NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|15235304|ref|NP_194573|]
View 

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 36-124 1.35e-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: 69.96  E-value: 1.35e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15235304  36 TLTVKVIEANIVVPVTRKTRPasslsrpsqpSRIVECLIGDETGCILFTARNDQV-DLMKPGATVILRNSRIDMFKGTMR 114
Cdd:cd04491   1 SVEGKVLSISEPREFTRDGSE----------GKVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLE 70

                        90
                ....*....|
gi 15235304 115 LGVDKWGRIE 124
Cdd:cd04491  71 LSVGKNSEIE 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 ...
 36-124 1.35e-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: 69.96  E-value: 1.35e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15235304  36 TLTVKVIEANIVVPVTRKTRPasslsrpsqpSRIVECLIGDETGCILFTARNDQV-DLMKPGATVILRNSRIDMFKGTMR 114
Cdd:cd04491   1 SVEGKVLSISEPREFTRDGSE----------GKVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLE 70

                        90
                ....*....|
gi 15235304 115 LGVDKWGRIE 124
Cdd:cd04491  71 LSVGKNSEIE 80
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 23-152 2.11e-12

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 60.44  E-value: 2.11e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15235304   23 VKVEQLKPGTTGHTLTVKVIEANivVPVTRKTRpasslsrpSQPSRIVECLIGDETGCILFTARNDQVDLMKPGATVILR 102
Cdd:PRK06461   5 TKIKDLKPGMERVNVTVRVLEVG--EPKVIQTK--------GGPRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIE 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 15235304  103 NSRIDMFKGTMRLGVDKWGRIEATGAASftVKEDNNLSLVEYELINVGGD 152
Cdd:PRK06461  75 NAWTTLYRGKVQLNVGKYGSISESDDEE--VPEAEEIPEETPEAPGGGGG 122
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
23-126 1.11e-09

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


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 55.07  E-value: 1.11e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15235304  23 VKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRpasslsrpsQPSRIVECLIGDETGCILFTARNDQVDL-MKPGATVIL 101
Cdd:COG1599  22 VKISDLSPGDRDVNVEGRVLEIGEERTFDRKDG---------SEGRVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRI 92

                        90       100
                ....*....|....*....|....*
gi 15235304 102 RNSRIDMFKGTMRLGVDKWGRIEAT 126
Cdd:COG1599  93 ENAYVREFNGGPELNLGERTTIEKL 117
 
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 ...
 36-124 1.35e-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: 69.96  E-value: 1.35e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15235304  36 TLTVKVIEANIVVPVTRKTRPasslsrpsqpSRIVECLIGDETGCILFTARNDQV-DLMKPGATVILRNSRIDMFKGTMR 114
Cdd:cd04491   1 SVEGKVLSISEPREFTRDGSE----------GKVQSGLVGDETGTIRFTLWDEKAaDDLEPGDVVRIENAYVREFNGRLE 70

                        90
                ....*....|
gi 15235304 115 LGVDKWGRIE 124
Cdd:cd04491  71 LSVGKNSEIE 80
PRK06461 PRK06461
single-stranded DNA-binding protein; Reviewed
 23-152 2.11e-12

single-stranded DNA-binding protein; Reviewed


Pssm-ID: 180574 [Multi-domain]  Cd Length: 129  Bit Score: 60.44  E-value: 2.11e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15235304   23 VKVEQLKPGTTGHTLTVKVIEANivVPVTRKTRpasslsrpSQPSRIVECLIGDETGCILFTARNDQVDLMKPGATVILR 102
Cdd:PRK06461   5 TKIKDLKPGMERVNVTVRVLEVG--EPKVIQTK--------GGPRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIE 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 15235304  103 NSRIDMFKGTMRLGVDKWGRIEATGAASftVKEDNNLSLVEYELINVGGD 152
Cdd:PRK06461  75 NAWTTLYRGKVQLNVGKYGSISESDDEE--VPEAEEIPEETPEAPGGGGG 122
RFA1 COG1599
ssDNA-binding replication factor A, large subunit [Replication, recombination and repair];
23-126 1.11e-09

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


Pssm-ID: 441207 [Multi-domain]  Cd Length: 282  Bit Score: 55.07  E-value: 1.11e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15235304  23 VKVEQLKPGTTGHTLTVKVIEANIVVPVTRKTRpasslsrpsQPSRIVECLIGDETGCILFTARNDQVDL-MKPGATVIL 101
Cdd:COG1599  22 VKISDLSPGDRDVNVEGRVLEIGEERTFDRKDG---------SEGRVQSGVIGDETGRIRFTLWDDKADLeLEEGDVVRI 92

                        90       100
                ....*....|....*....|....*
gi 15235304 102 RNSRIDMFKGTMRLGVDKWGRIEAT 126
Cdd:COG1599  93 ENAYVREFNGGPELNLGERTTIEKL 117
PRK07217 PRK07217
replication factor A; Reviewed
 36-126 5.72e-04

replication factor A; Reviewed


Pssm-ID: 235970 [Multi-domain]  Cd Length: 311  Bit Score: 38.85  E-value: 5.72e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15235304   36 TLTVKVIEanivvpvtrktrpassLSRPSQPSRIVECLIGDETGCILFT--ARNDQVDLMKpGATVILRNSRIDMFKGTM 113
Cdd:PRK07217  86 DVTAKVVQ----------------LWEPSSDSIAQVGLLGDETGTIKFTkwAKSDLPELEE-GKSYLLKNVVTDEYQGRF 148

                         90
                 ....*....|...
gi 15235304  114 RLGVDKWGRIEAT 126
Cdd:PRK07217 149 SVKLNRTTSIEEL 161
PRK07218 PRK07218
Single-stranded DNA binding protein;
23-149 8.35e-04

Single-stranded DNA binding protein;


Pssm-ID: 180890 [Multi-domain]  Cd Length: 423  Bit Score: 38.45  E-value: 8.35e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15235304   23 VKVEQLKPGTTGHTLTVKVIEANivvpvTRKTRPASSlsrpsqPSRIVECLIGDETGCILFTARNDqVDLmKPGATVILR 102
Cdd:PRK07218  59 KDIKELSTDDKNVTVTGRVLTIG-----ERSIRYQGD------DHVIYEGILADETGTISYTAWKD-FGL-SPGDTVTIG 125

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 15235304  103 NSridmfkgtmrlGVDKW-GRIEATGAASFTVKEDNNLSLVEYELINV 149
Cdd:PRK07218 126 NA-----------GVREWdGRPELNIGESTTVSLLDDSSLPPYSIGGD 162
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH