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Conserved domains on  [gi|79507214|ref|NP_196249|]
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Nucleic acid-binding, OB-fold-like protein [Arabidopsis thaliana]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 10139716)

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
hPOT1_OB1_like cd04497
hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection ...
 9-143 1.02e-41

hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. A second OB fold has not been predicted in S. pombe POT1. OnTEBP binds the extreme 3-prime end of telomeric DNA. It is heterodimeric and contains four OB folds - three in the alpha subunit (two in the N-terminal domain and one in the C-terminal domain) and one in the beta subunit. OB1Nalpha, together with the second OB fold of the N-terminal domain of OnTEBP alpha subunit and the beta subunit OB fold, forms a deep cleft that binds ssDNA.


:

Pssm-ID: 239943  Cd Length: 138  Bit Score: 144.73  E-value: 1.02e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79507214   9 YKFLRIQDAFKALHLHVNLIGVIVELGF---SNGSDCSCTLKIVDPW-YSGSGLPVKFVARTIRDLPRVeSIGDIILLSR 84
Cdd:cd04497   1 YKYTPLSSALKESGGSVNVIGVVVDAGPpvrSKGTDYCCTLTITDPSlANSDGLTVKLFRPNEESLPIV-KVGDIILLRR 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 79507214  85 VKIVLINRKITALCNETtSSSFALFNGKHSVDSIPYQSSPKFLMREQDKNFLSNLREWM 143
Cdd:cd04497  80 VKIQSYNGKPQGISNDR-GSSWAVFRGDDGVVPIPQQSSKPVEFGPEEEPSVEELRKWA 137
RPA_2b-aaRSs_OBF_like super family cl09930
Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with ...
 158-196 1.74e-05

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 pfam16686:

Pssm-ID: 471953  Cd Length: 152  Bit Score: 44.57  E-value: 1.74e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 79507214   158 LKDIKEGECSNLSCQIVHISKVYKDRWYLFVWDGTEMPP 196
Cdd:pfam16686   1 LKDVQPGQFFDLIVQVVKKAYDDGGKVLLYVWDYTENPP 39
 
Name Accession Description Interval E-value
hPOT1_OB1_like cd04497
hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection ...
 9-143 1.02e-41

hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. A second OB fold has not been predicted in S. pombe POT1. OnTEBP binds the extreme 3-prime end of telomeric DNA. It is heterodimeric and contains four OB folds - three in the alpha subunit (two in the N-terminal domain and one in the C-terminal domain) and one in the beta subunit. OB1Nalpha, together with the second OB fold of the N-terminal domain of OnTEBP alpha subunit and the beta subunit OB fold, forms a deep cleft that binds ssDNA.


Pssm-ID: 239943  Cd Length: 138  Bit Score: 144.73  E-value: 1.02e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79507214   9 YKFLRIQDAFKALHLHVNLIGVIVELGF---SNGSDCSCTLKIVDPW-YSGSGLPVKFVARTIRDLPRVeSIGDIILLSR 84
Cdd:cd04497   1 YKYTPLSSALKESGGSVNVIGVVVDAGPpvrSKGTDYCCTLTITDPSlANSDGLTVKLFRPNEESLPIV-KVGDIILLRR 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 79507214  85 VKIVLINRKITALCNETtSSSFALFNGKHSVDSIPYQSSPKFLMREQDKNFLSNLREWM 143
Cdd:cd04497  80 VKIQSYNGKPQGISNDR-GSSWAVFRGDDGVVPIPQQSSKPVEFGPEEEPSVEELRKWA 137
Telo_bind smart00976
Telomeric single stranded DNA binding POT1/CDC13; The telomere-binding protein forms a ...
 11-143 6.85e-37

Telomeric single stranded DNA binding POT1/CDC13; The telomere-binding protein forms a heterodimer in ciliates consisting of an alpha and a beta subunit. This complex may function as a protective cap for the single-stranded telomeric overhang. Alpha subunit consists of 3 structural domains, all with the same beta-barrel OB fold.


Pssm-ID: 214949  Cd Length: 137  Bit Score: 132.06  E-value: 6.85e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79507214     11 FLRIQDAFKALHLHVNLIGVIVELGF---SNGSDCSCTLKIVDPWY-SGSGLPVKFVARTIRDLPRVESIGDIILLSRVK 86
Cdd:smart00976   1 FTPIKDLTSATNKYVNVIGVVVDFKPpkrSRGTDFTCTLTITDPSYaDGYGLTVKLFSPTLESLPVIKYVGDIILLHRVK 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 79507214     87 IVLINRKITALCNETTsSSFALFNGKHSVDSIPYQSSPKFLMREQDKNFLSNLREWM 143
Cdd:smart00976  81 IQDFNNRIQGLCSFGT-SSWAVFGPLNGVVRERESSPPSTFTPEDEKQYVEELRNWA 136
POT1 pfam02765
Telomeric single stranded DNA binding POT1/CDC13; This domain binds single stranded telomeric ...
 11-143 4.84e-33

Telomeric single stranded DNA binding POT1/CDC13; This domain binds single stranded telomeric DNA and adopts an OB fold. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping. POT1 is one component of the shelterin complex that protects telomere-ends from attack by DNA-repair mechanisms.


Pssm-ID: 397060  Cd Length: 140  Bit Score: 121.69  E-value: 4.84e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79507214    11 FLRIQDAFKaLHLHVNLIGVIVELGF---SNGSDCSCTLKIVDPW---YSGSGLPVKFVARTIRDLPRVESIGDIILLSR 84
Cdd:pfam02765   1 FVDLDKALA-EGKVVNVIGVVIDASFpkkTGGSDYCCTFTIVDPSlkgDSNDGLRVVFFRKNFEDLPIVKKVGDIILLHR 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 79507214    85 VKIVLINRKITALCNETTSSSFALFNGKHSVD-SIPYQSSPKFLMREQDKNFLSNLREWM 143
Cdd:pfam02765  80 VKIQSFNGEPQGLANIGFSSSWALFNGKLNRLyTPPILGSNFFEFSAEEKKYLESLRKWA 139
POT1PC pfam16686
ssDNA-binding domain of telomere protection protein; POT1PC is the ssDNA-binding domain on a ...
 158-196 1.74e-05

ssDNA-binding domain of telomere protection protein; POT1PC is the ssDNA-binding domain on a family of fungal telomere protection protein 1 proteins. POT1PC is able to accommodate heterogeneous ssDNA ligands. Pot1 proteins are the proteins responsible for binding to and protecting the 3' single-stranded DNA (ssDNA) overhang at most eukaryotic telomeres.


Pssm-ID: 435514  Cd Length: 152  Bit Score: 44.57  E-value: 1.74e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 79507214   158 LKDIKEGECSNLSCQIVHISKVYKDRWYLFVWDGTEMPP 196
Cdd:pfam16686   1 LKDVQPGQFFDLIVQVVKKAYDDGGKVLLYVWDYTENPP 39
 
Name Accession Description Interval E-value
hPOT1_OB1_like cd04497
hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection ...
 9-143 1.02e-41

hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. A second OB fold has not been predicted in S. pombe POT1. OnTEBP binds the extreme 3-prime end of telomeric DNA. It is heterodimeric and contains four OB folds - three in the alpha subunit (two in the N-terminal domain and one in the C-terminal domain) and one in the beta subunit. OB1Nalpha, together with the second OB fold of the N-terminal domain of OnTEBP alpha subunit and the beta subunit OB fold, forms a deep cleft that binds ssDNA.


Pssm-ID: 239943  Cd Length: 138  Bit Score: 144.73  E-value: 1.02e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79507214   9 YKFLRIQDAFKALHLHVNLIGVIVELGF---SNGSDCSCTLKIVDPW-YSGSGLPVKFVARTIRDLPRVeSIGDIILLSR 84
Cdd:cd04497   1 YKYTPLSSALKESGGSVNVIGVVVDAGPpvrSKGTDYCCTLTITDPSlANSDGLTVKLFRPNEESLPIV-KVGDIILLRR 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 79507214  85 VKIVLINRKITALCNETtSSSFALFNGKHSVDSIPYQSSPKFLMREQDKNFLSNLREWM 143
Cdd:cd04497  80 VKIQSYNGKPQGISNDR-GSSWAVFRGDDGVVPIPQQSSKPVEFGPEEEPSVEELRKWA 137
Telo_bind smart00976
Telomeric single stranded DNA binding POT1/CDC13; The telomere-binding protein forms a ...
 11-143 6.85e-37

Telomeric single stranded DNA binding POT1/CDC13; The telomere-binding protein forms a heterodimer in ciliates consisting of an alpha and a beta subunit. This complex may function as a protective cap for the single-stranded telomeric overhang. Alpha subunit consists of 3 structural domains, all with the same beta-barrel OB fold.


Pssm-ID: 214949  Cd Length: 137  Bit Score: 132.06  E-value: 6.85e-37
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79507214     11 FLRIQDAFKALHLHVNLIGVIVELGF---SNGSDCSCTLKIVDPWY-SGSGLPVKFVARTIRDLPRVESIGDIILLSRVK 86
Cdd:smart00976   1 FTPIKDLTSATNKYVNVIGVVVDFKPpkrSRGTDFTCTLTITDPSYaDGYGLTVKLFSPTLESLPVIKYVGDIILLHRVK 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 79507214     87 IVLINRKITALCNETTsSSFALFNGKHSVDSIPYQSSPKFLMREQDKNFLSNLREWM 143
Cdd:smart00976  81 IQDFNNRIQGLCSFGT-SSWAVFGPLNGVVRERESSPPSTFTPEDEKQYVEELRNWA 136
POT1 pfam02765
Telomeric single stranded DNA binding POT1/CDC13; This domain binds single stranded telomeric ...
 11-143 4.84e-33

Telomeric single stranded DNA binding POT1/CDC13; This domain binds single stranded telomeric DNA and adopts an OB fold. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping. POT1 is one component of the shelterin complex that protects telomere-ends from attack by DNA-repair mechanisms.


Pssm-ID: 397060  Cd Length: 140  Bit Score: 121.69  E-value: 4.84e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 79507214    11 FLRIQDAFKaLHLHVNLIGVIVELGF---SNGSDCSCTLKIVDPW---YSGSGLPVKFVARTIRDLPRVESIGDIILLSR 84
Cdd:pfam02765   1 FVDLDKALA-EGKVVNVIGVVIDASFpkkTGGSDYCCTFTIVDPSlkgDSNDGLRVVFFRKNFEDLPIVKKVGDIILLHR 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 79507214    85 VKIVLINRKITALCNETTSSSFALFNGKHSVD-SIPYQSSPKFLMREQDKNFLSNLREWM 143
Cdd:pfam02765  80 VKIQSFNGEPQGLANIGFSSSWALFNGKLNRLyTPPILGSNFFEFSAEEKKYLESLRKWA 139
POT1PC pfam16686
ssDNA-binding domain of telomere protection protein; POT1PC is the ssDNA-binding domain on a ...
 158-196 1.74e-05

ssDNA-binding domain of telomere protection protein; POT1PC is the ssDNA-binding domain on a family of fungal telomere protection protein 1 proteins. POT1PC is able to accommodate heterogeneous ssDNA ligands. Pot1 proteins are the proteins responsible for binding to and protecting the 3' single-stranded DNA (ssDNA) overhang at most eukaryotic telomeres.


Pssm-ID: 435514  Cd Length: 152  Bit Score: 44.57  E-value: 1.74e-05
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 79507214   158 LKDIKEGECSNLSCQIVHISKVYKDRWYLFVWDGTEMPP 196
Cdd:pfam16686   1 LKDVQPGQFFDLIVQVVKKAYDDGGKVLLYVWDYTENPP 39
 
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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