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Q9RY80

- DDRB_DEIRA

UniProt

Q9RY80 - DDRB_DEIRA

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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

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
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 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 – 76Combined sources
Beta strandi13 – 208Combined sources
Helixi21 – 233Combined sources
Helixi24 – 329Combined sources
Turni33 – 353Combined sources
Beta strandi45 – 484Combined sources
Helixi50 – 523Combined sources
Helixi58 – 614Combined sources
Beta strandi64 – 685Combined sources
Turni69 – 713Combined sources
Beta strandi72 – 776Combined sources
Beta strandi80 – 878Combined sources
Beta strandi90 – 923Combined sources
Beta strandi95 – 973Combined sources
Beta strandi100 – 1067Combined sources
Helixi113 – 1153Combined sources
Beta strandi125 – 1317Combined sources
Helixi138 – 1403Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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

        10         20         30         40         50
MLQIEFITDL GARVTVNVEH ESRLLDVQRH YGRLGWTSGE IPSGGYQFPI
60 70 80 90 100
ENEADFDWSL IGARKWKSPE GEELVIHRGH AYRRRELEAV DSRKLKLPAA
110 120 130 140 150
IKYSRGAKVS DPQHVREKAD GDIEYVSLAI FRGGKRQERY AVPGGAAGNG
160 170 180
QGRPAPQGQP AQARPQATAA RPAARPPVQP GQEEETPF
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.Curated

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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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

« 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: October 29, 2014
This is version 60 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