVKGYEYGGRYVPLSDEELEQLKYKSE-PGLELLGFKPLSSLPPYYFLRPSYFLVPDDKSVIGSTKAFSALV 79
                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198  382 HALDDLDMVAIVRYAYDKRANPQVGVAFPHI-KHNYECLVYVQLPFMEDLRQYMFSSLKN 440
Cdd:smart00559  80 EALLETDKIAIARYTLRTKSNPRLVALRPYDeEDDGEGLVLVQLPFADDVRKLDFPELNT 139
vWA_ku cd01458
Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to ...
7-237 4.86e-47

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: 166.00  E-value: 4.86e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198   7 KAAVVLCMDVGFTMSNSIPGI-ESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDNPlsggDQYQNITVHRHLML 85
Cdd:cd01458     1 KESVVFLVDVSPSMFESKDGEyESPFEEALKCIRQLMKSKIISSPKDLVGVVFYGTEESKNP----VGYENIYVLLDLDT 76
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198  86 PDFDLLEDIESKIQPG----------SQQADFLDALIVSMDVIQHetIGKKFEKRHIEIFTDL-----SSRFSKSQLDII 150
Cdd:cd01458    77 PGAERVEDLKELIEPGglsfagqvgdSGQVSLSDALWVCLDLFSK--GKKKKSHKRIFLFTNNddphgGDSIKDSQAAVK 154
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 151 IHSLKKCDISLQFFLPFSLGKedgsgdrgdgpfrlgghgpsfplkgiteqQKEGLEIVKMVMISLEG--EDGLDEIYSFS 228
Cdd:cd01458   155 AEDLKDKGIELELFPLSSPGK-----------------------------KFDVSKFYKDIIALVEDanEELLDEFTEPS 205
                         250
                  ....*....|...
gi 2222400198 229 ----ESLRKLCVF 237
Cdd:cd01458   206 kdleDLLKRLRAK 218
Ku_PK_bind pfam08785
Ku C terminal domain like; The non-homologous end joining (NHEJ) pathway is one method by ...
593-706 3.62e-37

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: 135.02  E-value: 3.62e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 593 NPAENFRVLVKQKK--ASFEEASNQLINHIEQFLDTNETP-YFMKSIDCIRAFREEAIKFSEEQRFNNFLKALQEKVEIK 669
Cdd:pfam08785   1 NPVPDFKQLLARGDdvDAVEKAVKQMGNIIEDLVRDSFGDsNYDKALECLRALREECIEEEEPDLYNDFLRDLKKKLLEG 80
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2222400198 670 QLNHFWEIVVQDGITLITKEEASGSSVTAEEAKKFLA 706
Cdd:pfam08785  81 DRREFWELVRKNKLGLITKDEAEDSDVTEEEAKEFLS 117
Ku_C pfam03730
Ku70/Ku80 C-terminal arm; The Ku heterodimer (composed of Ku70 and Ku80) contributes to ...
476-569 1.14e-17

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: 78.08  E-value: 1.14e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 476 LFPTTKIPNPRFQRLFQCLLHRALHPREPLppiqQHIWNMLNPPAEVTTKSQIPLSKIKTLFPLIEAKKkdqvtaqeifq 555
Cdd:pfam03730   1 SYNPDKFPNPSLQRHYQNLQALALDEDEPE----EPEDLTLPKYEAIDKRIGKLLEEFKELFELEDYKP----------- 65
                          90
                  ....*....|....
gi 2222400198 556 DNHEDGPTAKKLKT 569
Cdd:pfam03730  66 DEDEEGPAAKKAKI 79
KU70 cd00788
Ku-core domain, Ku70 subfamily; Ku70 is a subunit of the Ku protein, which plays a key role in ...
249-499 3.91e-13

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: 70.39  E-value: 3.91e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 249 CRLTIG--SNLSIRIAAYkSILQERVK--KTWTVVDAKTLKKEdIQKETVYcLNDDDETEVLKEDIIQGFRYGSDIVPFS 324
Cdd:cd00788     6 LPLELGpgNKLVISVKGY-SLVSHAKKprKYKLDREKNEERRE-VKSKRKF-FDVESGKTLEKADIKKGYKIGGEKIIFT 82
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 325 KVDEEQMKYKSEgKCFSVLGFCKSSQVQRRFfmgnqVLK--VFAARDDE---AAAVALSSLIHALDDLDMVAIVRYAYDK 399
Cdd:cd00788    83 KEELKKIKSFGE-PGLRLIGFKPRSTLKPYH-----NIKksYFIYPDESdykGSTRLFAALLRSCLKKNKVAICWYILRK 156
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198 400 RANPQVGVAFP------HIKHNY--ECLVYVQLPFMEDLRQYMFSSLKNSKKYAPTEAQLNAVDALIDSMSLAKkdektd 471
Cdd:cd00788   157 NSPPRLVALVPqeeeldEPDGQVlpPGFHLVPLPFADDIRKLPSLLEENASAESASDELVDKAKQIIKKLRLLS------ 230
                         250       260
                  ....*....|....*....|....*...
gi 2222400198 472 tledlFPTTKIPNPRFQRLFQCLLHRAL 499
Cdd:cd00788   231 -----YDPDKFPNPSLQKHYKILEALAL 253
VWA smart00327
von Willebrand factor (vWF) type A domain; VWA domains in extracellular eukaryotic proteins ...
10-156 2.67e-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: 51.30  E-value: 2.67e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198   10 VVLCMDVgftmSNSIpgIESPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDgtdnplsggdqyqnitVHRHLMLPDFD 89
Cdd:smart00327   2 VVFLLDG----SGSM--GGNRFELAKEFVLKLVEQLDIGPDGDRVGLVTFSDD----------------ARVLFPLNDSR 59
                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2222400198   90 LLEDIESKIQ----PGSQQADFLDALIVSMDVIQHETIG-KKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKK 156
Cdd:smart00327  60 SKDALLEALAslsyKLGGGTNLGAALQYALENLFSKSAGsRRGAPKVVILITDGESNDGPKDLLKAAKELKR 131
vWFA cd00198
Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation ...
8-161 2.62e-05

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: 45.25  E-value: 2.62e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2222400198   8 AAVVLCMDVgftmSNSIPGieSPFEQAKKVITMFVQRQVFAENKDEIALVLFGTDGTDnpLSGGDQYQNitvhrhlmlpD 87
Cdd:cd00198     1 ADIVFLLDV----SGSMGG--EKLDKAKEALKALVSSLSASPPGDRVGLVTFGSNARV--VLPLTTDTD----------K 62
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2222400198  88 FDLLEDIESKIQPGSQQADFLDALIVSMDVIQheTIGKKFEKRHIEIFTDLSSRFSKSQLDIIIHSLKKCDISL 161
Cdd:cd00198    63 ADLLEAIDALKKGLGGGTNIGAALRLALELLK--SAKRPNARRVIILLTDGEPNDGPELLAEAARELRKLGITV 134
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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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