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Conserved domains on  [gi|15232092|ref|NP_189768|]
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Nucleic acid-binding proteins superfamily [Arabidopsis thaliana]

Protein Classification

replication protein A OB-fold DNA-binding domain-containing protein; single-stranded DNA-binding protein( domain architecture ID 10138918)

replication protein A (RPA) OB-fold DNA-binding domain-containing protein| single-stranded DNA (ssDNA)-binding protein plays a key role in DNA replication, recombination, and repair

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPA1_DBD_C cd04476
RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding ...
 110-252 1.73e-25

RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large 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). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding function of this domain. It appears that zinc itself may not be required for ssDNA binding.


:

Pssm-ID: 239922 [Multi-domain]  Cd Length: 166  Bit Score: 99.69  E-value: 1.73e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232092 110 FELQDLGLPPGR-EDLIHVDCEVKTNRlricfveaMPKWYYIAYKVCGKKVQPYPQGShgdaspiYSCGVCDCDVTNVNY 188
Cdd:cd04476   2 AEIKEENLGEGEkPDYFTVKATIVFIK--------PDNWWYPACPGCNKKVVEEGNGT-------YRCEKCNKSVPNPEY 66

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15232092 189 RYKLILRASYGaSPEVKLLIFDGLAQRLIGKTTAMLFAEVPEsDPSILSDVLADLMGKIHEMIV 252
Cdd:cd04476  67 RYILSLNVADH-TGEAWLTLFDEVAEQIFGKSAEELLELKEE-DPDAFPDAIQDLVGKTFLFRV 128
RPA1_DBD_A_like cd04480
RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB ...
 23-80 3.03e-13

RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large 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). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.


:

Pssm-ID: 239926 [Multi-domain]  Cd Length: 86  Bit Score: 64.20  E-value: 3.03e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15232092  23 KIKKRVVRLWRLF-----KSIEMVLVDGEGTRIHASIEEGLVKRFQHQLVNGESRIIDTFSFV 80
Cdd:cd04480   1 KICVRVLRLWDVYnnasgESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVA 63
 
Name Accession Description Interval E-value
RPA1_DBD_C cd04476
RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding ...
 110-252 1.73e-25

RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large 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). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding function of this domain. It appears that zinc itself may not be required for ssDNA binding.


Pssm-ID: 239922 [Multi-domain]  Cd Length: 166  Bit Score: 99.69  E-value: 1.73e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232092 110 FELQDLGLPPGR-EDLIHVDCEVKTNRlricfveaMPKWYYIAYKVCGKKVQPYPQGShgdaspiYSCGVCDCDVTNVNY 188
Cdd:cd04476   2 AEIKEENLGEGEkPDYFTVKATIVFIK--------PDNWWYPACPGCNKKVVEEGNGT-------YRCEKCNKSVPNPEY 66

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15232092 189 RYKLILRASYGaSPEVKLLIFDGLAQRLIGKTTAMLFAEVPEsDPSILSDVLADLMGKIHEMIV 252
Cdd:cd04476  67 RYILSLNVADH-TGEAWLTLFDEVAEQIFGKSAEELLELKEE-DPDAFPDAIQDLVGKTFLFRV 128
RPA1_DBD_A_like cd04480
RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB ...
 23-80 3.03e-13

RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large 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). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.


Pssm-ID: 239926 [Multi-domain]  Cd Length: 86  Bit Score: 64.20  E-value: 3.03e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15232092  23 KIKKRVVRLWRLF-----KSIEMVLVDGEGTRIHASIEEGLVKRFQHQLVNGESRIIDTFSFV 80
Cdd:cd04480   1 KICVRVLRLWDVYnnasgESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVA 63
DUF223 pfam02721
Domain of unknown function DUF223;
39-78 1.09e-03

Domain of unknown function DUF223;


Pssm-ID: 145722  Cd Length: 95  Bit Score: 37.66  E-value: 1.09e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 15232092    39 EMVLVDGEGTRIHASIEEGLVKRFQHQLVNGESRIIDTFS 78
Cdd:pfam02721   1 GLILADENGDKIEATIRRRLAAFYADRISEGEWKTITTFV 40
 
Name Accession Description Interval E-value
RPA1_DBD_C cd04476
RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding ...
 110-252 1.73e-25

RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large 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). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding function of this domain. It appears that zinc itself may not be required for ssDNA binding.


Pssm-ID: 239922 [Multi-domain]  Cd Length: 166  Bit Score: 99.69  E-value: 1.73e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15232092 110 FELQDLGLPPGR-EDLIHVDCEVKTNRlricfveaMPKWYYIAYKVCGKKVQPYPQGShgdaspiYSCGVCDCDVTNVNY 188
Cdd:cd04476   2 AEIKEENLGEGEkPDYFTVKATIVFIK--------PDNWWYPACPGCNKKVVEEGNGT-------YRCEKCNKSVPNPEY 66

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15232092 189 RYKLILRASYGaSPEVKLLIFDGLAQRLIGKTTAMLFAEVPEsDPSILSDVLADLMGKIHEMIV 252
Cdd:cd04476  67 RYILSLNVADH-TGEAWLTLFDEVAEQIFGKSAEELLELKEE-DPDAFPDAIQDLVGKTFLFRV 128
RPA1_DBD_A_like cd04480
RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB ...
 23-80 3.03e-13

RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large 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). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.


Pssm-ID: 239926 [Multi-domain]  Cd Length: 86  Bit Score: 64.20  E-value: 3.03e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15232092  23 KIKKRVVRLWRLF-----KSIEMVLVDGEGTRIHASIEEGLVKRFQHQLVNGESRIIDTFSFV 80
Cdd:cd04480   1 KICVRVLRLWDVYnnasgESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVA 63
DUF223 pfam02721
Domain of unknown function DUF223;
39-78 1.09e-03

Domain of unknown function DUF223;


Pssm-ID: 145722  Cd Length: 95  Bit Score: 37.66  E-value: 1.09e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 15232092    39 EMVLVDGEGTRIHASIEEGLVKRFQHQLVNGESRIIDTFS 78
Cdd:pfam02721   1 GLILADENGDKIEATIRRRLAAFYADRISEGEWKTITTFV 40
 
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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