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Conserved domains on  [gi|2783007121|ref|NP_001419695|]
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non-homologous end-joining factor 1 isoform 1 [Rattus norvegicus]

Protein Classification

HD_XLF_N domain-containing protein( domain architecture ID 10558230)

HD_XLF_N domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XLF pfam09302
XLF-Cernunnos, XRcc4-like factor, NHEJ component; XLF (also called Cernunnos) is ...
 12-180 1.32e-39

XLF-Cernunnos, XRcc4-like factor, NHEJ component; XLF (also called Cernunnos) is Xrcc4-like-factor, and interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated down-regulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining. This family contains Nej1 (non-homologous end-joining factor), and Lif1, ligase-interacting factor. XLF forms one of the components of the NHEJ machinery for DNA non-homologous end-joining.


:

Pssm-ID: 462749  Cd Length: 180  Bit Score: 137.01  E-value: 1.32e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2783007121  12 PWAWLQLAENS----LLAKASITKHGYALLISDLQQVWHEQVDTLEVSQRAKELNKRLT-----APPAAFLHHLDEVLRP 82
Cdd:pfam09302   1 PWRPLPLSGQGglppLLVKYSFSSDSYEVYLTDLANVWSERLDRKAILKRAKEENTSIDpseddEQLSVLLEKIRDALDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2783007121  83 LfkdsahQDAAHPSKaTFSCDRGEEVLILRVRSELSGL--PFNWHFHCLPASSLLVSQHLICPLMGVSLALHSHVRELAA 160
Cdd:pfam09302  81 S------KGTATFSL-SLSSDAGGDSLKLHVTSKLPGPlqPLEWPFHLTKAPPSALAQHLVLPLLQASAALQRQVESLID 153

                         170       180
                  ....*....|....*....|....
gi 2783007121 161 LLRMKDLEIQA----YQESGAVLS 180
Cdd:pfam09302 154 LLKEKDAVIGKlldkLEASGADLS 177
 
Name Accession Description Interval E-value
XLF pfam09302
XLF-Cernunnos, XRcc4-like factor, NHEJ component; XLF (also called Cernunnos) is ...
 12-180 1.32e-39

XLF-Cernunnos, XRcc4-like factor, NHEJ component; XLF (also called Cernunnos) is Xrcc4-like-factor, and interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated down-regulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining. This family contains Nej1 (non-homologous end-joining factor), and Lif1, ligase-interacting factor. XLF forms one of the components of the NHEJ machinery for DNA non-homologous end-joining.


Pssm-ID: 462749  Cd Length: 180  Bit Score: 137.01  E-value: 1.32e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2783007121  12 PWAWLQLAENS----LLAKASITKHGYALLISDLQQVWHEQVDTLEVSQRAKELNKRLT-----APPAAFLHHLDEVLRP 82
Cdd:pfam09302   1 PWRPLPLSGQGglppLLVKYSFSSDSYEVYLTDLANVWSERLDRKAILKRAKEENTSIDpseddEQLSVLLEKIRDALDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2783007121  83 LfkdsahQDAAHPSKaTFSCDRGEEVLILRVRSELSGL--PFNWHFHCLPASSLLVSQHLICPLMGVSLALHSHVRELAA 160
Cdd:pfam09302  81 S------KGTATFSL-SLSSDAGGDSLKLHVTSKLPGPlqPLEWPFHLTKAPPSALAQHLVLPLLQASAALQRQVESLID 153

                         170       180
                  ....*....|....*....|....
gi 2783007121 161 LLRMKDLEIQA----YQESGAVLS 180
Cdd:pfam09302 154 LLKEKDAVIGKlldkLEASGADLS 177
HD_XLF_N cd22285
N-terminal head domain found in XRCC4-like factor and similar proteins; XRCC4-like factor (XLF) ...
 12-131 7.67e-29

N-terminal head domain found in XRCC4-like factor and similar proteins; XRCC4-like factor (XLF), also known as non-homologous end-joining factor 1 (NHEJ1) or protein cernunnos, is involved in DNA nonhomologous end joining (NHEJ), which is required for double-strand break (DSB) repair and V(D)J recombination. It interacts with the XRCC4-DNA ligase IV complex to promote NHEJ. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are non-complementary or partially complementary. XLF binds DNA in a length-dependent manner. Similar to XRCC4, XLF 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, XLF and XRCC4 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 XLF, which is structurally related to other XRCC4-superfamily members, XRCC4, PAXX, SAS6, and CCDC61.


Pssm-ID: 409002  Cd Length: 109  Bit Score: 106.62  E-value: 7.67e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2783007121  12 PWAWLQLAENSLLAKASITKHGYALLISDLQQVWHEQVDTLEVSQRAKELNKRLTAPPAAFLHHLDEVLRPLFKDSahqd 91
Cdd:cd22285     1 PWKPLPISNPPYLIKFSFSDDSYEILLTDLVSVWSEELSRDEILKRAKELNPSIEAQLEELLEHLEDLLSGLDSDT---- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2783007121  92 aahpskaTFSCDRGEEVLILRVRSELSGLPFNWHFHCLPA 131
Cdd:cd22285    77 -------TLSIEESNDKLKLKLKSKLPGVPFKWEFELQKA 109
 
Name Accession Description Interval E-value
XLF pfam09302
XLF-Cernunnos, XRcc4-like factor, NHEJ component; XLF (also called Cernunnos) is ...
 12-180 1.32e-39

XLF-Cernunnos, XRcc4-like factor, NHEJ component; XLF (also called Cernunnos) is Xrcc4-like-factor, and interacts with the XRCC4-DNA ligase IV complex to promote DNA non-homologous end-joining. It directly interacts with the XRCC4-Ligase IV complex and siRNA-mediated down-regulation of XLF in human cell lines leads to radio-sensitivity and impaired DNA non-homologous end-joining. This family contains Nej1 (non-homologous end-joining factor), and Lif1, ligase-interacting factor. XLF forms one of the components of the NHEJ machinery for DNA non-homologous end-joining.


Pssm-ID: 462749  Cd Length: 180  Bit Score: 137.01  E-value: 1.32e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2783007121  12 PWAWLQLAENS----LLAKASITKHGYALLISDLQQVWHEQVDTLEVSQRAKELNKRLT-----APPAAFLHHLDEVLRP 82
Cdd:pfam09302   1 PWRPLPLSGQGglppLLVKYSFSSDSYEVYLTDLANVWSERLDRKAILKRAKEENTSIDpseddEQLSVLLEKIRDALDG 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2783007121  83 LfkdsahQDAAHPSKaTFSCDRGEEVLILRVRSELSGL--PFNWHFHCLPASSLLVSQHLICPLMGVSLALHSHVRELAA 160
Cdd:pfam09302  81 S------KGTATFSL-SLSSDAGGDSLKLHVTSKLPGPlqPLEWPFHLTKAPPSALAQHLVLPLLQASAALQRQVESLID 153

                         170       180
                  ....*....|....*....|....
gi 2783007121 161 LLRMKDLEIQA----YQESGAVLS 180
Cdd:pfam09302 154 LLKEKDAVIGKlldkLEASGADLS 177
HD_XLF_N cd22285
N-terminal head domain found in XRCC4-like factor and similar proteins; XRCC4-like factor (XLF) ...
 12-131 7.67e-29

N-terminal head domain found in XRCC4-like factor and similar proteins; XRCC4-like factor (XLF), also known as non-homologous end-joining factor 1 (NHEJ1) or protein cernunnos, is involved in DNA nonhomologous end joining (NHEJ), which is required for double-strand break (DSB) repair and V(D)J recombination. It interacts with the XRCC4-DNA ligase IV complex to promote NHEJ. It may act in concert with XRCC6/XRCC5 (Ku) to stimulate XRCC4-mediated joining of blunt ends and several types of mismatched ends that are non-complementary or partially complementary. XLF binds DNA in a length-dependent manner. Similar to XRCC4, XLF 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, XLF and XRCC4 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 XLF, which is structurally related to other XRCC4-superfamily members, XRCC4, PAXX, SAS6, and CCDC61.


Pssm-ID: 409002  Cd Length: 109  Bit Score: 106.62  E-value: 7.67e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2783007121  12 PWAWLQLAENSLLAKASITKHGYALLISDLQQVWHEQVDTLEVSQRAKELNKRLTAPPAAFLHHLDEVLRPLFKDSahqd 91
Cdd:cd22285     1 PWKPLPISNPPYLIKFSFSDDSYEILLTDLVSVWSEELSRDEILKRAKELNPSIEAQLEELLEHLEDLLSGLDSDT---- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 2783007121  92 aahpskaTFSCDRGEEVLILRVRSELSGLPFNWHFHCLPA 131
Cdd:cd22285    77 -------TLSIEESNDKLKLKLKSKLPGVPFKWEFELQKA 109
HD_XRCC4-like_N cd22210
N-terminal head domain found in the XRCC4 superfamily of proteins; The XRCC4 superfamily ...
 12-131 2.45e-22

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: 89.52  E-value: 2.45e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2783007121  12 PWAWLQLA--ENSLLAKASITKH---GYALLISDLQQVWHEQVDTLEVSQRAKELNKRltAPPAAFLHHLDEVLRPLFKD 86
Cdd:cd22210     1 PWRPLPLHvvLEELTFKVETEVAnerGLRLHVSDDAFLWTGEVSESDISQLKNDQGIL--VDFASFPGKLRSALEKCILA 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2783007121  87 sahqdaahPSKATFSCDRGEEVLILRVRSELSGLPFNWHFHCLPA 131
Cdd:cd22210    79 --------SDRFTFVLTIRGDEAYLKLVEILDEQLPHITFALRKV 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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