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Conserved domains on  [gi|1576727548|ref|NP_001355634|]
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DNA damage-induced apoptosis suppressor protein [Mus musculus]

Protein Classification

single stranded DNA-binding domain-containing protein( domain architecture ID 489)

single stranded DNA-binding domain-containing protein may bind preferentially to single-stranded DNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RPA_2b-aaRSs_OBF_like super family cl09930
Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with ...
 8-102 1.49e-14

Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with oligonucleotide/oligosaccharide (OB) fold.; This superfamily includes two oligonucleotide/oligosaccharide binding fold (OBF) domain families. One of these contains the OBF domains of the large (RPA1, 70kDa), middle (RPA2, RPA4, 32kDa) and small (RPA3, 14 kDa) subunits of human heterotrimeric Replication protein A (RPA), and similar domains. RPA is a nuclear single-strand (ss) DNA-binding protein involved in most aspects of DNA metabolism. This family includes the four OBF domains of RPA1 [DNA-binding domain (DBD)-A, DBD-B, DBD-C, and RPA1N], the OBF domain of RPA2 (RPA2 DBD-D), RPA3, and the OBF domain of RPA4. The major DNA binding activity of human RPA and Saccharomyces cerevisiae RPA appears to be associated with DBD-A and -B, of RPA1. RPA1 DBD-C shows only weak ssDNA-binding activity and is involved in trimerization. The other OBF domain family in this superfamily is the N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids to their cognate tRNAs during protein biosynthesis. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases.


The actual alignment was detected with superfamily member cd04476:

Pssm-ID: 471953 [Multi-domain]  Cd Length: 166  Bit Score: 72.34  E-value: 1.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1576727548   8 LFASVLAVQNWNFIYPSCQRCFSKIILESK-RFTCPKCGSSGDTgsTNYRYKLSLKVAESSKLFFITVFGSCLDTFFGLT 86
Cdd:cd04476    20 VKATIVFIKPDNWWYPACPGCNKKVVEEGNgTYRCEKCNKSVPN--PEYRYILSLNVADHTGEAWLTLFDEVAEQIFGKS 97

                          90
                  ....*....|....*.
gi 1576727548  87 ATGLHRYLEDSIKNLE 102
Cdd:cd04476    98 AEELLELKEEDPDAFP 113
 
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 ...
 8-102 1.49e-14

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: 72.34  E-value: 1.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1576727548   8 LFASVLAVQNWNFIYPSCQRCFSKIILESK-RFTCPKCGSSGDTgsTNYRYKLSLKVAESSKLFFITVFGSCLDTFFGLT 86
Cdd:cd04476    20 VKATIVFIKPDNWWYPACPGCNKKVVEEGNgTYRCEKCNKSVPN--PEYRYILSLNVADHTGEAWLTLFDEVAEQIFGKS 97

                          90
                  ....*....|....*.
gi 1576727548  87 ATGLHRYLEDSIKNLE 102
Cdd:cd04476    98 AEELLELKEEDPDAFP 113
Rep_fac-A_C pfam08646
Replication factor-A C terminal domain; This domain is found at the C terminal of replication ...
 10-95 2.78e-05

Replication factor-A C terminal domain; This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA.


Pssm-ID: 462546 [Multi-domain]  Cd Length: 146  Bit Score: 44.91  E-value: 2.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1576727548  10 ASVLAVQNWNFIYPSCQR--CFSKIILE-SKRFTCPKCGSSGDTgsTNYRYKLSLKVAESSKLFFITVFGSCLDTFFGLT 86
Cdd:pfam08646   6 ATVVFIKQDNFWYPACPSedCNKKVVEQgDGTWRCEKCDKNFPE--PKYRYILSINVSDHTGQLWVTLFNEAAEKILGKS 83


                  ....*....
gi 1576727548  87 ATGLHRYLE 95
Cdd:pfam08646  84 ADELMKLKE 92
 
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 ...
 8-102 1.49e-14

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: 72.34  E-value: 1.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1576727548   8 LFASVLAVQNWNFIYPSCQRCFSKIILESK-RFTCPKCGSSGDTgsTNYRYKLSLKVAESSKLFFITVFGSCLDTFFGLT 86
Cdd:cd04476    20 VKATIVFIKPDNWWYPACPGCNKKVVEEGNgTYRCEKCNKSVPN--PEYRYILSLNVADHTGEAWLTLFDEVAEQIFGKS 97

                          90
                  ....*....|....*.
gi 1576727548  87 ATGLHRYLEDSIKNLE 102
Cdd:cd04476    98 AEELLELKEEDPDAFP 113
Rep_fac-A_C pfam08646
Replication factor-A C terminal domain; This domain is found at the C terminal of replication ...
 10-95 2.78e-05

Replication factor-A C terminal domain; This domain is found at the C terminal of replication factor A. Replication factor A (RPA) binds single-stranded DNA and is involved in replication, repair, and recombination of DNA.


Pssm-ID: 462546 [Multi-domain]  Cd Length: 146  Bit Score: 44.91  E-value: 2.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1576727548  10 ASVLAVQNWNFIYPSCQR--CFSKIILE-SKRFTCPKCGSSGDTgsTNYRYKLSLKVAESSKLFFITVFGSCLDTFFGLT 86
Cdd:pfam08646   6 ATVVFIKQDNFWYPACPSedCNKKVVEQgDGTWRCEKCDKNFPE--PKYRYILSINVSDHTGQLWVTLFNEAAEKILGKS 83


                  ....*....
gi 1576727548  87 ATGLHRYLE 95
Cdd:pfam08646  84 ADELMKLKE 92
 
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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