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Conserved domains on  [gi|46854555|gb|AAH69791|]
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Replication protein A4, 34kDa [Homo sapiens]

Protein Classification

RPA2_DBD_D and RPA_C domain-containing protein( domain architecture ID 13423533)

RPA2_DBD_D and RPA_C domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPA2_DBD_D cd04478
RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding ...
 73-166 2.34e-31

RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro.


:

Pssm-ID: 239924  Cd Length: 95  Bit Score: 111.54  E-value: 2.34e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46854555  73 QVSIVGVIRGAEKASNHICYKIDDMTAkPIEARQWF--GREKVKQVTPLSVGVYVKVFGILKCPTGTKSLEVLKIHVLED 150
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTG-TIEVRQWLddDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTD 79

                        90
                ....*....|....*.
gi 46854555 151 MNEFTVHILETVNAHM 166
Cdd:cd04478  80 FNEVTYHLLEVIYVHL 95
RFA2 super family cl34949
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 32-259 3.28e-24

Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair];


The actual alignment was detected with superfamily member COG5235:

Pssm-ID: 227560 [Multi-domain]  Cd Length: 258  Bit Score: 97.74  E-value: 3.28e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46854555  32 PAIKTQRPKVRIQDVVPCNVNQLLSST--VFDPVFKVRGIIVSQVSIVGVIRGAEKASNHICYKIDDMTAKpIEARQWFG 109
Cdd:COG5235  25 PPMDRSEGGYIVNTLRPVTIKQILSCDqdETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIEDGTGS-IEVRFWPG 103

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46854555 110 RE-KVKQVTPLSVGVYVKVFGILKCPTGTKSLEVLKIHVLEDMNEFTVHILETVNAHMMLDKARRDTTVESVPVSPSEVN 188
Cdd:COG5235 104 NSyEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTRQLQRPLEEEVKNDGQSLF 183

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 46854555 189 DAGDNDESHRNF-IQDEVLRLIHECPHQEGKSIHELRAQLCD-LSVKAIKEAIDYLTVEGHIYPTVDREHFKS 259
Cdd:COG5235 184 AKLDNDTSSGSSrLQEDILECYRRNQDENGLHINVVIKMLSQsYSEDETRVNIDVLLRDGHIYPTVDGNEFKT 256
 
Name Accession Description Interval E-value
RPA2_DBD_D cd04478
RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding ...
 73-166 2.34e-31

RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro.


Pssm-ID: 239924  Cd Length: 95  Bit Score: 111.54  E-value: 2.34e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46854555  73 QVSIVGVIRGAEKASNHICYKIDDMTAkPIEARQWF--GREKVKQVTPLSVGVYVKVFGILKCPTGTKSLEVLKIHVLED 150
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTG-TIEVRQWLddDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTD 79

                        90
                ....*....|....*.
gi 46854555 151 MNEFTVHILETVNAHM 166
Cdd:cd04478  80 FNEVTYHLLEVIYVHL 95
RFA2 COG5235
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 32-259 3.28e-24

Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair];


Pssm-ID: 227560 [Multi-domain]  Cd Length: 258  Bit Score: 97.74  E-value: 3.28e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46854555  32 PAIKTQRPKVRIQDVVPCNVNQLLSST--VFDPVFKVRGIIVSQVSIVGVIRGAEKASNHICYKIDDMTAKpIEARQWFG 109
Cdd:COG5235  25 PPMDRSEGGYIVNTLRPVTIKQILSCDqdETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIEDGTGS-IEVRFWPG 103

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46854555 110 RE-KVKQVTPLSVGVYVKVFGILKCPTGTKSLEVLKIHVLEDMNEFTVHILETVNAHMMLDKARRDTTVESVPVSPSEVN 188
Cdd:COG5235 104 NSyEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTRQLQRPLEEEVKNDGQSLF 183

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 46854555 189 DAGDNDESHRNF-IQDEVLRLIHECPHQEGKSIHELRAQLCD-LSVKAIKEAIDYLTVEGHIYPTVDREHFKS 259
Cdd:COG5235 184 AKLDNDTSSGSSrLQEDILECYRRNQDENGLHINVVIKMLSQsYSEDETRVNIDVLLRDGHIYPTVDGNEFKT 256
RPA_C pfam08784
Replication protein A C terminal; This domain corresponds to the C terminal of the single ...
 202-253 3.36e-11

Replication protein A C terminal; This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.


Pssm-ID: 400920  Cd Length: 106  Bit Score: 58.54  E-value: 3.36e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 46854555   202 QDEVLRLIH-ECPHQEGKSIHELRAQLcDLSVKAIKEAIDYLTVEGHIYPTVD 253
Cdd:pfam08784  53 QDQVLNLIKqPPNGNEGVHVDEIAQRL-GLPVNDVKQAVDFLSNEGHIYSTID 104
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 74-148 4.62e-04

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.


Pssm-ID: 460164 [Multi-domain]  Cd Length: 75  Bit Score: 37.98  E-value: 4.62e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 46854555    74 VSIVGVIRGAEK-ASNHICYKIDDMTAKpIEARqWFGREKVKQVTPLSVGVYVKVFGILKC-PTGTKSLEVLKIHVL 148
Cdd:pfam01336   1 VTVAGRVTSIRRsGGKLLFLTLRDGTGS-IQVV-VFKEEAEKLAKKLKEGDVVRVTGKVKKrKGGELELVVEEIELL 75
 
Name Accession Description Interval E-value
RPA2_DBD_D cd04478
RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding ...
 73-166 2.34e-31

RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA damage. RPA2 interacts physically with menin; the gene encoding menin is a tumor suppressor gene disrupted in multiple endocrine neoplasia type I. This subfamily also includes RPA2 from Cryptosporidium parvum (CpRPA2). CpRPA2 is an SSB, which can be phosphorylated by DNA-PK in vitro.


Pssm-ID: 239924  Cd Length: 95  Bit Score: 111.54  E-value: 2.34e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46854555  73 QVSIVGVIRGAEKASNHICYKIDDMTAkPIEARQWF--GREKVKQVTPLSVGVYVKVFGILKCPTGTKSLEVLKIHVLED 150
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTG-TIEVRQWLddDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTD 79

                        90
                ....*....|....*.
gi 46854555 151 MNEFTVHILETVNAHM 166
Cdd:cd04478  80 FNEVTYHLLEVIYVHL 95
RFA2 COG5235
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 32-259 3.28e-24

Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair];


Pssm-ID: 227560 [Multi-domain]  Cd Length: 258  Bit Score: 97.74  E-value: 3.28e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46854555  32 PAIKTQRPKVRIQDVVPCNVNQLLSST--VFDPVFKVRGIIVSQVSIVGVIRGAEKASNHICYKIDDMTAKpIEARQWFG 109
Cdd:COG5235  25 PPMDRSEGGYIVNTLRPVTIKQILSCDqdETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIEDGTGS-IEVRFWPG 103

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46854555 110 RE-KVKQVTPLSVGVYVKVFGILKCPTGTKSLEVLKIHVLEDMNEFTVHILETVNAHMMLDKARRDTTVESVPVSPSEVN 188
Cdd:COG5235 104 NSyEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTRQLQRPLEEEVKNDGQSLF 183

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 46854555 189 DAGDNDESHRNF-IQDEVLRLIHECPHQEGKSIHELRAQLCD-LSVKAIKEAIDYLTVEGHIYPTVDREHFKS 259
Cdd:COG5235 184 AKLDNDTSSGSSrLQEDILECYRRNQDENGLHINVVIKMLSQsYSEDETRVNIDVLLRDGHIYPTVDGNEFKT 256
RPA_C pfam08784
Replication protein A C terminal; This domain corresponds to the C terminal of the single ...
 202-253 3.36e-11

Replication protein A C terminal; This domain corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints.


Pssm-ID: 400920  Cd Length: 106  Bit Score: 58.54  E-value: 3.36e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 46854555   202 QDEVLRLIH-ECPHQEGKSIHELRAQLcDLSVKAIKEAIDYLTVEGHIYPTVD 253
Cdd:pfam08784  53 QDQVLNLIKqPPNGNEGVHVDEIAQRL-GLPVNDVKQAVDFLSNEGHIYSTID 104
tRNA_anti-codon pfam01336
OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic ...
 74-148 4.62e-04

OB-fold nucleic acid binding domain; This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyze the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a hetero-trimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.


Pssm-ID: 460164 [Multi-domain]  Cd Length: 75  Bit Score: 37.98  E-value: 4.62e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 46854555    74 VSIVGVIRGAEK-ASNHICYKIDDMTAKpIEARqWFGREKVKQVTPLSVGVYVKVFGILKC-PTGTKSLEVLKIHVL 148
Cdd:pfam01336   1 VTVAGRVTSIRRsGGKLLFLTLRDGTGS-IQVV-VFKEEAEKLAKKLKEGDVVRVTGKVKKrKGGELELVVEEIELL 75
 
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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