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Conserved domains on  [gi|672041085|ref|XP_008758858|]
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DNA repair protein XRCC4 isoform X1 [Rattus norvegicus]

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 ...
 2-334 0e+00

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: 506.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085    2 ERKVSRISLASEPNVTYFLQVSWEGTIGSGFVITLTDGHSAWTAKgnldnnpvsskISESEIAQEADDMAMEQEKYMDEL 81
Cdd:pfam06632   1 EKKVRRIHISSEPDTIYFLQVSWEKDLGSGFDIILTDGQSAWTGT-----------VSEEEISREADDMEMEREKYVDEL 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085   82 RRALVPESGAAGAYKFIFSKDTQ-----HFSLEKELKDVSFRLGSFNLDKVTNPTEVIRELICYCLDTIAEKQAKNEHLQ 156
Cdd:pfam06632  70 RKALTLGAEPAGKYNFDLSKDGPnpdclHFSYEKVLKDVSFRLGSVKLQKVPEPAEVIRELISYCLDCIAELQAKNEHLQ 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085  157 KENERLLRDWTDVQGRFEKCVSDKEALEADLYQRFILVLNEKKTKIRSL---LSEVQQLEKSTKPERETP-SSDKIPEED 232
Cdd:pfam06632 150 KENERLQRDWNDVTGRLEKCVKAKEELEADLYKRFILVLNEKKAKIRSLqklLNELQESEESTEQKREDPaTSDRTPDEE 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085  233 GLYDGSTDEESGA----PVLGADTLDKDDSLFSSPDVTDIAPSRKRRHRMQTNLGTEPKMAPQELPLQEKERLGSSPPQT 308
Cdd:pfam06632 230 SDYDGSTDEESENlpspPSSKPAASPRDDSLLSSPDITDVAPSRKRRQRHQKTLGTEAKVATQEPQLQEKEKPDSSAPKS 309

                         330       340
                  ....*....|....*....|....*..
gi 672041085  309 LKEEGTSAAKMSLETLRNS-SPEDLFD 334
Cdd:pfam06632 310 SKKTPQSAEGMSLETLKNSpEPEDLFD 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 ...
 2-334 0e+00

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: 506.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085    2 ERKVSRISLASEPNVTYFLQVSWEGTIGSGFVITLTDGHSAWTAKgnldnnpvsskISESEIAQEADDMAMEQEKYMDEL 81
Cdd:pfam06632   1 EKKVRRIHISSEPDTIYFLQVSWEKDLGSGFDIILTDGQSAWTGT-----------VSEEEISREADDMEMEREKYVDEL 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085   82 RRALVPESGAAGAYKFIFSKDTQ-----HFSLEKELKDVSFRLGSFNLDKVTNPTEVIRELICYCLDTIAEKQAKNEHLQ 156
Cdd:pfam06632  70 RKALTLGAEPAGKYNFDLSKDGPnpdclHFSYEKVLKDVSFRLGSVKLQKVPEPAEVIRELISYCLDCIAELQAKNEHLQ 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085  157 KENERLLRDWTDVQGRFEKCVSDKEALEADLYQRFILVLNEKKTKIRSL---LSEVQQLEKSTKPERETP-SSDKIPEED 232
Cdd:pfam06632 150 KENERLQRDWNDVTGRLEKCVKAKEELEADLYKRFILVLNEKKAKIRSLqklLNELQESEESTEQKREDPaTSDRTPDEE 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085  233 GLYDGSTDEESGA----PVLGADTLDKDDSLFSSPDVTDIAPSRKRRHRMQTNLGTEPKMAPQELPLQEKERLGSSPPQT 308
Cdd:pfam06632 230 SDYDGSTDEESENlpspPSSKPAASPRDDSLLSSPDITDVAPSRKRRQRHQKTLGTEAKVATQEPQLQEKEKPDSSAPKS 309

                         330       340
                  ....*....|....*....|....*..
gi 672041085  309 LKEEGTSAAKMSLETLRNS-SPEDLFD 334
Cdd:pfam06632 310 SKKTPQSAEGMSLETLKNSpEPEDLFD 336
HD_XRCC4_N cd22283
N-terminal head domain found in X-ray repair cross-complementing protein 4 and similar ...
 2-127 1.12e-26

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: 101.97  E-value: 1.12e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085   2 ERKVSRISLASePNVTYFLQVSWEGTIGSGFVITLTDGHSAWTAkgnldnnpvssKISESEIAQEADDMAMEQEKYMDEL 81
Cdd:cd22283    1 EKTLCRIELDS-PGKTYYLLTSWKDEGNDGFKLTLTDGESAWTG-----------TVSEEDISQMAKKLKMSEEDYVEET 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 672041085  82 RRALVPESGAAGAYKFIFSKDTQ--HFSLEKEL-KDVSFRLGSFNLDKV 127
Cdd:cd22283   69 KKALTGEASGDSNFTFQLKKEENslEFSWKKVLdDDIKFKLGSVTLKKV 117
 
Name Accession Description Interval E-value
XRCC4 pfam06632
DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of ...
 2-334 0e+00

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: 506.56  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085    2 ERKVSRISLASEPNVTYFLQVSWEGTIGSGFVITLTDGHSAWTAKgnldnnpvsskISESEIAQEADDMAMEQEKYMDEL 81
Cdd:pfam06632   1 EKKVRRIHISSEPDTIYFLQVSWEKDLGSGFDIILTDGQSAWTGT-----------VSEEEISREADDMEMEREKYVDEL 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085   82 RRALVPESGAAGAYKFIFSKDTQ-----HFSLEKELKDVSFRLGSFNLDKVTNPTEVIRELICYCLDTIAEKQAKNEHLQ 156
Cdd:pfam06632  70 RKALTLGAEPAGKYNFDLSKDGPnpdclHFSYEKVLKDVSFRLGSVKLQKVPEPAEVIRELISYCLDCIAELQAKNEHLQ 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085  157 KENERLLRDWTDVQGRFEKCVSDKEALEADLYQRFILVLNEKKTKIRSL---LSEVQQLEKSTKPERETP-SSDKIPEED 232
Cdd:pfam06632 150 KENERLQRDWNDVTGRLEKCVKAKEELEADLYKRFILVLNEKKAKIRSLqklLNELQESEESTEQKREDPaTSDRTPDEE 229

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085  233 GLYDGSTDEESGA----PVLGADTLDKDDSLFSSPDVTDIAPSRKRRHRMQTNLGTEPKMAPQELPLQEKERLGSSPPQT 308
Cdd:pfam06632 230 SDYDGSTDEESENlpspPSSKPAASPRDDSLLSSPDITDVAPSRKRRQRHQKTLGTEAKVATQEPQLQEKEKPDSSAPKS 309

                         330       340
                  ....*....|....*....|....*..
gi 672041085  309 LKEEGTSAAKMSLETLRNS-SPEDLFD 334
Cdd:pfam06632 310 SKKTPQSAEGMSLETLKNSpEPEDLFD 336
HD_XRCC4_N cd22283
N-terminal head domain found in X-ray repair cross-complementing protein 4 and similar ...
 2-127 1.12e-26

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: 101.97  E-value: 1.12e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085   2 ERKVSRISLASePNVTYFLQVSWEGTIGSGFVITLTDGHSAWTAkgnldnnpvssKISESEIAQEADDMAMEQEKYMDEL 81
Cdd:cd22283    1 EKTLCRIELDS-PGKTYYLLTSWKDEGNDGFKLTLTDGESAWTG-----------TVSEEDISQMAKKLKMSEEDYVEET 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 672041085  82 RRALVPESGAAGAYKFIFSKDTQ--HFSLEKEL-KDVSFRLGSFNLDKV 127
Cdd:cd22283   69 KKALTGEASGDSNFTFQLKKEENslEFSWKKVLdDDIKFKLGSVTLKKV 117
HD_XRCC4-like_N cd22210
N-terminal head domain found in the XRCC4 superfamily of proteins; The XRCC4 superfamily ...
 4-127 1.45e-16

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: 74.50  E-value: 1.45e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672041085   4 KVSRISLASEPNvTYFLQVSWEGTIGSGFVITLTDGHSAWTakgnldnnpvsSKISESEIAQEADDMAM--EQEKYMDEL 81
Cdd:cd22210    1 PWRPLPLHVVLE-ELTFKVETEVANERGLRLHVSDDAFLWT-----------GEVSESDISQLKNDQGIlvDFASFPGKL 68

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 672041085  82 RRALVPESGAAGAYKFIFSK--DTQHFSLEKELKDvSFRLGSFNLDKV 127
Cdd:cd22210   69 RSALEKCILASDRFTFVLTIrgDEAYLKLVEILDE-QLPHITFALRKV 115
 
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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