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Conserved domains on  [gi|2200755242|pdb|1IN1|A]
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Chain A, DNA LIGASE III

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LIG3_BRCT pfam16759
DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT ...
 12-82 6.60e-38

DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT domain of the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1) and mediates homo- and heterodimerization.


:

Pssm-ID: 465260  Cd Length: 77  Bit Score: 121.32  E-value: 6.60e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
1IN1_A        12 VLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSRD------KNPAAQQVSPEWIWACIRKR 82
Cdd:pfam16759  1 PLPDIFTGVRLFLPPSVPDFSKLRRYFIAYDGDLVQEYDLDSATHVVVPKDsakekeESSGAKHVTASWIWECIKKR 77
 
Name Accession Description Interval E-value
LIG3_BRCT pfam16759
DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT ...
 12-82 6.60e-38

DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT domain of the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1) and mediates homo- and heterodimerization.


Pssm-ID: 465260  Cd Length: 77  Bit Score: 121.32  E-value: 6.60e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
1IN1_A        12 VLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSRD------KNPAAQQVSPEWIWACIRKR 82
Cdd:pfam16759  1 PLPDIFTGVRLFLPPSVPDFSKLRRYFIAYDGDLVQEYDLDSATHVVVPKDsakekeESSGAKHVTASWIWECIKKR 77
BRCT_DNA_ligase_III cd18431
BRCT domain of DNA ligase 3 (LIG3) and similar proteins; LIG3 (EC 6.5.1.1), also termed DNA ...
 13-86 2.12e-35

BRCT domain of DNA ligase 3 (LIG3) and similar proteins; LIG3 (EC 6.5.1.1), also termed DNA ligase III, or polydeoxyribonucleotide synthase [ATP] 3, functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents.


Pssm-ID: 349384 [Multi-domain]  Cd Length: 78  Bit Score: 115.10  E-value: 2.12e-35
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
1IN1_A      13 LLDIFTGVRLYLPPSTPD-FSRLRRYFVAFDGDLVQEFDMTSATHVLGSRD---KNPAAQQVSPEWIWACIRKRRLVA 86
Cdd:cd18431  1 LPDIFTGVKVYLPGSVEDdYKKLKRYFIAYDGDVVEEYDEEDATHVVVDRDdklGNPSAKVVSPEWLWDCIKKQKLVP 78
BRCT smart00292
breast cancer carboxy-terminal domain;
15-79 1.67e-08

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 46.98  E-value: 1.67e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
1IN1_A         15 DIFTGVRLYL--PPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSRDKNP-----AAQQ-----VSPEWIWACI 79
Cdd:smart00292  2 KLFKGKTFYItgSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGklellKAIAlgipiVKEEWLLDCL 78
 
Name Accession Description Interval E-value
LIG3_BRCT pfam16759
DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT ...
 12-82 6.60e-38

DNA ligase 3 BRCT domain; The BRCT domain of DNA ligase 3 (LIG3) binds to the C-terminal BRCT domain of the scaffolding protein X-ray repair cross-complementing protein 1 (XRCC1) and mediates homo- and heterodimerization.


Pssm-ID: 465260  Cd Length: 77  Bit Score: 121.32  E-value: 6.60e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
1IN1_A        12 VLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSRD------KNPAAQQVSPEWIWACIRKR 82
Cdd:pfam16759  1 PLPDIFTGVRLFLPPSVPDFSKLRRYFIAYDGDLVQEYDLDSATHVVVPKDsakekeESSGAKHVTASWIWECIKKR 77
BRCT_DNA_ligase_III cd18431
BRCT domain of DNA ligase 3 (LIG3) and similar proteins; LIG3 (EC 6.5.1.1), also termed DNA ...
 13-86 2.12e-35

BRCT domain of DNA ligase 3 (LIG3) and similar proteins; LIG3 (EC 6.5.1.1), also termed DNA ligase III, or polydeoxyribonucleotide synthase [ATP] 3, functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents.


Pssm-ID: 349384 [Multi-domain]  Cd Length: 78  Bit Score: 115.10  E-value: 2.12e-35
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
1IN1_A      13 LLDIFTGVRLYLPPSTPD-FSRLRRYFVAFDGDLVQEFDMTSATHVLGSRD---KNPAAQQVSPEWIWACIRKRRLVA 86
Cdd:cd18431  1 LPDIFTGVKVYLPGSVEDdYKKLKRYFIAYDGDVVEEYDEEDATHVVVDRDdklGNPSAKVVSPEWLWDCIKKQKLVP 78
BRCT_XRCC1_rpt2 cd17707
Second (C-terminal) BRCT domain in X-ray repair cross-complementing protein 1 (XRCC1) and ...
 13-88 1.54e-08

Second (C-terminal) BRCT domain in X-ray repair cross-complementing protein 1 (XRCC1) and similar proteins; XRCC1 is a DNA repair protein that corrects defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. It forms homodimers and interacts with polynucleotide kinase (PNK), DNA polymerase-beta (POLB), DNA ligase III (LIG3), APTX, APLF, and APEX1. XRCC1 contains an N-terminal XRCC1-specific domain and two BRCT domains. This model corresponds to the second BRCT domain.


Pssm-ID: 349340  Cd Length: 94  Bit Score: 47.26  E-value: 1.54e-08
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1IN1_A      13 LLDIFTGVRLYLPPSTPDFSR--LRRYFVAFDGdLVQEFDMTSATHVL--GSRDK--------NPAAQQVSPEWIWACIR 80
Cdd:cd17707  2 LPDFFSGKHFFLYGDFPADERrlLKRYITAFNG-EVEDYMSDKVTFVVtnQEWDDnfdealaeNPSLAFVRPRWIYACHE 80


               ....*...
1IN1_A      81 KRRLVaPC 88
Cdd:cd17707 81 KQKLL-PC 87
BRCT smart00292
breast cancer carboxy-terminal domain;
15-79 1.67e-08

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 46.98  E-value: 1.67e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
1IN1_A         15 DIFTGVRLYL--PPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSRDKNP-----AAQQ-----VSPEWIWACI 79
Cdd:smart00292  2 KLFKGKTFYItgSFDKEERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGklellKAIAlgipiVKEEWLLDCL 78
BRCT_2 pfam16589
BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found ...
 15-85 6.46e-08

BRCT domain, a BRCA1 C-terminus domain; This BRCT domain, a BRCA1 C-terminus region, is found on many RAP1 proteins, usually at the very N-terminus. The function in human at least of a BRCT is to contribute to the heterogeneity of the telomere DNA length, but that may not be its general function, which remains unknown.


Pssm-ID: 465186 [Multi-domain]  Cd Length: 84  Bit Score: 45.43  E-value: 6.46e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
1IN1_A        15 DIFTGVRLYL-PPSTPDFSRLRRYFVAFDGDLVQEFDmTSATHVLGSRDKNPAAQQ------VSPEWIWACIRKRRLV 85
Cdd:pfam16589  3 NLFEPLRFYInAIPSPSRSKLKRLIEANGGTVVDNIN-PAVYIVIAPYNKTDKLAEntklgvVSPQWIFDCVKKGKLL 79
BRCT_polymerase_lambda cd17715
BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed ...
 17-85 2.04e-06

BRCT domain of DNA polymerase lambda and similar proteins; DNA polymerase lambda, also termed Pol Lambda, or DNA polymerase beta-2 (Pol beta2), or DNA polymerase kappa, is involved in base excision repair (BER) and is responsible for repair of lesions that give rise to abasic (AP) sites in DNA. It also contributes to DNA double-strand break repair by non-homologous end joining and homologous recombination. DNA polymerase lambda has both template-dependent and template-independent (terminal transferase) DNA polymerase activities, as well as a 5'-deoxyribose-5-phosphate lyase (dRP lyase) activity. DNA polymerase lambda contains one BRCT domain.


Pssm-ID: 349347  Cd Length: 80  Bit Score: 41.71  E-value: 2.04e-06
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1IN1_A      17 FTGVRLYLPPSTPDFSR---LRRYFVAFDGDLVQEFDmTSATHVL---GSRDK------NPAAQQVSPEWIWACIRKRRL 84
Cdd:cd17715  1 FEGLTIHLVRTGIGRARaelFQRYIVQYGGQIVEDFG-EGVTHVVvddGMDAErkvdrdPPGAQLVKSGWLSACIQEKRL 79


               .
1IN1_A      85 V 85
Cdd:cd17715 80 V 80
BRCT_Rev1 cd17719
BRCT domain of DNA repair protein Rev1 and similar proteins; REV1, also termed alpha ...
 16-85 1.68e-05

BRCT domain of DNA repair protein Rev1 and similar proteins; REV1, also termed alpha integrin-binding protein 80, or AIBP80, or Rev1-like terminal deoxycytidyl transferase, is a DNA template-dependent dCMP transferase required for mutagenesis induced by UV light.


Pssm-ID: 349351 [Multi-domain]  Cd Length: 87  Bit Score: 39.09  E-value: 1.68e-05
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1IN1_A      16 IFTGVRLYLPPST-PDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSRDKNPAAQQ---------VSPEWIWACIRKRRLV 85
Cdd:cd17719  1 IFKGVVIYVNGYTdPSADELKRLILLHGGQYEHYYSRSRVTHIIATNLPGSKIKKlkkarnykvVRPEWIVDSIKAGRLL 80
BRCT cd00027
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 27-78 1.32e-03

C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The BRCT (BRCA1 C-terminus) domain is found within many DNA damage repair and cell cycle checkpoint proteins. BRCT domains interact with each other forming homo/hetero BRCT multimers, but are also involved in BRCT-non-BRCT interactions and interactions within DNA strand breaks. BRCT tandem repeats bind to phosphopeptides; it has been shown that the repeats in human BRCA1 bind specifically to pS-X-X-F motifs, mediating the interaction between BRCA1 and the DNA helicase BACH1, or BRCA1 and CtIP, a transcriptional corepressor. It is assumed that BRCT repeats play similar roles in many signaling pathways associated with the response to DNA damage.


Pssm-ID: 349339 [Multi-domain]  Cd Length: 68  Bit Score: 33.87  E-value: 1.32e-03
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|.
1IN1_A      27 STPDFSRLRRYFVAFDGDLVQEFDmTSATHVLGSRDKNPAAQQ---------VSPEWIWAC 78
Cdd:cd00027  9 DDEEREELKKLIEALGGKVSESLS-SKVTHLIAKSPSGEKYYLaalawgipiVSPEWLLDC 68
 
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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