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Conserved domains on  [gi|564333959|ref|XP_006231536|]
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CST complex subunit STN1 isoform X2 [Rattus norvegicus]

Protein Classification

single-stranded DNA-binding protein( domain architecture ID 10138995)

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 ...
 211-376 2.95e-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: 281.11  E-value: 2.95e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333959  211 AGLTALLSEKVKEFLQEKKVQSFYQKELEMVEPLQSLASQPVTHSTCSDQVELKNDAASD-IHSVFKNALHLLQEKGFVF 289
Cdd:pfam09170   1 PGLVSLLSEKIKEFLLENKVQTFYQQELETVESLVSLASRPVQHSSCSQQVDSKGPSTSKqIHSLFKEAIQLLQEKGLVF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333959  290 QRDGGSDKLYYVTSKDKDLHQKIYQIIKEDCQKPNHVEKGCHLMHVLNCVLLNLRWDLNKAVLQQVLELLEDQSDIVSTG 369
Cdd:pfam09170  81 QKDSSFDDLYYVTDQDKDLHKKILDIIREDCQKPKHAEKGCHFLHILSCVRQSYSPNLSEAVLQQVLDLLEDNSDIVSTM 160


                  ....*..
gi 564333959  370 DHYYTAF 376
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 ...
 65-165 6.51e-37

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: 128.71  E-value: 6.51e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333959  65 DIMGAVISVKERETFYSYGVDDATGVINCVCWKRPSNAESSSDPailstsrelSMTSQLKKLQETIEQKTKIGIGDIIRV 144
Cdd:cd04483    1 DILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRS---------DAARILKSALMALKQAKVLEIGDLLRV 71

                         90       100
                 ....*....|....*....|.
gi 564333959 145 RGYVRMFREEREICATIYYKV 165
Cdd:cd04483   72 RGSIRTYRGEREINASVVYKV 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 ...
 211-376 2.95e-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: 281.11  E-value: 2.95e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333959  211 AGLTALLSEKVKEFLQEKKVQSFYQKELEMVEPLQSLASQPVTHSTCSDQVELKNDAASD-IHSVFKNALHLLQEKGFVF 289
Cdd:pfam09170   1 PGLVSLLSEKIKEFLLENKVQTFYQQELETVESLVSLASRPVQHSSCSQQVDSKGPSTSKqIHSLFKEAIQLLQEKGLVF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333959  290 QRDGGSDKLYYVTSKDKDLHQKIYQIIKEDCQKPNHVEKGCHLMHVLNCVLLNLRWDLNKAVLQQVLELLEDQSDIVSTG 369
Cdd:pfam09170  81 QKDSSFDDLYYVTDQDKDLHKKILDIIREDCQKPKHAEKGCHFLHILSCVRQSYSPNLSEAVLQQVLDLLEDNSDIVSTM 160


                  ....*..
gi 564333959  370 DHYYTAF 376
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 ...
 65-165 6.51e-37

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: 128.71  E-value: 6.51e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333959  65 DIMGAVISVKERETFYSYGVDDATGVINCVCWKRPSNAESSSDPailstsrelSMTSQLKKLQETIEQKTKIGIGDIIRV 144
Cdd:cd04483    1 DILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRS---------DAARILKSALMALKQAKVLEIGDLLRV 71

                         90       100
                 ....*....|....*....|.
gi 564333959 145 RGYVRMFREEREICATIYYKV 165
Cdd:cd04483   72 RGSIRTYRGEREINASVVYKV 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 ...
 211-376 2.95e-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: 281.11  E-value: 2.95e-95
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333959  211 AGLTALLSEKVKEFLQEKKVQSFYQKELEMVEPLQSLASQPVTHSTCSDQVELKNDAASD-IHSVFKNALHLLQEKGFVF 289
Cdd:pfam09170   1 PGLVSLLSEKIKEFLLENKVQTFYQQELETVESLVSLASRPVQHSSCSQQVDSKGPSTSKqIHSLFKEAIQLLQEKGLVF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333959  290 QRDGGSDKLYYVTSKDKDLHQKIYQIIKEDCQKPNHVEKGCHLMHVLNCVLLNLRWDLNKAVLQQVLELLEDQSDIVSTG 369
Cdd:pfam09170  81 QKDSSFDDLYYVTDQDKDLHKKILDIIREDCQKPKHAEKGCHFLHILSCVRQSYSPNLSEAVLQQVLDLLEDNSDIVSTM 160


                  ....*..
gi 564333959  370 DHYYTAF 376
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 ...
 65-165 6.51e-37

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: 128.71  E-value: 6.51e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333959  65 DIMGAVISVKERETFYSYGVDDATGVINCVCWKRPSNAESSSDPailstsrelSMTSQLKKLQETIEQKTKIGIGDIIRV 144
Cdd:cd04483    1 DILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRS---------DAARILKSALMALKQAKVLEIGDLLRV 71

                         90       100
                 ....*....|....*....|.
gi 564333959 145 RGYVRMFREEREICATIYYKV 165
Cdd:cd04483   72 RGSIRTYRGEREINASVVYKV 92
RPA2_DBD_D cd04478
RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding ...
 64-168 4.39e-04

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: 39.12  E-value: 4.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 564333959  64 VDIMGAVISVKERETFYSYGVDDATGVINCVCWKrpsNAESSSDpailstsrelsmtsqlkklqetiEQKTKIGIGDIIR 143
Cdd:cd04478    2 VTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWL---DDDNDDS-----------------------SEVEPIEEGTYVR 55

                         90       100
                 ....*....|....*....|....*
gi 564333959 144 VRGYVRMFREEREICATIYYKVDDP 168
Cdd:cd04478   56 VFGNLKSFQGKKSIMAFSIRPVTDF 80
 
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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