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Conserved domains on  [gi|578832635|ref|XP_006722583|]
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DNA endonuclease RBBP8 isoform X1 [Homo sapiens]

Protein Classification

DNA endonuclease RBBP8( domain architecture ID 10564642)

DNA endonuclease RBBP8 similar to human RBBP8 that cooperates with the MRE11-RAD50-NBN complex in DNA-end resection, the first step of double-strand break (DSB) repair through the homologous recombination pathway

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CtIP_N pfam10482
Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that ...
 20-139 5.61e-63

Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. This N-terminal domain carries a coiled-coil region and is essential for homodimerization of the protein. The C-terminal domain is family pfam08573.


:

Pssm-ID: 463107 [Multi-domain]  Cd Length: 120  Bit Score: 207.98  E-value: 5.61e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635   20 FKDLWTKLKECHDREVQGLQVKVTKLKQERILDAQRLEEFFTKNQQLREQQKVLHETIKVLEDRLRAGLCDRCAVTEEHM 99
Cdd:pfam10482   1 FEELLNKLKEIHDKEVQGLQAKVSELKKERCLDAQRLEELFSKNQQLREQQKALQENIKVLENRLRAGLCDRCAVTQELA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 578832635  100 RKKQQEFENIRQQNLKLITELMNERNTLQEENKKLSEQLQ 139
Cdd:pfam10482  81 KKKQQEFENSQLQSLQHITILTNEMNTLKDENRKLKEELK 120
SAE2 pfam08573
DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing ...
 797-860 3.78e-14

DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling. SAE2 is homologous to the CtIP proteins in mammals and an homologous protein in plants. Crucial sequence motifs that are highly conserved are the CxxC and the RHR motifs in this C-terminal part of the protein. In budding yeast, genetic evidence suggests that the SAE2 protein is essential for the processing of hairpin DNA intermediates and meiotic double-strand breaks by Mre11/Rad50 complexes. SAE2 binds DNA and exhibits endonuclease activity on single-stranded DNA independently of Mre11/Rad50 complexes, but hairpin DNA structures are cleaved cooperatively in the presence of Mre11/Rad50 or Mre11/Rad50/Xrs2. Hairpin structures are not processed at the tip by SAE2 but rather at single-stranded DNA regions adjacent to the hairpin. The catalytic activities of SAE2 are important for its biological functions. Although proteins containing this domain were described as endonucleases, it is now known that they actually function as endonuclease activators. This domain contains highly conserved residues at its 15-residue extreme that are indispensable for MRN (Mre11-Rad50-Nbs1) complex activation, through the stimulation of Mre11 endonuclease activity.


:

Pssm-ID: 462525  Cd Length: 108  Bit Score: 69.31  E-value: 3.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635  797 EVVRKKEERRKLLGHTCKEC--EIYYA------------------------------DMPAEERE--------KKLASC- 835
Cdd:pfam08573   4 EVVRGKDERKCLPGCTCPCCcgDYFRAmaplpgrlrqkeedqklledylgdeayklgTMSAEEREellveaktRKLANKy 83

                          90       100
                  ....*....|....*....|....*
gi 578832635  836 SRHRFRYIPPNTPENFWEVGFPSTQ 860
Cdd:pfam08573  84 GRHRHHFERAPTPPGFWRTDFPSTQ 108
 
Name Accession Description Interval E-value
CtIP_N pfam10482
Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that ...
 20-139 5.61e-63

Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. This N-terminal domain carries a coiled-coil region and is essential for homodimerization of the protein. The C-terminal domain is family pfam08573.


Pssm-ID: 463107 [Multi-domain]  Cd Length: 120  Bit Score: 207.98  E-value: 5.61e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635   20 FKDLWTKLKECHDREVQGLQVKVTKLKQERILDAQRLEEFFTKNQQLREQQKVLHETIKVLEDRLRAGLCDRCAVTEEHM 99
Cdd:pfam10482   1 FEELLNKLKEIHDKEVQGLQAKVSELKKERCLDAQRLEELFSKNQQLREQQKALQENIKVLENRLRAGLCDRCAVTQELA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 578832635  100 RKKQQEFENIRQQNLKLITELMNERNTLQEENKKLSEQLQ 139
Cdd:pfam10482  81 KKKQQEFENSQLQSLQHITILTNEMNTLKDENRKLKEELK 120
SAE2 pfam08573
DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing ...
 797-860 3.78e-14

DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling. SAE2 is homologous to the CtIP proteins in mammals and an homologous protein in plants. Crucial sequence motifs that are highly conserved are the CxxC and the RHR motifs in this C-terminal part of the protein. In budding yeast, genetic evidence suggests that the SAE2 protein is essential for the processing of hairpin DNA intermediates and meiotic double-strand breaks by Mre11/Rad50 complexes. SAE2 binds DNA and exhibits endonuclease activity on single-stranded DNA independently of Mre11/Rad50 complexes, but hairpin DNA structures are cleaved cooperatively in the presence of Mre11/Rad50 or Mre11/Rad50/Xrs2. Hairpin structures are not processed at the tip by SAE2 but rather at single-stranded DNA regions adjacent to the hairpin. The catalytic activities of SAE2 are important for its biological functions. Although proteins containing this domain were described as endonucleases, it is now known that they actually function as endonuclease activators. This domain contains highly conserved residues at its 15-residue extreme that are indispensable for MRN (Mre11-Rad50-Nbs1) complex activation, through the stimulation of Mre11 endonuclease activity.


Pssm-ID: 462525  Cd Length: 108  Bit Score: 69.31  E-value: 3.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635  797 EVVRKKEERRKLLGHTCKEC--EIYYA------------------------------DMPAEERE--------KKLASC- 835
Cdd:pfam08573   4 EVVRGKDERKCLPGCTCPCCcgDYFRAmaplpgrlrqkeedqklledylgdeayklgTMSAEEREellveaktRKLANKy 83

                          90       100
                  ....*....|....*....|....*
gi 578832635  836 SRHRFRYIPPNTPENFWEVGFPSTQ 860
Cdd:pfam08573  84 GRHRHHFERAPTPPGFWRTDFPSTQ 108
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
34-152 2.40e-05

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 48.23  E-value: 2.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635  34 EVQGLQVKVTKLKQERILDAQRLEEFFTKNQQLRE---QQKVLHETIKVLEDRLRAGLCDRCAVTEEHMRKKQQEFENIR 110
Cdd:COG4717  126 QLLPLYQELEALEAELAELPERLEELEERLEELREleeELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEELQ 205

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 578832635 111 QQnlklITELMNERNTLQEENKKLSEQLQQkIENDQQHQAAE 152
Cdd:COG4717  206 QR----LAELEEELEEAQEELEELEEELEQ-LENELEAAALE 242
PRK12704 PRK12704
phosphodiesterase; Provisional
 21-153 6.31e-04

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 43.23  E-value: 6.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635  21 KDLWTKLKECHDREV----QGLQVKVTKLKQ-ERILDaQRLEEFFTKNQQLREQQKVLHETIKVLEdrlraglcdrcavt 95
Cdd:PRK12704  63 KEEIHKLRNEFEKELrerrNELQKLEKRLLQkEENLD-RKLELLEKREEELEKKEKELEQKQQELE-------------- 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 578832635  96 eehmrKKQQEFENIRQQNLKLITELMNerntLQEENKKlsEQLQQKIENDQQHQAAEL 153
Cdd:PRK12704 128 -----KKEEELEELIEEQLQELERISG----LTAEEAK--EILLEKVEEEARHEAAVL 174
 
Name Accession Description Interval E-value
CtIP_N pfam10482
Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that ...
 20-139 5.61e-63

Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. This N-terminal domain carries a coiled-coil region and is essential for homodimerization of the protein. The C-terminal domain is family pfam08573.


Pssm-ID: 463107 [Multi-domain]  Cd Length: 120  Bit Score: 207.98  E-value: 5.61e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635   20 FKDLWTKLKECHDREVQGLQVKVTKLKQERILDAQRLEEFFTKNQQLREQQKVLHETIKVLEDRLRAGLCDRCAVTEEHM 99
Cdd:pfam10482   1 FEELLNKLKEIHDKEVQGLQAKVSELKKERCLDAQRLEELFSKNQQLREQQKALQENIKVLENRLRAGLCDRCAVTQELA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 578832635  100 RKKQQEFENIRQQNLKLITELMNERNTLQEENKKLSEQLQ 139
Cdd:pfam10482  81 KKKQQEFENSQLQSLQHITILTNEMNTLKDENRKLKEELK 120
SAE2 pfam08573
DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing ...
 797-860 3.78e-14

DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling. SAE2 is homologous to the CtIP proteins in mammals and an homologous protein in plants. Crucial sequence motifs that are highly conserved are the CxxC and the RHR motifs in this C-terminal part of the protein. In budding yeast, genetic evidence suggests that the SAE2 protein is essential for the processing of hairpin DNA intermediates and meiotic double-strand breaks by Mre11/Rad50 complexes. SAE2 binds DNA and exhibits endonuclease activity on single-stranded DNA independently of Mre11/Rad50 complexes, but hairpin DNA structures are cleaved cooperatively in the presence of Mre11/Rad50 or Mre11/Rad50/Xrs2. Hairpin structures are not processed at the tip by SAE2 but rather at single-stranded DNA regions adjacent to the hairpin. The catalytic activities of SAE2 are important for its biological functions. Although proteins containing this domain were described as endonucleases, it is now known that they actually function as endonuclease activators. This domain contains highly conserved residues at its 15-residue extreme that are indispensable for MRN (Mre11-Rad50-Nbs1) complex activation, through the stimulation of Mre11 endonuclease activity.


Pssm-ID: 462525  Cd Length: 108  Bit Score: 69.31  E-value: 3.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635  797 EVVRKKEERRKLLGHTCKEC--EIYYA------------------------------DMPAEERE--------KKLASC- 835
Cdd:pfam08573   4 EVVRGKDERKCLPGCTCPCCcgDYFRAmaplpgrlrqkeedqklledylgdeayklgTMSAEEREellveaktRKLANKy 83

                          90       100
                  ....*....|....*....|....*
gi 578832635  836 SRHRFRYIPPNTPENFWEVGFPSTQ 860
Cdd:pfam08573  84 GRHRHHFERAPTPPGFWRTDFPSTQ 108
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
34-152 2.40e-05

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 48.23  E-value: 2.40e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635  34 EVQGLQVKVTKLKQERILDAQRLEEFFTKNQQLRE---QQKVLHETIKVLEDRLRAGLCDRCAVTEEHMRKKQQEFENIR 110
Cdd:COG4717  126 QLLPLYQELEALEAELAELPERLEELEERLEELREleeELEELEAELAELQEELEELLEQLSLATEEELQDLAEELEELQ 205

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 578832635 111 QQnlklITELMNERNTLQEENKKLSEQLQQkIENDQQHQAAE 152
Cdd:COG4717  206 QR----LAELEEELEEAQEELEELEEELEQ-LENELEAAALE 242
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
34-154 4.26e-04

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 43.74  E-value: 4.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635  34 EVQGLQVKVTKLKQERILDAQRLEEFFTKNQQLREQQKVLHETIKVLEDRLRAGLcDRCAVTEEHMRKKQQEFENIRQQn 113
Cdd:COG4372   39 ELDKLQEELEQLREELEQAREELEQLEEELEQARSELEQLEEELEELNEQLQAAQ-AELAQAQEELESLQEEAEELQEE- 116

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 578832635 114 lklITELMNERNTLQEENKKLSEQlQQKIENDQQHQAAELE 154
Cdd:COG4372  117 ---LEELQKERQDLEQQRKQLEAQ-IAELQSEIAEREEELK 153
PRK12704 PRK12704
phosphodiesterase; Provisional
 21-153 6.31e-04

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 43.23  E-value: 6.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635  21 KDLWTKLKECHDREV----QGLQVKVTKLKQ-ERILDaQRLEEFFTKNQQLREQQKVLHETIKVLEdrlraglcdrcavt 95
Cdd:PRK12704  63 KEEIHKLRNEFEKELrerrNELQKLEKRLLQkEENLD-RKLELLEKREEELEKKEKELEQKQQELE-------------- 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 578832635  96 eehmrKKQQEFENIRQQNLKLITELMNerntLQEENKKlsEQLQQKIENDQQHQAAEL 153
Cdd:PRK12704 128 -----KKEEELEELIEEQLQELERISG----LTAEEAK--EILLEKVEEEARHEAAVL 174
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
15-157 2.80e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 41.29  E-value: 2.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635  15 DTSSDFKDLWTKLKECHDREVQgLQVKVTKLKQERIL---DAQRLEEFFTKNQQLREQQKvLHETIKVLEDRLRAGLCDR 91
Cdd:COG4717  341 ELLDRIEELQELLREAEELEEE-LQLEELEQEIAALLaeaGVEDEEELRAALEQAEEYQE-LKEELEELEEQLEELLGEL 418

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 578832635  92 CAVTEEHMRKK-QQEFENIRQQnlklITELMNERNTLQEENKKLSEQLQQkIENDQQHQAAELECEE 157
Cdd:COG4717  419 EELLEALDEEElEEELEELEEE----LEELEEELEELREELAELEAELEQ-LEEDGELAELLQELEE 480
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
19-158 8.07e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 39.75  E-value: 8.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 578832635  19 DFKDLWTKLKEChDREVQGLQVKVTKLKQE--RILDAQRLEEFFTKNQQLREQQKVLHETIKVLEDRL--RAGLCDRCAV 94
Cdd:COG4717   89 EYAELQEELEEL-EEELEELEAELEELREEleKLEKLLQLLPLYQELEALEAELAELPERLEELEERLeeLRELEEELEE 167

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 578832635  95 TEEHMRKKQQEFENIRQQ----NLKLITELMNERNTLQEENKKLSEQLQQKIENDQQHQAAELECEED 158
Cdd:COG4717  168 LEAELAELQEELEELLEQlslaTEEELQDLAEELEELQQRLAELEEELEEAQEELEELEEELEQLENE 235
 
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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