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Conserved domains on  [gi|564333961|ref|XP_006231537|]
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CST complex subunit STN1 isoform X3 [Rattus norvegicus]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 10293560)

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
STN1_2 pfam09170
CST, complex subunit STN1, C terminal; STN1 is a component of the CST complex, a complex that ...
 175-340 3.90e-95

CST, complex subunit STN1, C terminal; STN1 is a component of the CST complex, a complex that binds to single-stranded DNA and is required for protecting telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity on their own. In addition to telomere protection, the CST complex probably has a more general role in DNA metabolism at non-telomeric sites. This entry represents the C-terminal region of Stn1 which has two winged helix-turn-helix (wHTH) motifs, wHTH1 and wHTH2. wHTH1 is structurally similar to that in RPA32 with a large insertion between helices alpha2 and alpha3, unique to Stn1, that may allow interaction with a different set of proteins that function at telomeres such as Ctc1. wHTH2 is most similar to the DNA-binding wHTH motifs of the pur operon repressor and RepE replication initiator, but it does not bind double-stranded DNA.


:

Pssm-ID: 462701  Cd Length: 167  Bit Score: 279.57  E-value: 3.90e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333961  175 AGLTALLSEKVKEFLQEKKVQSFYQKELEMVEPLQSLASQPVTHSTCSDQVELKNDAASD-IHSVFKNALHLLQEKGFVF 253
Cdd:pfam09170   1 PGLVSLLSEKIKEFLLENKVQTFYQQELETVESLVSLASRPVQHSSCSQQVDSKGPSTSKqIHSLFKEAIQLLQEKGLVF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333961  254 QRDGGSDKLYYVTSKDKDLHQKIYQIIKEDCQKPNHVEKGCHLMHVLNCVLLNLRWDLNKAVLQQVLELLEDQSDIVSTG 333
Cdd:pfam09170  81 QKDSSFDDLYYVTDQDKDLHKKILDIIREDCQKPKHAEKGCHFLHILSCVRQSYSPNLSEAVLQQVLDLLEDNSDIVSTM 160


                  ....*..
gi 564333961  334 DHYYTAF 340
Cdd:pfam09170 161 EGYYTAF 167
RPA_2b-aaRSs_OBF_like super family cl09930
Replication protein A, class 2b aminoacyl-tRNA synthetases, and related proteins with ...
 44-128 1.13e-23

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 cd04483:

Pssm-ID: 471953  Cd Length: 92  Bit Score: 93.27  E-value: 1.13e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333961  44 MLTVDDATGVINCVCWKRPSNAESSSDPailstsrelSMTSQLKKLQETIEQKTKIGIGDIIRVRGYVRMFREEREICAT 123
Cdd:cd04483   17 SFGVDDGTGVVNCVCWKNLSYAEVSSRS---------DAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRGEREINAS 87


                 ....*
gi 564333961 124 IYYKV 128
Cdd:cd04483   88 VVYKV 92
 
Name Accession Description Interval E-value
STN1_2 pfam09170
CST, complex subunit STN1, C terminal; STN1 is a component of the CST complex, a complex that ...
 175-340 3.90e-95

CST, complex subunit STN1, C terminal; STN1 is a component of the CST complex, a complex that binds to single-stranded DNA and is required for protecting telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity on their own. In addition to telomere protection, the CST complex probably has a more general role in DNA metabolism at non-telomeric sites. This entry represents the C-terminal region of Stn1 which has two winged helix-turn-helix (wHTH) motifs, wHTH1 and wHTH2. wHTH1 is structurally similar to that in RPA32 with a large insertion between helices alpha2 and alpha3, unique to Stn1, that may allow interaction with a different set of proteins that function at telomeres such as Ctc1. wHTH2 is most similar to the DNA-binding wHTH motifs of the pur operon repressor and RepE replication initiator, but it does not bind double-stranded DNA.


Pssm-ID: 462701  Cd Length: 167  Bit Score: 279.57  E-value: 3.90e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333961  175 AGLTALLSEKVKEFLQEKKVQSFYQKELEMVEPLQSLASQPVTHSTCSDQVELKNDAASD-IHSVFKNALHLLQEKGFVF 253
Cdd:pfam09170   1 PGLVSLLSEKIKEFLLENKVQTFYQQELETVESLVSLASRPVQHSSCSQQVDSKGPSTSKqIHSLFKEAIQLLQEKGLVF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333961  254 QRDGGSDKLYYVTSKDKDLHQKIYQIIKEDCQKPNHVEKGCHLMHVLNCVLLNLRWDLNKAVLQQVLELLEDQSDIVSTG 333
Cdd:pfam09170  81 QKDSSFDDLYYVTDQDKDLHKKILDIIREDCQKPKHAEKGCHFLHILSCVRQSYSPNLSEAVLQQVLDLLEDNSDIVSTM 160


                  ....*..
gi 564333961  334 DHYYTAF 340
Cdd:pfam09170 161 EGYYTAF 167
hOBFC1_like cd04483
hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein ...
 44-128 1.13e-23

hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. 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 OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.


Pssm-ID: 239929  Cd Length: 92  Bit Score: 93.27  E-value: 1.13e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333961  44 MLTVDDATGVINCVCWKRPSNAESSSDPailstsrelSMTSQLKKLQETIEQKTKIGIGDIIRVRGYVRMFREEREICAT 123
Cdd:cd04483   17 SFGVDDGTGVVNCVCWKNLSYAEVSSRS---------DAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRGEREINAS 87


                 ....*
gi 564333961 124 IYYKV 128
Cdd:cd04483   88 VVYKV 92
 
Name Accession Description Interval E-value
STN1_2 pfam09170
CST, complex subunit STN1, C terminal; STN1 is a component of the CST complex, a complex that ...
 175-340 3.90e-95

CST, complex subunit STN1, C terminal; STN1 is a component of the CST complex, a complex that binds to single-stranded DNA and is required for protecting telomeres from DNA degradation. The CST complex binds single-stranded DNA with high affinity in a sequence-independent manner, while isolated subunits bind DNA with low affinity on their own. In addition to telomere protection, the CST complex probably has a more general role in DNA metabolism at non-telomeric sites. This entry represents the C-terminal region of Stn1 which has two winged helix-turn-helix (wHTH) motifs, wHTH1 and wHTH2. wHTH1 is structurally similar to that in RPA32 with a large insertion between helices alpha2 and alpha3, unique to Stn1, that may allow interaction with a different set of proteins that function at telomeres such as Ctc1. wHTH2 is most similar to the DNA-binding wHTH motifs of the pur operon repressor and RepE replication initiator, but it does not bind double-stranded DNA.


Pssm-ID: 462701  Cd Length: 167  Bit Score: 279.57  E-value: 3.90e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333961  175 AGLTALLSEKVKEFLQEKKVQSFYQKELEMVEPLQSLASQPVTHSTCSDQVELKNDAASD-IHSVFKNALHLLQEKGFVF 253
Cdd:pfam09170   1 PGLVSLLSEKIKEFLLENKVQTFYQQELETVESLVSLASRPVQHSSCSQQVDSKGPSTSKqIHSLFKEAIQLLQEKGLVF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333961  254 QRDGGSDKLYYVTSKDKDLHQKIYQIIKEDCQKPNHVEKGCHLMHVLNCVLLNLRWDLNKAVLQQVLELLEDQSDIVSTG 333
Cdd:pfam09170  81 QKDSSFDDLYYVTDQDKDLHKKILDIIREDCQKPKHAEKGCHFLHILSCVRQSYSPNLSEAVLQQVLDLLEDNSDIVSTM 160


                  ....*..
gi 564333961  334 DHYYTAF 340
Cdd:pfam09170 161 EGYYTAF 167
hOBFC1_like cd04483
hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein ...
 44-128 1.13e-23

hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. 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 OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.


Pssm-ID: 239929  Cd Length: 92  Bit Score: 93.27  E-value: 1.13e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333961  44 MLTVDDATGVINCVCWKRPSNAESSSDPailstsrelSMTSQLKKLQETIEQKTKIGIGDIIRVRGYVRMFREEREICAT 123
Cdd:cd04483   17 SFGVDDGTGVVNCVCWKNLSYAEVSSRS---------DAARILKSALMALKQAKVLEIGDLLRVRGSIRTYRGEREINAS 87


                 ....*
gi 564333961 124 IYYKV 128
Cdd:cd04483   88 VVYKV 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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