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Conserved domains on  [gi|1912393391|ref|XP_036259933|]
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DNA repair protein XRCC4 isoform X1 [Molothrus ater]

Protein Classification

HD_XRCC4_N domain-containing protein( domain architecture ID 10535161)

HD_XRCC4_N domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRCC4 pfam06632
DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of ...
 2-329 8.40e-163

DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalyzed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks.


:

Pssm-ID: 369011 [Multi-domain]  Cd Length: 336  Bit Score: 457.26  E-value: 8.40e-163
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391   2 EKTLNRIHPVSDPEATYFLQVSWEKDLGTGFALLLSDCQCAWTGTVSESDISREAADIEMDREKYVEELRKALIAGEESA 81
Cdd:pfam06632   1 EKKVRRIHISSEPDTIYFLQVSWEKDLGSGFDIILTDGQSAWTGTVSEEEISREADDMEMEREKYVDELRKALTLGAEPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391  82 GKYNFVISRDEQNKAC-HFSYERNLKDGSFRLGSLKLKEVPNPAEVIKELIGYCLDSLGKLQAKTEHLQRENERLFSNWS 160
Cdd:pfam06632  81 GKYNFDLSKDGPNPDClHFSYEKVLKDVSFRLGSVKLQKVPEPAEVIRELISYCLDCIAELQAKNEHLQKENERLQRDWN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391 161 EVEKRLEKCVEAKEELEADLYSRFVLVLNEKKAKIRNLQKLLSEAKESAVDAKCARDSIATTQVVVKRENNYEASTDEES 240
Cdd:pfam06632 161 DVTGRLEKCVKAKEELEADLYKRFILVLNEKKAKIRSLQKLLNELQESEESTEQKREDPATSDRTPDEESDYDGSTDEES 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391 241 ENPAQ--ASLPSAPERRDsSLLGSPDIVDPAPRRKRRQRTAKPAGTGAKVAAYEAEQPAQEKAGPAS------SGQRCPD 312
Cdd:pfam06632 241 ENLPSppSSKPAASPRDD-SLLSSPDITDVAPSRKRRQRHQKTLGTEAKVATQEPQLQEKEKPDSSApksskkTPQSAEG 319

                         330
                  ....*....|....*..
gi 1912393391 313 WDLETLENSCEPGELLE 329
Cdd:pfam06632 320 MSLETLKNSPEPEDLFD 336
 
Name Accession Description Interval E-value
XRCC4 pfam06632
DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of ...
 2-329 8.40e-163

DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalyzed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks.


Pssm-ID: 369011 [Multi-domain]  Cd Length: 336  Bit Score: 457.26  E-value: 8.40e-163
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391   2 EKTLNRIHPVSDPEATYFLQVSWEKDLGTGFALLLSDCQCAWTGTVSESDISREAADIEMDREKYVEELRKALIAGEESA 81
Cdd:pfam06632   1 EKKVRRIHISSEPDTIYFLQVSWEKDLGSGFDIILTDGQSAWTGTVSEEEISREADDMEMEREKYVDELRKALTLGAEPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391  82 GKYNFVISRDEQNKAC-HFSYERNLKDGSFRLGSLKLKEVPNPAEVIKELIGYCLDSLGKLQAKTEHLQRENERLFSNWS 160
Cdd:pfam06632  81 GKYNFDLSKDGPNPDClHFSYEKVLKDVSFRLGSVKLQKVPEPAEVIRELISYCLDCIAELQAKNEHLQKENERLQRDWN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391 161 EVEKRLEKCVEAKEELEADLYSRFVLVLNEKKAKIRNLQKLLSEAKESAVDAKCARDSIATTQVVVKRENNYEASTDEES 240
Cdd:pfam06632 161 DVTGRLEKCVKAKEELEADLYKRFILVLNEKKAKIRSLQKLLNELQESEESTEQKREDPATSDRTPDEESDYDGSTDEES 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391 241 ENPAQ--ASLPSAPERRDsSLLGSPDIVDPAPRRKRRQRTAKPAGTGAKVAAYEAEQPAQEKAGPAS------SGQRCPD 312
Cdd:pfam06632 241 ENLPSppSSKPAASPRDD-SLLSSPDITDVAPSRKRRQRHQKTLGTEAKVATQEPQLQEKEKPDSSApksskkTPQSAEG 319

                         330
                  ....*....|....*..
gi 1912393391 313 WDLETLENSCEPGELLE 329
Cdd:pfam06632 320 MSLETLKNSPEPEDLFD 336
HD_XRCC4_N cd22283
N-terminal head domain found in X-ray repair cross-complementing protein 4 and similar ...
 2-120 3.19e-37

N-terminal head domain found in X-ray repair cross-complementing protein 4 and similar proteins; X-ray repair cross-complementing protein 4 (XRCC4) is a DNA repair protein involved in DNA non-homologous end-joining (NHEJ), which is required for double-strand break repair and V(D)J recombination. The DNA ligase IV (LIG4)- XRCC4 complex is responsible for the ligation step of NHEJ, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. XRCC4 monomers are comprised of an N-terminal globular head domain, a centrally located coiled-coil, and a C-terminal region. These monomers homodimerize through two dimerization domains, the N-terminal globular head domains and long extended alpha-helical coiled-coil regions. In addition, XRCC4 and XLF form symmetric heterodimers that interact through their globular head domains at the opposite end of the homodimer interface, and may form XLF-XRCC4 filaments. This model corresponds to the N-terminal head domain of XRCC4, which is structurally related to other XRCC4-superfamily members, PAXX, XLF, SAS6, and CCDC61.


Pssm-ID: 409000  Cd Length: 117  Bit Score: 129.31  E-value: 3.19e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391   2 EKTLNRIHPVSdPEATYFLQVSWEKDLGTGFALLLSDCQCAWTGTVSESDISREAADIEMDREKYVEELRKALIAGEESA 81
Cdd:cd22283     1 EKTLCRIELDS-PGKTYYLLTSWKDEGNDGFKLTLTDGESAWTGTVSEEDISQMAKKLKMSEEDYVEETKKALTGEASGD 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1912393391  82 GKYNFVISRDEQNkaCHFSYERNL-KDGSFRLGSLKLKEV 120
Cdd:cd22283    80 SNFTFQLKKEENS--LEFSWKKVLdDDIKFKLGSVTLKKV 117
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 155-312 4.21e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 39.00  E-value: 4.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391  155 LFSNWSEVEKRLEKCVEAKEELEADLYSRfVLVLNEKKAKIRNLQKLL--SEAKESAVDAKCARDSIATTQvvvkrennY 232
Cdd:PHA03307   757 LFSNPSLVPAKLAEALALLEPAEPQRGAG-SSPPVRAEAAFRRPGRLRrsGPAADAASRTASKRKSRSHTP--------D 827

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391  233 EASTDEESENPAQASLPSAPERRDSSLLGSPDIVDPAPRRKRRQRTAKPAGTGAKVAAyeAEQPAQEKAGPASSGQRCPD 312
Cdd:PHA03307   828 GGSESSGPARPPGAAARPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGA--AAPPKAAAAAPPAGAPAPRP 905
 
Name Accession Description Interval E-value
XRCC4 pfam06632
DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of ...
 2-329 8.40e-163

DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of several eukaryotic DNA double-strand break repair and V(D)J recombination protein XRCC4 sequences. In the non-homologous end joining pathway of DNA double-strand break repair, the ligation step is catalyzed by a complex of XRCC4 and DNA ligase IV. It is thought that XRCC4 and ligase IV are essential for alignment-based gap filling, as well as for final ligation of the breaks.


Pssm-ID: 369011 [Multi-domain]  Cd Length: 336  Bit Score: 457.26  E-value: 8.40e-163
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391   2 EKTLNRIHPVSDPEATYFLQVSWEKDLGTGFALLLSDCQCAWTGTVSESDISREAADIEMDREKYVEELRKALIAGEESA 81
Cdd:pfam06632   1 EKKVRRIHISSEPDTIYFLQVSWEKDLGSGFDIILTDGQSAWTGTVSEEEISREADDMEMEREKYVDELRKALTLGAEPA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391  82 GKYNFVISRDEQNKAC-HFSYERNLKDGSFRLGSLKLKEVPNPAEVIKELIGYCLDSLGKLQAKTEHLQRENERLFSNWS 160
Cdd:pfam06632  81 GKYNFDLSKDGPNPDClHFSYEKVLKDVSFRLGSVKLQKVPEPAEVIRELISYCLDCIAELQAKNEHLQKENERLQRDWN 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391 161 EVEKRLEKCVEAKEELEADLYSRFVLVLNEKKAKIRNLQKLLSEAKESAVDAKCARDSIATTQVVVKRENNYEASTDEES 240
Cdd:pfam06632 161 DVTGRLEKCVKAKEELEADLYKRFILVLNEKKAKIRSLQKLLNELQESEESTEQKREDPATSDRTPDEESDYDGSTDEES 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391 241 ENPAQ--ASLPSAPERRDsSLLGSPDIVDPAPRRKRRQRTAKPAGTGAKVAAYEAEQPAQEKAGPAS------SGQRCPD 312
Cdd:pfam06632 241 ENLPSppSSKPAASPRDD-SLLSSPDITDVAPSRKRRQRHQKTLGTEAKVATQEPQLQEKEKPDSSApksskkTPQSAEG 319

                         330
                  ....*....|....*..
gi 1912393391 313 WDLETLENSCEPGELLE 329
Cdd:pfam06632 320 MSLETLKNSPEPEDLFD 336
HD_XRCC4_N cd22283
N-terminal head domain found in X-ray repair cross-complementing protein 4 and similar ...
 2-120 3.19e-37

N-terminal head domain found in X-ray repair cross-complementing protein 4 and similar proteins; X-ray repair cross-complementing protein 4 (XRCC4) is a DNA repair protein involved in DNA non-homologous end-joining (NHEJ), which is required for double-strand break repair and V(D)J recombination. The DNA ligase IV (LIG4)- XRCC4 complex is responsible for the ligation step of NHEJ, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends. XRCC4 monomers are comprised of an N-terminal globular head domain, a centrally located coiled-coil, and a C-terminal region. These monomers homodimerize through two dimerization domains, the N-terminal globular head domains and long extended alpha-helical coiled-coil regions. In addition, XRCC4 and XLF form symmetric heterodimers that interact through their globular head domains at the opposite end of the homodimer interface, and may form XLF-XRCC4 filaments. This model corresponds to the N-terminal head domain of XRCC4, which is structurally related to other XRCC4-superfamily members, PAXX, XLF, SAS6, and CCDC61.


Pssm-ID: 409000  Cd Length: 117  Bit Score: 129.31  E-value: 3.19e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391   2 EKTLNRIHPVSdPEATYFLQVSWEKDLGTGFALLLSDCQCAWTGTVSESDISREAADIEMDREKYVEELRKALIAGEESA 81
Cdd:cd22283     1 EKTLCRIELDS-PGKTYYLLTSWKDEGNDGFKLTLTDGESAWTGTVSEEDISQMAKKLKMSEEDYVEETKKALTGEASGD 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1912393391  82 GKYNFVISRDEQNkaCHFSYERNL-KDGSFRLGSLKLKEV 120
Cdd:cd22283    80 SNFTFQLKKEENS--LEFSWKKVLdDDIKFKLGSVTLKKV 117
HD_XRCC4-like_N cd22210
N-terminal head domain found in the XRCC4 superfamily of proteins; The XRCC4 superfamily ...
 7-120 2.88e-13

N-terminal head domain found in the XRCC4 superfamily of proteins; The XRCC4 superfamily includes five families: XRCC4, XLF, PAXX, SAS6 and CCDC61. XRCC4 (X-ray repair cross-complementing protein 4), XLF (XRCC4-like factor) and PAXX (paralog of XRCC4 and XLF) play crucial roles in the non-homologous end-joining (NHEJ) DNA repair pathway. SAS6 (spindle assembly abnormal protein 6) and CCDC61 (coiled-coil domain-containing protein 61) have a centrosomal/centriolar function. Members of this superfamily have an N-terminal globular head domain, a centrally located coiled-coil, and a C-terminal low-complexity region. They form homodimers through two homodimerization domains: an N-terminal globular head domain and a parallel coiled-coil domain. In addition, some members such as XRCC4 and XLF form symmetric heterodimers that interact through their globular head domains at the opposite end of the homodimer interface, and may form XLF-XRCC4 filaments. This model corresponds to the N-terminal head domain of XRCC4 superfamily proteins.


Pssm-ID: 408999  Cd Length: 115  Bit Score: 65.26  E-value: 2.88e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391   7 RIHPVSDPEaTYFLQVSWEKDLGTGFALLLSDCQCAWTGTVSESDISREAADIEM--DREKYVEELRKALIAGEESAGKY 84
Cdd:cd22210     4 PLPLHVVLE-ELTFKVETEVANERGLRLHVSDDAFLWTGEVSESDISQLKNDQGIlvDFASFPGKLRSALEKCILASDRF 82

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1912393391  85 NFVISRDEQNKACHFSYErnlKDGSFRLGSLKLKEV 120
Cdd:cd22210    83 TFVLTIRGDEAYLKLVEI---LDEQLPHITFALRKV 115
PHA03307 PHA03307
transcriptional regulator ICP4; Provisional
 155-312 4.21e-03

transcriptional regulator ICP4; Provisional


Pssm-ID: 223039 [Multi-domain]  Cd Length: 1352  Bit Score: 39.00  E-value: 4.21e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391  155 LFSNWSEVEKRLEKCVEAKEELEADLYSRfVLVLNEKKAKIRNLQKLL--SEAKESAVDAKCARDSIATTQvvvkrennY 232
Cdd:PHA03307   757 LFSNPSLVPAKLAEALALLEPAEPQRGAG-SSPPVRAEAAFRRPGRLRrsGPAADAASRTASKRKSRSHTP--------D 827

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912393391  233 EASTDEESENPAQASLPSAPERRDSSLLGSPDIVDPAPRRKRRQRTAKPAGTGAKVAAyeAEQPAQEKAGPASSGQRCPD 312
Cdd:PHA03307   828 GGSESSGPARPPGAAARPPPARSSESSKSKPAAAGGRARGKNGRRRPRPPEPRARPGA--AAPPKAAAAAPPAGAPAPRP 905
 
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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