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Q9RY80 (DDRB_DEIRA) Reviewed, UniProtKB/Swiss-Prot

Last modified February 19, 2014. Version 57. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Single-stranded DNA-binding protein DdrB
Alternative name(s):
DNA damage response protein B
Gene names
Name:ddrB
Ordered Locus Names:DR_0070
OrganismDeinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) [Reference proteome] [HAMAP]
Taxonomic identifier243230 [NCBI]
Taxonomic lineageBacteriaDeinococcus-ThermusDeinococciDeinococcalesDeinococcaceaeDeinococcus

Protein attributes

Sequence length188 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2 Ref.3 Ref.4 Ref.5

Subunit structure

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. Ref.3 Ref.4 Ref.6

Induction

Induced to high levels following extreme ionizing radiation exposure. Also highly induced in response to desiccation stress. Ref.2

Domain

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.

Disruption phenotype

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. Ref.2 Ref.4 Ref.5

Mass spectrometry

Molecular mass is 25236.7 Da from positions 1 - 188. Determined by SELDI. Tagged N-terminally with 6 His residues. Ref.4

Sequence caution

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 188188Single-stranded DNA-binding protein DdrB
PRO_0000394491

Experimental info

Mutagenesis511E → A: Forms pentamers but not higher-ordered structures; binds ssDNA normally. Ref.6
Mutagenesis641R → A: Reduced ssDNA-binding. Ref.6
Mutagenesis661W → A: Reduced ssDNA-binding. Ref.6
Mutagenesis831R → A: Forms pentamers but not higher-ordered structures, reduced ssDNA-binding. Ref.6
Mutagenesis851R → A: Reduced ssDNA-binding. Ref.6
Mutagenesis941K → A: Reduced ssDNA-binding. Ref.6
Mutagenesis1021K → A: Reduced ssDNA-binding. Ref.6
Mutagenesis1081K → A: Reduced ssDNA-binding. Ref.6
Mutagenesis1321R → A: Reduced ssDNA-binding. Ref.6
Mutagenesis1351K → A: Reduced ssDNA-binding. Ref.6

Secondary structure

................................ 188
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9RY80 [UniParc].

Last modified June 15, 2010. Version 2.
Checksum: 997F38C92EB9AE06

FASTA18820,830
        10         20         30         40         50         60 
MLQIEFITDL GARVTVNVEH ESRLLDVQRH YGRLGWTSGE IPSGGYQFPI ENEADFDWSL 

        70         80         90        100        110        120 
IGARKWKSPE GEELVIHRGH AYRRRELEAV DSRKLKLPAA IKYSRGAKVS DPQHVREKAD 

       130        140        150        160        170        180 
GDIEYVSLAI FRGGKRQERY AVPGGAAGNG QGRPAPQGQP AQARPQATAA RPAARPPVQP 


GQEEETPF 

« Hide

References

« Hide 'large scale' references
[1]"Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1."
White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D., Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L., Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M., Vamathevan J.J., Lam P. expand/collapse author list , McDonald L.A., Utterback T.R., Zalewski C., Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D., Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C., Fraser C.M.
Science 286:1571-1577(1999) [PubMed] [Europe PMC] [Abstract]
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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE000513 Genomic DNA. Translation: AAF09667.1. Different initiation.
BK006794 Genomic DNA. Translation: DAA06535.1.
PIRD75563.
RefSeqNP_293796.1. NC_001263.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4HQBX-ray2.30A/B/C/D/E1-144[»]
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING243230.DR_0070.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAF09667; AAF09667; DR_0070.
GeneID1798604.
KEGGdra:DR_0070.
PATRIC21627611. VBIDeiRad64572_0233.

Phylogenomic databases

eggNOGNOG70958.
HOGENOMHOG000099548.
OrthoDBEOG61KBJ8.
ProtClustDBCLSK880928.

Enzyme and pathway databases

BioCycDRAD243230:GH46-74-MONOMER.

Family and domain databases

InterProIPR024305. ssDNA-bd_DdrB-like.
[Graphical view]
PfamPF12747. DdrB. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameDDRB_DEIRA
AccessionPrimary (citable) accession number: Q9RY80
Secondary accession number(s): C6SUN7
Entry history
Integrated into UniProtKB/Swiss-Prot: June 15, 2010
Last sequence update: June 15, 2010
Last modified: February 19, 2014
This is version 57 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references