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Q9RY80

- DDRB_DEIRA

UniProt

Q9RY80 - DDRB_DEIRA

Protein

Single-stranded DNA-binding protein DdrB

Gene

ddrB

Organism
Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 59 (01 Oct 2014)
      Sequence version 2 (15 Jun 2010)
      Previous versions | rss
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    Functioni

    ssDNA-binding protein that contributes to the ionizing radiation resistance of D.radiodurans. Plays a role in DNA repair and genome reconstitution in a RecA-independent process. Required for recovery from severe genomic fragmentation as a result of exposure to severe levels of ionizing radiation. Binds ssDNA but not dsDNA. Stimulates annealing of complementary ssDNA. Does not complement an ssb disruption.4 Publications

    GO - Molecular functioni

    1. single-stranded DNA binding Source: UniProtKB

    GO - Biological processi

    1. cellular response to desiccation Source: UniProtKB
    2. cellular response to gamma radiation Source: UniProtKB
    3. DNA repair Source: UniProtKB

    Keywords - Biological processi

    DNA damage, DNA repair, Stress response

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    BioCyciDRAD243230:GH46-74-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Single-stranded DNA-binding protein DdrB
    Alternative name(s):
    DNA damage response protein B
    Gene namesi
    Name:ddrB
    Ordered Locus Names:DR_0070
    OrganismiDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422)
    Taxonomic identifieri243230 [NCBI]
    Taxonomic lineageiBacteriaDeinococcus-ThermusDeinococciDeinococcalesDeinococcaceaeDeinococcus
    ProteomesiUP000002524: Chromosome I

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene show a normal growth rate, do not exhibit a decrease in the efficiency of natural transformation, but display a reduced capacity to survive ionizing radiation when exposed at doses superior to 2.5 kGy. DNA repair folowing irradiations is slower. Cannot be complemented by ssb. A double recA-ddrB disruption shows no signs of DNA repair 24 hours after irradiation.3 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi51 – 511E → A: Forms pentamers but not higher-ordered structures; binds ssDNA normally. 1 Publication
    Mutagenesisi64 – 641R → A: Reduced ssDNA-binding. 1 Publication
    Mutagenesisi66 – 661W → A: Reduced ssDNA-binding. 1 Publication
    Mutagenesisi83 – 831R → A: Forms pentamers but not higher-ordered structures, reduced ssDNA-binding. 1 Publication
    Mutagenesisi85 – 851R → A: Reduced ssDNA-binding. 1 Publication
    Mutagenesisi94 – 941K → A: Reduced ssDNA-binding. 1 Publication
    Mutagenesisi102 – 1021K → A: Reduced ssDNA-binding. 1 Publication
    Mutagenesisi108 – 1081K → A: Reduced ssDNA-binding. 1 Publication
    Mutagenesisi132 – 1321R → A: Reduced ssDNA-binding. 1 Publication
    Mutagenesisi135 – 1351K → A: Reduced ssDNA-binding. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 188188Single-stranded DNA-binding protein DdrBPRO_0000394491Add
    BLAST

    Expressioni

    Inductioni

    Induced to high levels following extreme ionizing radiation exposure. Also highly induced in response to desiccation stress.1 Publication

    Interactioni

    Subunit structurei

    Homopentamer arranged in a ring-structure; DNA binds between subunits and along the top of the ring. The pentamers self-associate to coat ssDNA in higher-ordered structures; oligomerization facilitates the assembly of extended nucleoprotein complexes. Self-assembly does not however require ssDNA-binding. Interacts with SSB.3 Publications

    Protein-protein interaction databases

    STRINGi243230.DR_0070.

    Structurei

    Secondary structure

    1
    188
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi2 – 76
    Beta strandi13 – 208
    Helixi21 – 233
    Helixi24 – 329
    Turni33 – 353
    Beta strandi45 – 484
    Helixi50 – 523
    Helixi58 – 614
    Beta strandi64 – 685
    Turni69 – 713
    Beta strandi72 – 776
    Beta strandi80 – 878
    Beta strandi90 – 923
    Beta strandi95 – 973
    Beta strandi100 – 1067
    Helixi113 – 1153
    Beta strandi125 – 1317
    Helixi138 – 1403

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4HQBX-ray2.30A/B/C/D/E1-144[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domaini

    Contains a novel ssDNA-binding fold, which is structurally and topologically distinct from the OB-fold universally found in standard SSB proteins. The disordered C-terminus of DdrB may mediate interactions with other proteins important for DNA damage recovery (By similarity).By similarity

    Phylogenomic databases

    eggNOGiNOG70958.
    HOGENOMiHOG000099548.
    OrthoDBiEOG61KBJ8.

    Family and domain databases

    InterProiIPR024305. ssDNA-bd_DdrB-like.
    [Graphical view]
    PfamiPF12747. DdrB. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9RY80-1 [UniParc]FASTAAdd to Basket

    « Hide

    MLQIEFITDL GARVTVNVEH ESRLLDVQRH YGRLGWTSGE IPSGGYQFPI    50
    ENEADFDWSL IGARKWKSPE GEELVIHRGH AYRRRELEAV DSRKLKLPAA 100
    IKYSRGAKVS DPQHVREKAD GDIEYVSLAI FRGGKRQERY AVPGGAAGNG 150
    QGRPAPQGQP AQARPQATAA RPAARPPVQP GQEEETPF 188
    Length:188
    Mass (Da):20,830
    Last modified:June 15, 2010 - v2
    Checksum:i997F38C92EB9AE06
    GO

    Sequence cautioni

    The sequence AAF09667.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

    Mass spectrometryi

    Molecular mass is 25236.7 Da from positions 1 - 188. Determined by SELDI. Tagged N-terminally with 6 His residues.1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000513 Genomic DNA. Translation: AAF09667.1. Different initiation.
    BK006794 Genomic DNA. Translation: DAA06535.1.
    PIRiD75563.
    RefSeqiNP_293796.1. NC_001263.1.

    Genome annotation databases

    EnsemblBacteriaiAAF09667; AAF09667; DR_0070.
    GeneIDi1798604.
    KEGGidra:DR_0070.
    PATRICi21627611. VBIDeiRad64572_0233.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000513 Genomic DNA. Translation: AAF09667.1 . Different initiation.
    BK006794 Genomic DNA. Translation: DAA06535.1 .
    PIRi D75563.
    RefSeqi NP_293796.1. NC_001263.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4HQB X-ray 2.30 A/B/C/D/E 1-144 [» ]
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 243230.DR_0070.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAF09667 ; AAF09667 ; DR_0070 .
    GeneIDi 1798604.
    KEGGi dra:DR_0070.
    PATRICi 21627611. VBIDeiRad64572_0233.

    Phylogenomic databases

    eggNOGi NOG70958.
    HOGENOMi HOG000099548.
    OrthoDBi EOG61KBJ8.

    Enzyme and pathway databases

    BioCyci DRAD243230:GH46-74-MONOMER.

    Family and domain databases

    InterProi IPR024305. ssDNA-bd_DdrB-like.
    [Graphical view ]
    Pfami PF12747. DdrB. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
    2. "Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance."
      Tanaka M., Earl A.M., Howell H.A., Park M.J., Eisen J.A., Peterson S.N., Battista J.R.
      Genetics 168:21-33(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION, ROLE IN RADIORESISTANCE, DISRUPTION PHENOTYPE.
      Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
    3. "DdrB protein, an alternative Deinococcus radiodurans SSB induced by ionizing radiation."
      Norais C.A., Chitteni-Pattu S., Wood E.A., Inman R.B., Cox M.M.
      J. Biol. Chem. 284:21402-21411(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION OF START CODON, FUNCTION AS A SSB PROTEIN, SUBUNIT.
      Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
    4. "DdrB stimulates single-stranded DNA annealing and facilitates RecA-independent DNA repair in Deinococcus radiodurans."
      Xu G., Lu H., Wang L., Chen H., Xu Z., Hu Y., Tian B., Hua Y.
      DNA Repair 9:805-812(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH SSB, MASS SPECTROMETRY, SSDNA-BINDING, DISRUPTION PHENOTYPE.
      Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
    5. "The essential role of the Deinococcus radiodurans ssb gene in cell survival and radiation tolerance."
      Lockhart J.S., DeVeaux L.C.
      PLoS ONE 8:E71651-E71651(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
      Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.
    6. "Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans reveals a DNA binding surface involving higher-order oligomeric states."
      Sugiman-Marangos S.N., Peel J.K., Weiss Y.M., Ghirlando R., Junop M.S.
      Nucleic Acids Res. 41:9934-9944(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-144 IN COMPLEX WITH SSDNA, SUBUNIT, MUTAGENESIS OF GLU-51; ARG-64; TRP-66; ARG-83; ARG-85; LYS-94; LYS-102; LYS-108; ARG-132 AND LYS-135.
      Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422.

    Entry informationi

    Entry nameiDDRB_DEIRA
    AccessioniPrimary (citable) accession number: Q9RY80
    Secondary accession number(s): C6SUN7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 15, 2010
    Last sequence update: June 15, 2010
    Last modified: October 1, 2014
    This is version 59 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references

    External Data

    Dasty 3