Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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: 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

  • single-stranded DNA binding Source: UniProtKB

GO - Biological processi

  • cellular response to desiccation Source: UniProtKB
  • cellular response to gamma radiation Source: UniProtKB
  • DNA repair Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

DNA damage, DNA repair, Stress response

Keywords - Ligandi

DNA-binding

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
Proteomesi
  • UP000002524 Componenti: 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 following 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)DescriptionActionsGraphical viewLength
Mutagenesisi51E → A: Forms pentamers but not higher-ordered structures; binds ssDNA normally. 1 Publication1
Mutagenesisi64R → A: Reduced ssDNA-binding. 1 Publication1
Mutagenesisi66W → A: Reduced ssDNA-binding. 1 Publication1
Mutagenesisi83R → A: Forms pentamers but not higher-ordered structures, reduced ssDNA-binding. 1 Publication1
Mutagenesisi85R → A: Reduced ssDNA-binding. 1 Publication1
Mutagenesisi94K → A: Reduced ssDNA-binding. 1 Publication1
Mutagenesisi102K → A: Reduced ssDNA-binding. 1 Publication1
Mutagenesisi108K → A: Reduced ssDNA-binding. 1 Publication1
Mutagenesisi132R → A: Reduced ssDNA-binding. 1 Publication1
Mutagenesisi135K → A: Reduced ssDNA-binding. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003944911 – 188Single-stranded DNA-binding protein DdrBAdd BLAST188

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

1188
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 7Combined sources6
Beta strandi13 – 20Combined sources8
Helixi21 – 23Combined sources3
Helixi24 – 33Combined sources10
Beta strandi46 – 48Combined sources3
Helixi50 – 52Combined sources3
Helixi58 – 61Combined sources4
Beta strandi64 – 66Combined sources3
Turni69 – 71Combined sources3
Beta strandi74 – 77Combined sources4
Beta strandi80 – 87Combined sources8
Beta strandi90 – 92Combined sources3
Beta strandi93 – 97Combined sources5
Beta strandi100 – 106Combined sources7
Helixi113 – 115Combined sources3
Helixi120 – 122Combined sources3
Beta strandi124 – 131Combined sources8
Helixi138 – 140Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4HQBX-ray2.30A/B/C/D/E1-144[»]
4NOEX-ray2.20A/B/C/D/E1-144[»]
SMRiQ9RY80.
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

HOGENOMiHOG000099548.
OrthoDBiPOG091H3KDX.

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 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.
WP_027480237.1. NZ_CP015081.1.

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.
PIRiD75563.
RefSeqiNP_293796.1. NC_001263.1.
WP_027480237.1. NZ_CP015081.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4HQBX-ray2.30A/B/C/D/E1-144[»]
4NOEX-ray2.20A/B/C/D/E1-144[»]
SMRiQ9RY80.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243230.DR_0070.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

HOGENOMiHOG000099548.
OrthoDBiPOG091H3KDX.

Family and domain databases

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

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: November 2, 2016
This is version 72 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.