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Q9RY80

- DDRB_DEIRA

UniProt

Q9RY80 - DDRB_DEIRA

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Protein
Single-stranded DNA-binding protein DdrB
Gene
ddrB, DR_0070
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

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
Complete GO annotation...

GO - Biological processi

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

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 DdrB
PRO_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

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[»]

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).

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...

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

« Hide 'large scale' publications
  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: May 14, 2014
This is version 58 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

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