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Conserved domains on  [gi|51036584|ref|NP_067593|]
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replication protein A 32 kDa subunit isoform 1 [Rattus norvegicus]

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 ...
 73-167 2.13e-42

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: 140.04  E-value: 2.13e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584  73 QVTIVGIIRHAEKAPTNIVYKIDDMTAaPMDVRQWVDTD-DTSGENTVVPPETYVKVAGHLRSFQNKKSLVAFKIIPLED 151
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTG-TIEVRQWLDDDnDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTD 79

                        90
                ....*....|....*.
gi 51036584 152 MNEFTAHILEVVNSHL 167
Cdd:cd04478  80 FNEVTYHLLEVIYVHL 95
RFA2 super family cl34949
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 25-267 3.99e-36

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: 129.32  E-value: 3.99e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584  25 GGF---GSPTPSQaEKKSRARAQHIVPCTISQLLSAT--LTDEVFKIGDVEISQVTIVGIIRHAEKAPTNIVYKIDDMTA 99
Cdd:COG5235  16 GQIfgtGSPPPMD-RSEGGYIVNTLRPVTIKQILSCDqdETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIEDGTG 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584 100 ApMDVRQWVDTDDTSGENTVVPPETYVKVAGHLRSFQNKKSLVAFKIIPLEDMNEFTAHILEVVNSHLMLSKansqaSVG 179
Cdd:COG5235  95 S-IEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTR-----QLQ 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584 180 RPSMSN-PGMGEpGNFSGNNFMPANGLTVVQNQVLNLIKACPRPEGLNFQDLRSQL-QHMPVASIKQAVDFLCNEGHIYS 257
Cdd:COG5235 169 RPLEEEvKNDGQ-SLFAKLDNDTSSGSSRLQEDILECYRRNQDENGLHINVVIKMLsQSYSEDETRVNIDVLLRDGHIYP 247

                       250
                ....*....|
gi 51036584 258 TVDDDHFKST 267
Cdd:COG5235 248 TVDGNEFKTT 257
 
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 ...
 73-167 2.13e-42

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: 140.04  E-value: 2.13e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584  73 QVTIVGIIRHAEKAPTNIVYKIDDMTAaPMDVRQWVDTD-DTSGENTVVPPETYVKVAGHLRSFQNKKSLVAFKIIPLED 151
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTG-TIEVRQWLDDDnDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTD 79

                        90
                ....*....|....*.
gi 51036584 152 MNEFTAHILEVVNSHL 167
Cdd:cd04478  80 FNEVTYHLLEVIYVHL 95
RFA2 COG5235
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 25-267 3.99e-36

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: 129.32  E-value: 3.99e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584  25 GGF---GSPTPSQaEKKSRARAQHIVPCTISQLLSAT--LTDEVFKIGDVEISQVTIVGIIRHAEKAPTNIVYKIDDMTA 99
Cdd:COG5235  16 GQIfgtGSPPPMD-RSEGGYIVNTLRPVTIKQILSCDqdETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIEDGTG 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584 100 ApMDVRQWVDTDDTSGENTVVPPETYVKVAGHLRSFQNKKSLVAFKIIPLEDMNEFTAHILEVVNSHLMLSKansqaSVG 179
Cdd:COG5235  95 S-IEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTR-----QLQ 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584 180 RPSMSN-PGMGEpGNFSGNNFMPANGLTVVQNQVLNLIKACPRPEGLNFQDLRSQL-QHMPVASIKQAVDFLCNEGHIYS 257
Cdd:COG5235 169 RPLEEEvKNDGQ-SLFAKLDNDTSSGSSRLQEDILECYRRNQDENGLHINVVIKMLsQSYSEDETRVNIDVLLRDGHIYP 247

                       250
                ....*....|
gi 51036584 258 TVDDDHFKST 267
Cdd:COG5235 248 TVDGNEFKTT 257
RPA_C pfam08784
Replication protein A C terminal; This domain corresponds to the C terminal of the single ...
 166-262 1.36e-28

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: 105.15  E-value: 1.36e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584   166 HLMLSKANSQASVG-----RPSMSNPGMGEPGNFSGNNFMPAN----GLTVVQNQVLNLIK-ACPRPEGLNFQDLRSQLq 235
Cdd:pfam08784   1 HLFLTKGASGSSGGgattpAVSNGGSSMGTQGAYSGGDASVVNanngGLTPLQDQVLNLIKqPPNGNEGVHVDEIAQRL- 79

                          90       100
                  ....*....|....*....|....*..
gi 51036584   236 HMPVASIKQAVDFLCNEGHIYSTVDDD 262
Cdd:pfam08784  80 GLPVNDVKQAVDFLSNEGHIYSTIDDD 106
 
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 ...
 73-167 2.13e-42

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: 140.04  E-value: 2.13e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584  73 QVTIVGIIRHAEKAPTNIVYKIDDMTAaPMDVRQWVDTD-DTSGENTVVPPETYVKVAGHLRSFQNKKSLVAFKIIPLED 151
Cdd:cd04478   1 QVTLVGVVRNVEEQSTNITYTIDDGTG-TIEVRQWLDDDnDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAFSIRPVTD 79

                        90
                ....*....|....*.
gi 51036584 152 MNEFTAHILEVVNSHL 167
Cdd:cd04478  80 FNEVTYHLLEVIYVHL 95
RFA2 COG5235
Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA ...
 25-267 3.99e-36

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: 129.32  E-value: 3.99e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584  25 GGF---GSPTPSQaEKKSRARAQHIVPCTISQLLSAT--LTDEVFKIGDVEISQVTIVGIIRHAEKAPTNIVYKIDDMTA 99
Cdd:COG5235  16 GQIfgtGSPPPMD-RSEGGYIVNTLRPVTIKQILSCDqdETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIEDGTG 94

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584 100 ApMDVRQWVDTDDTSGENTVVPPETYVKVAGHLRSFQNKKSLVAFKIIPLEDMNEFTAHILEVVNSHLMLSKansqaSVG 179
Cdd:COG5235  95 S-IEVRFWPGNSYEEEQCKDLEEQNYVKVNGSLKTFNGKRSISASHISAIEDSNEVTYHFLECIYQHLFYTR-----QLQ 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584 180 RPSMSN-PGMGEpGNFSGNNFMPANGLTVVQNQVLNLIKACPRPEGLNFQDLRSQL-QHMPVASIKQAVDFLCNEGHIYS 257
Cdd:COG5235 169 RPLEEEvKNDGQ-SLFAKLDNDTSSGSSRLQEDILECYRRNQDENGLHINVVIKMLsQSYSEDETRVNIDVLLRDGHIYP 247

                       250
                ....*....|
gi 51036584 258 TVDDDHFKST 267
Cdd:COG5235 248 TVDGNEFKTT 257
RPA_C pfam08784
Replication protein A C terminal; This domain corresponds to the C terminal of the single ...
 166-262 1.36e-28

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: 105.15  E-value: 1.36e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 51036584   166 HLMLSKANSQASVG-----RPSMSNPGMGEPGNFSGNNFMPAN----GLTVVQNQVLNLIK-ACPRPEGLNFQDLRSQLq 235
Cdd:pfam08784   1 HLFLTKGASGSSGGgattpAVSNGGSSMGTQGAYSGGDASVVNanngGLTPLQDQVLNLIKqPPNGNEGVHVDEIAQRL- 79

                          90       100
                  ....*....|....*....|....*..
gi 51036584   236 HMPVASIKQAVDFLCNEGHIYSTVDDD 262
Cdd:pfam08784  80 GLPVNDVKQAVDFLSNEGHIYSTIDDD 106
RPA2_OBF_family cd03524
RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold ...
 75-148 5.90e-07

RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-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). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyrococcus abyssi DNA polymerase II (Pol II) small subunit, Sulfolobus solfataricus SSB, and Bacillus subtilis YhaM (a 3'-to-5'exoribonuclease). It also includes the OB folds of breast cancer susceptibility gene 2 protein (BRCA2), Oxytricha nova telomere end binding protein (TEBP), Saccharomyces cerevisiae telomere-binding protein (Cdc13), and human protection of telomeres 1 protein (POT1).


Pssm-ID: 239601 [Multi-domain]  Cd Length: 75  Bit Score: 46.20  E-value: 5.90e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 51036584  75 TIVGIIRHAEKAPTN---IVYKIDDMTAAPMDVRQWVDTDDTSgeNTVVPPETYVKVAGHLRSFQNKKSLVAFKIIP 148
Cdd:cd03524   1 TIVGIVVAVEEIRTEgkvLIFTLTDGTGGTIRVTLFGELAEEL--ENLLKEGQVVYIKGKVKKFRGRLQLIVESIEL 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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