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Conserved domains on  [gi|238479872|ref|NP_001154639|]
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DNA ligase IV-binding protein [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRCC4 super family cl05919
DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of ...
 47-255 3.14e-10

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.


The actual alignment was detected with superfamily member pfam06632:

Pssm-ID: 369011 [Multi-domain]  Cd Length: 336  Bit Score: 59.73  E-value: 3.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872   47 SRFDISVTDGSSSWICNATEEEVAERAAQWDQPVSEYLK-LAEQYLGFQQPNSVYSFSDALEGSKR--LSWTFEKEGTKL 123
Cdd:pfam06632  29 SGFDIILTDGQSAWTGTVSEEEISREADDMEMEREKYVDeLRKALTLGAEPAGKYNFDLSKDGPNPdcLHFSYEKVLKDV 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872  124 EWRWKC-------KPSDDSKKITVGILDFLME---ANIRLSEEvvNktrsfEKMRSEAERCLAQGEKLCDEKTEFESATY 193
Cdd:pfam06632 109 SFRLGSvklqkvpEPAEVIRELISYCLDCIAElqaKNEHLQKE--N-----ERLQRDWNDVTGRLEKCVKAKEELEADLY 181

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872  194 AKFLSVLNAKKAKLRALRDKEDSVRVVEEEESTDKAESFESGRSDDEKS--------EEEASKKATSSKA 255
Cdd:pfam06632 182 KRFILVLNEKKAKIRSLQKLLNELQESEESTEQKREDPATSDRTPDEESdydgstdeESENLPSPPSSKP 251
 
Name Accession Description Interval E-value
XRCC4 pfam06632
DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of ...
 47-255 3.14e-10

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: 59.73  E-value: 3.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872   47 SRFDISVTDGSSSWICNATEEEVAERAAQWDQPVSEYLK-LAEQYLGFQQPNSVYSFSDALEGSKR--LSWTFEKEGTKL 123
Cdd:pfam06632  29 SGFDIILTDGQSAWTGTVSEEEISREADDMEMEREKYVDeLRKALTLGAEPAGKYNFDLSKDGPNPdcLHFSYEKVLKDV 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872  124 EWRWKC-------KPSDDSKKITVGILDFLME---ANIRLSEEvvNktrsfEKMRSEAERCLAQGEKLCDEKTEFESATY 193
Cdd:pfam06632 109 SFRLGSvklqkvpEPAEVIRELISYCLDCIAElqaKNEHLQKE--N-----ERLQRDWNDVTGRLEKCVKAKEELEADLY 181

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872  194 AKFLSVLNAKKAKLRALRDKEDSVRVVEEEESTDKAESFESGRSDDEKS--------EEEASKKATSSKA 255
Cdd:pfam06632 182 KRFILVLNEKKAKIRSLQKLLNELQESEESTEQKREDPATSDRTPDEESdydgstdeESENLPSPPSSKP 251
HD_XLF_N cd22285
N-terminal head domain found in XRCC4-like factor and similar proteins; XRCC4-like factor (XLF) ...
 39-131 1.27e-05

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: 43.07  E-value: 1.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872  39 FVKGTWHNSRFDISVTDGSSSWICNATEEEVAERAAQW----DQPVSEYLKLAEQYLGFQQPNSVYSFSDALEGSKrLSW 114
Cdd:cd22285   13 LIKFSFSDDSYEILLTDLVSVWSEELSRDEILKRAKELnpsiEAQLEELLEHLEDLLSGLDSDTTLSIEESNDKLK-LKL 91

                         90
                 ....*....|....*..
gi 238479872 115 TFEKEGTKLEWRWKCKP 131
Cdd:cd22285   92 KSKLPGVPFKWEFELQK 108
 
Name Accession Description Interval E-value
XRCC4 pfam06632
DNA double-strand break repair and V(D)J recombination protein XRCC4; This family consists of ...
 47-255 3.14e-10

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: 59.73  E-value: 3.14e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872   47 SRFDISVTDGSSSWICNATEEEVAERAAQWDQPVSEYLK-LAEQYLGFQQPNSVYSFSDALEGSKR--LSWTFEKEGTKL 123
Cdd:pfam06632  29 SGFDIILTDGQSAWTGTVSEEEISREADDMEMEREKYVDeLRKALTLGAEPAGKYNFDLSKDGPNPdcLHFSYEKVLKDV 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872  124 EWRWKC-------KPSDDSKKITVGILDFLME---ANIRLSEEvvNktrsfEKMRSEAERCLAQGEKLCDEKTEFESATY 193
Cdd:pfam06632 109 SFRLGSvklqkvpEPAEVIRELISYCLDCIAElqaKNEHLQKE--N-----ERLQRDWNDVTGRLEKCVKAKEELEADLY 181

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872  194 AKFLSVLNAKKAKLRALRDKEDSVRVVEEEESTDKAESFESGRSDDEKS--------EEEASKKATSSKA 255
Cdd:pfam06632 182 KRFILVLNEKKAKIRSLQKLLNELQESEESTEQKREDPATSDRTPDEESdydgstdeESENLPSPPSSKP 251
HD_XLF_N cd22285
N-terminal head domain found in XRCC4-like factor and similar proteins; XRCC4-like factor (XLF) ...
 39-131 1.27e-05

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: 43.07  E-value: 1.27e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872  39 FVKGTWHNSRFDISVTDGSSSWICNATEEEVAERAAQW----DQPVSEYLKLAEQYLGFQQPNSVYSFSDALEGSKrLSW 114
Cdd:cd22285   13 LIKFSFSDDSYEILLTDLVSVWSEELSRDEILKRAKELnpsiEAQLEELLEHLEDLLSGLDSDTTLSIEESNDKLK-LKL 91

                         90
                 ....*....|....*..
gi 238479872 115 TFEKEGTKLEWRWKCKP 131
Cdd:cd22285   92 KSKLPGVPFKWEFELQK 108
HD_XRCC4_N cd22283
N-terminal head domain found in X-ray repair cross-complementing protein 4 and similar ...
 29-136 1.98e-04

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: 39.95  E-value: 1.98e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 238479872  29 RLEISGAD-PIFVKGTWHN---SRFDISVTDGSSSWICNATEEEVAERAAQWDQPVSEYLKLAEQYLGFQ-QPNSVYSFs 103
Cdd:cd22283    6 RIELDSPGkTYYLLTSWKDegnDGFKLTLTDGESAWTGTVSEEDISQMAKKLKMSEEDYVEETKKALTGEaSGDSNFTF- 84

                         90       100       110
                 ....*....|....*....|....*....|...
gi 238479872 104 dalegskrlswTFEKEGTKLEWRWKCKPSDDSK 136
Cdd:cd22283   85 -----------QLKKEENSLEFSWKKVLDDDIK 106
 
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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