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Conserved domains on  [gi|18403397|ref|NP_565774|]
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Nucleic acid-binding, OB-fold-like protein [Arabidopsis thaliana]

Protein Classification

SOSS complex subunit B family protein( domain architecture ID 10139587)

SOSS complex subunit B family protein that contains an OB-fold nucleic acid binding domain; such as human SOSS complex subunit B2 (SSB2/NABP1), a component of the SOSS multiprotein complex that functions downstream of the MRN complex to promote DNA repair and G2/M checkpoint

Gene Ontology:  GO:0006281|GO:0005634|GO:0070876|GO:0003697
PubMed:  19683501|19683490

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 71-154 1.03e-16

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


:

Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 71.11  E-value: 1.03e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18403397  71 TLTVKVVDQNSVPQKPGAASSShlrpaRISECLVGDETACILFTARNDQVEL-MKPGATVNLRNAKIDMFKGSMRLAVDK 149
Cdd:cd04491   1 SVEGKVLSISEPREFTRDGSEG-----KVQSGLVGDETGTIRFTLWDEKAADdLEPGDVVRIENAYVREFNGRLELSVGK 75


                ....*
gi 18403397 150 WGRIE 154
Cdd:cd04491  76 NSEIE 80
 
Name Accession Description Interval E-value
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 71-154 1.03e-16

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 71.11  E-value: 1.03e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18403397  71 TLTVKVVDQNSVPQKPGAASSShlrpaRISECLVGDETACILFTARNDQVEL-MKPGATVNLRNAKIDMFKGSMRLAVDK 149
Cdd:cd04491   1 SVEGKVLSISEPREFTRDGSEG-----KVQSGLVGDETGTIRFTLWDEKAADdLEPGDVVRIENAYVREFNGRLELSVGK 75


                ....*
gi 18403397 150 WGRIE 154
Cdd:cd04491  76 NSEIE 80
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
58-166 4.36e-13

ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 65.47  E-value: 4.36e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18403397  58 VKVDQLKPGTSGHTLTVKVVDQNSVPQKPGAASSshlrPARISECLVGDETACILFTARNDQVEL-MKPGATVNLRNAKI 136
Cdd:COG1599  22 VKISDLSPGDRDVNVEGRVLEIGEERTFDRKDGS----EGRVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYV 97

                        90       100       110
                ....*....|....*....|....*....|
gi 18403397 137 DMFKGSMRLAVDKWGRIEATEpADITVKED 166
Cdd:COG1599  98 REFNGGPELNLGERTTIEKLD-EDVEVIPD 126
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 58-175 5.84e-13

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 62.36  E-value: 5.84e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18403397   58 VKVDQLKPGTSGHTLTVKVV---DQNSVPQKPGaassshlrPARISECLVGDETACILFTARNDQVELMKPGATVNLRNA 134
Cdd:PRK06461   5 TKIKDLKPGMERVNVTVRVLevgEPKVIQTKGG--------PRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENA 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 18403397  135 KIDMFKGSMRLAVDKWGRIEATEpaDITVKEDNNLSLVEYE 175
Cdd:PRK06461  77 WTTLYRGKVQLNVGKYGSISESD--DEEVPEAEEIPEETPE 115
 
Name Accession Description Interval E-value
SoSSB_OBF cd04491
SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus ...
 71-154 1.03e-16

SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating the DNA helicase activity of MCM.


Pssm-ID: 239937 [Multi-domain]  Cd Length: 82  Bit Score: 71.11  E-value: 1.03e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18403397  71 TLTVKVVDQNSVPQKPGAASSShlrpaRISECLVGDETACILFTARNDQVEL-MKPGATVNLRNAKIDMFKGSMRLAVDK 149
Cdd:cd04491   1 SVEGKVLSISEPREFTRDGSEG-----KVQSGLVGDETGTIRFTLWDEKAADdLEPGDVVRIENAYVREFNGRLELSVGK 75


                ....*
gi 18403397 150 WGRIE 154
Cdd:cd04491  76 NSEIE 80
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
58-166 4.36e-13

ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 65.47  E-value: 4.36e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18403397  58 VKVDQLKPGTSGHTLTVKVVDQNSVPQKPGAASSshlrPARISECLVGDETACILFTARNDQVEL-MKPGATVNLRNAKI 136
Cdd:COG1599  22 VKISDLSPGDRDVNVEGRVLEIGEERTFDRKDGS----EGRVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRIENAYV 97

                        90       100       110
                ....*....|....*....|....*....|
gi 18403397 137 DMFKGSMRLAVDKWGRIEATEpADITVKED 166
Cdd:COG1599  98 REFNGGPELNLGERTTIEKLD-EDVEVIPD 126
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 58-175 5.84e-13

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 62.36  E-value: 5.84e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18403397   58 VKVDQLKPGTSGHTLTVKVV---DQNSVPQKPGaassshlrPARISECLVGDETACILFTARNDQVELMKPGATVNLRNA 134
Cdd:PRK06461   5 TKIKDLKPGMERVNVTVRVLevgEPKVIQTKGG--------PRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENA 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 18403397  135 KIDMFKGSMRLAVDKWGRIEATEpaDITVKEDNNLSLVEYE 175
Cdd:PRK06461  77 WTTLYRGKVQLNVGKYGSISESD--DEEVPEAEEIPEETPE 115
PRK07217 PRK07217
replication factor A; Reviewed
 103-179 6.30e-04

replication factor A; Reviewed


Pssm-ID: 235970 [Multi-domain]  Cd Length: 311  Bit Score: 39.23  E-value: 6.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18403397  103 LVGDETACILFT--ARNDQVELMKpGATVNLRNAKIDMFKGSMRLAVDKWGRIEATEpADITVKEDNnlslVEYE--LVN 178
Cdd:PRK07217 107 LLGDETGTIKFTkwAKSDLPELEE-GKSYLLKNVVTDEYQGRFSVKLNRTTSIEELD-EDIEVGDDE----VEVEgaLVD 180


                 .
gi 18403397  179 V 179
Cdd:PRK07217 181 I 181
PRK07218 PRK07218
Single-stranded DNA binding protein;
58-145 8.70e-04

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 38.84  E-value: 8.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18403397   58 VKVDQLKPGTSGHTLTVKVVDQNSvpqkpgaaSSSHLR--PARISECLVGDETACILFTARNDqVELmKPGATVNLRNAK 135
Cdd:PRK07218  59 KDIKELSTDDKNVTVTGRVLTIGE--------RSIRYQgdDHVIYEGILADETGTISYTAWKD-FGL-SPGDTVTIGNAG 128

                         90
                 ....*....|
gi 18403397  136 IDMFKGSMRL 145
Cdd:PRK07218 129 VREWDGRPEL 138
PRK07218 PRK07218
Single-stranded DNA binding protein;
63-166 3.35e-03

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 37.30  E-value: 3.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18403397   63 LKPGTSGHTLTVKV--VDQNSVPQKPGaassshlrPARISECLVGDETACILFTARnDQVELMKPGATVNLRNAKIDMFK 140
Cdd:PRK07218 168 LGPGDRGVNVEARVleLEHREIDGRDG--------ETTILSGVLADETGRLPFTDW-DPLPEIEIGASIRIEDAYVREFR 238

                         90       100
                 ....*....|....*....|....*.
gi 18403397  141 GSMRLAVDKWGRIEATEPaDITVKED 166
Cdd:PRK07218 239 GVPSVNVSEFTTVEALDR-EVSVSKD 263
 
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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