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Conserved domains on  [gi|196049675|pdb|2VXB|B]
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Chain B, DNA REPAIR PROTEIN RHP9

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
BRCT_p53bp1_rpt1 cd17745
first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, ...
 2-107 1.75e-28

first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, also termed 53BP1, or TP53-binding protein 1 (TP53BP1) , is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis. TP53BP1 contains two tandem BRCT repeats. This family also includes Schizosaccharomyces pombe Crb2, which is a checkpoint mediator required for the cellular response to DNA damage. This model corresponds to the first BRCT domain.


:

Pssm-ID: 349376 [Multi-domain]  Cd Length: 99  Bit Score: 103.54  E-value: 1.75e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2VXB_B        2 IFDDCVFAFSGPVHEDA-YDRSALETVVQDHGGLVLDTGLRPLFNDPfkskqkklRHLKPQKRSKSWNQAFVVSDTFSRK 80
Cdd:cd17745   1 IFSGCAFLLTGAEETDKpFDKERLESQIEANGGTVLEDFDEELFNDG--------RSSTRKSRSKDLRFVFLIADSPSRT 72

                        90       100
                ....*....|....*....|....*..
2VXB_B       81 VKYLEALAFNIPCVHPQFIKQCLKMNR 107
Cdd:cd17745  73 PKYLQALALGIPCVSHKWILDCIEAGK 99
BRCT super family cl00038
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 204-236 9.20e-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.


The actual alignment was detected with superfamily member cd17724:

Pssm-ID: 469589  Cd Length: 87  Bit Score: 34.27  E-value: 9.20e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
2VXB_B      204 ECDLILTMDG------NIVDETNCPVVDPEWIVECLISQ 236
Cdd:cd17724  49 KIDVVVTDGScpstvlKKARQLGIPVVSTEWVIQCLING 87
 
Name Accession Description Interval E-value
BRCT_p53bp1_rpt1 cd17745
first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, ...
 2-107 1.75e-28

first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, also termed 53BP1, or TP53-binding protein 1 (TP53BP1) , is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis. TP53BP1 contains two tandem BRCT repeats. This family also includes Schizosaccharomyces pombe Crb2, which is a checkpoint mediator required for the cellular response to DNA damage. This model corresponds to the first BRCT domain.


Pssm-ID: 349376 [Multi-domain]  Cd Length: 99  Bit Score: 103.54  E-value: 1.75e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2VXB_B        2 IFDDCVFAFSGPVHEDA-YDRSALETVVQDHGGLVLDTGLRPLFNDPfkskqkklRHLKPQKRSKSWNQAFVVSDTFSRK 80
Cdd:cd17745   1 IFSGCAFLLTGAEETDKpFDKERLESQIEANGGTVLEDFDEELFNDG--------RSSTRKSRSKDLRFVFLIADSPSRT 72

                        90       100
                ....*....|....*....|....*..
2VXB_B       81 VKYLEALAFNIPCVHPQFIKQCLKMNR 107
Cdd:cd17745  73 PKYLQALALGIPCVSHKWILDCIEAGK 99
BRCT smart00292
breast cancer carboxy-terminal domain;
2-103 2.95e-10

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 55.07  E-value: 2.95e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2VXB_B           2 IFDDCVFAFSGpvHEDAYDRSALETVVQDHGGLVLDTGlrplfndpfkskqkklrhlkpqkrSKSWNQAFVVSDTFSRKV 81
Cdd:smart00292   3 LFKGKTFYITG--SFDKEERDELKELIEALGGKVTSSL------------------------SSKTTTHVIVGSPEGGKL 56

                           90       100
                   ....*....|....*....|..
2VXB_B          82 KYLEALAFNIPCVHPQFIKQCL 103
Cdd:smart00292  57 ELLKAIALGIPIVKEEWLLDCL 78
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 2-103 2.76e-04

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 38.43  E-value: 2.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2VXB_B          2 IFDDCVFAFSGpvhEDAYDRSALETVVQDHGGlvldtglrplfndpfkskqkklrhlkpqKRSKSWNQA--FVVSDtfSR 79
Cdd:pfam00533   5 LFSGKTFVITG---LDGLERDELKELIEKLGG----------------------------KVTDSLSKKttHVIVE--AR 51

                          90       100
                  ....*....|....*....|....
2VXB_B         80 KVKYLEALAFNIPCVHPQFIKQCL 103
Cdd:pfam00533  52 TKKYLKAKELGIPIVTEEWLLDCI 75
BRCT_p53bp1_rpt2 cd17724
Second (C-terminal) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, ...
 204-236 9.20e-03

Second (C-terminal) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, also termed 53BP1, or TP53-binding protein 1 (TP53BP1) , is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics, and class-switch recombination (CSR) during antibody genesis. TP53BP1 contains two tandem BRCT repeats. This family corresponds to the second BRCT domain.


Pssm-ID: 349356  Cd Length: 87  Bit Score: 34.27  E-value: 9.20e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
2VXB_B      204 ECDLILTMDG------NIVDETNCPVVDPEWIVECLISQ 236
Cdd:cd17724  49 KIDVVVTDGScpstvlKKARQLGIPVVSTEWVIQCLING 87
 
Name Accession Description Interval E-value
BRCT_p53bp1_rpt1 cd17745
first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, ...
 2-107 1.75e-28

first (central) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, also termed 53BP1, or TP53-binding protein 1 (TP53BP1) , is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics and class-switch recombination (CSR) during antibody genesis. TP53BP1 contains two tandem BRCT repeats. This family also includes Schizosaccharomyces pombe Crb2, which is a checkpoint mediator required for the cellular response to DNA damage. This model corresponds to the first BRCT domain.


Pssm-ID: 349376 [Multi-domain]  Cd Length: 99  Bit Score: 103.54  E-value: 1.75e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2VXB_B        2 IFDDCVFAFSGPVHEDA-YDRSALETVVQDHGGLVLDTGLRPLFNDPfkskqkklRHLKPQKRSKSWNQAFVVSDTFSRK 80
Cdd:cd17745   1 IFSGCAFLLTGAEETDKpFDKERLESQIEANGGTVLEDFDEELFNDG--------RSSTRKSRSKDLRFVFLIADSPSRT 72

                        90       100
                ....*....|....*....|....*..
2VXB_B       81 VKYLEALAFNIPCVHPQFIKQCLKMNR 107
Cdd:cd17745  73 PKYLQALALGIPCVSHKWILDCIEAGK 99
BRCT smart00292
breast cancer carboxy-terminal domain;
2-103 2.95e-10

breast cancer carboxy-terminal domain;


Pssm-ID: 214602 [Multi-domain]  Cd Length: 78  Bit Score: 55.07  E-value: 2.95e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2VXB_B           2 IFDDCVFAFSGpvHEDAYDRSALETVVQDHGGLVLDTGlrplfndpfkskqkklrhlkpqkrSKSWNQAFVVSDTFSRKV 81
Cdd:smart00292   3 LFKGKTFYITG--SFDKEERDELKELIEALGGKVTSSL------------------------SSKTTTHVIVGSPEGGKL 56

                           90       100
                   ....*....|....*....|..
2VXB_B          82 KYLEALAFNIPCVHPQFIKQCL 103
Cdd:smart00292  57 ELLKAIALGIPIVKEEWLLDCL 78
BRCT cd00027
C-terminal domain of the breast cancer suppressor protein (BRCA1) and related domains; The ...
 6-102 2.87e-05

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: 40.81  E-value: 2.87e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2VXB_B        6 CVFAFSGPVHEDaydRSALETVVQDHGGLVLdtglrplfndpfKSKQKKLRHLkpqkrskswnqafvVSDTFSRKVKYLE 85
Cdd:cd00027   1 LVICFSGLDDEE---REELKKLIEALGGKVS------------ESLSSKVTHL--------------IAKSPSGEKYYLA 51

                        90
                ....*....|....*..
2VXB_B       86 ALAFNIPCVHPQFIKQC 102
Cdd:cd00027  52 ALAWGIPIVSPEWLLDC 68
BRCT_MDC1_rpt1 cd17744
first BRCT domain of mediator of DNA damage checkpoint protein 1 (MDC1) and similar proteins; ...
 72-109 4.54e-05

first BRCT domain of mediator of DNA damage checkpoint protein 1 (MDC1) and similar proteins; MDC1, also termed nuclear factor with BRCT domains 1 (NFBD1), is a nuclear chromatin-associated protein that is required for checkpoint mediated cell cycle arrest in response to DNA damage within both the S phase and G2/M phases of the cell cycle. It directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. MDC1 contains a forkhead-associated (FHA) domain and two BRCT domains, as well as an internal 41-amino acid repeat sequence. The family corresponds to the first BRCT domain.


Pssm-ID: 349375 [Multi-domain]  Cd Length: 72  Bit Score: 40.68  E-value: 4.54e-05
                        10        20        30
                ....*....|....*....|....*....|....*...
2VXB_B       72 VVSDTFSRKVKYLEALAFNIPCVHPQFIKQCLKMNRVV 109
Cdd:cd17744  35 LVTDKVRRTVKFLCALARGIPIVSPDWLEASIKANKFL 72
BRCT pfam00533
BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in ...
 2-103 2.76e-04

BRCA1 C Terminus (BRCT) domain; The BRCT domain is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage. The BRCT domain of XRCC1 forms a homodimer in the crystal structure. This suggests that pairs of BRCT domains associate as homo- or heterodimers. BRCT domains are often found as tandem-repeat pairs. Structures of the BRCA1 BRCT domains revealed a basis for a widely utilized head-to-tail BRCT-BRCT oligomerization mode. This conserved tandem BRCT architecture facilitates formation of the canonical BRCT phospho-peptide interaction cleft at a groove between the BRCT domains. Disease associated missense and nonsense mutations in the BRCA1 BRCT domains disrupt peptide binding by directly occluding this peptide binding groove, or by disrupting key conserved BRCT core folding determinants.


Pssm-ID: 425736 [Multi-domain]  Cd Length: 75  Bit Score: 38.43  E-value: 2.76e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2VXB_B          2 IFDDCVFAFSGpvhEDAYDRSALETVVQDHGGlvldtglrplfndpfkskqkklrhlkpqKRSKSWNQA--FVVSDtfSR 79
Cdd:pfam00533   5 LFSGKTFVITG---LDGLERDELKELIEKLGG----------------------------KVTDSLSKKttHVIVE--AR 51

                          90       100
                  ....*....|....*....|....
2VXB_B         80 KVKYLEALAFNIPCVHPQFIKQCL 103
Cdd:pfam00533  52 TKKYLKAKELGIPIVTEEWLLDCI 75
RTT107_BRCT_5 pfam16770
Regulator of Ty1 transposition protein 107 BRCT domain; This is the fifth BRCT domain of ...
 79-116 4.74e-04

Regulator of Ty1 transposition protein 107 BRCT domain; This is the fifth BRCT domain of regulator of Ty1 transposition protein 107 (RTT107). It is involved in binding phosphorylated histone H2A.


Pssm-ID: 465266  Cd Length: 91  Bit Score: 38.27  E-value: 4.74e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
2VXB_B         79 RKVKYLEALAFNIPCVHPQFIKQCLKMNRVVDFSPYLL 116
Cdd:pfam16770  54 RTEKFLCALAFAPYILSPDFITDCLKEGKLPDEEDYLL 91
BRCT_p53bp1_rpt2 cd17724
Second (C-terminal) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, ...
 204-236 9.20e-03

Second (C-terminal) BRCT domain in p53-binding protein 1 (p53BP1) and similar proteins; p53BP1, also termed 53BP1, or TP53-binding protein 1 (TP53BP1) , is a double-strand break (DSB) repair protein involved in response to DNA damage, telomere dynamics, and class-switch recombination (CSR) during antibody genesis. TP53BP1 contains two tandem BRCT repeats. This family corresponds to the second BRCT domain.


Pssm-ID: 349356  Cd Length: 87  Bit Score: 34.27  E-value: 9.20e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
2VXB_B      204 ECDLILTMDG------NIVDETNCPVVDPEWIVECLISQ 236
Cdd:cd17724  49 KIDVVVTDGScpstvlKKARQLGIPVVSTEWVIQCLING 87
 
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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