DDRB_DEIRA
ID DDRB_DEIRA Reviewed; 188 AA.
AC Q9RY80; C6SUN7;
DT 15-JUN-2010, integrated into UniProtKB/Swiss-Prot.
DT 15-JUN-2010, sequence version 2.
DT 25-MAY-2022, entry version 85.
DE RecName: Full=Single-stranded DNA-binding protein DdrB;
DE AltName: Full=DNA damage response protein B;
GN Name=ddrB; OrderedLocusNames=DR_0070;
OS Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG
OS 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422).
OC Bacteria; Deinococcus-Thermus; Deinococci; Deinococcales; Deinococcaceae;
OC Deinococcus.
OX NCBI_TaxID=243230;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=10567266; DOI=10.1126/science.286.5444.1571;
RA White O., Eisen J.A., Heidelberg J.F., Hickey E.K., Peterson J.D.,
RA Dodson R.J., Haft D.H., Gwinn M.L., Nelson W.C., Richardson D.L.,
RA Moffat K.S., Qin H., Jiang L., Pamphile W., Crosby M., Shen M.,
RA Vamathevan J.J., Lam P., McDonald L.A., Utterback T.R., Zalewski C.,
RA Makarova K.S., Aravind L., Daly M.J., Minton K.W., Fleischmann R.D.,
RA Ketchum K.A., Nelson K.E., Salzberg S.L., Smith H.O., Venter J.C.,
RA Fraser C.M.;
RT "Genome sequence of the radioresistant bacterium Deinococcus radiodurans
RT R1.";
RL Science 286:1571-1577(1999).
RN [2]
RP INDUCTION, ROLE IN RADIORESISTANCE, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=15454524; DOI=10.1534/genetics.104.029249;
RA Tanaka M., Earl A.M., Howell H.A., Park M.J., Eisen J.A., Peterson S.N.,
RA Battista J.R.;
RT "Analysis of Deinococcus radiodurans's transcriptional response to ionizing
RT radiation and desiccation reveals novel proteins that contribute to extreme
RT radioresistance.";
RL Genetics 168:21-33(2004).
RN [3]
RP IDENTIFICATION OF START CODON, FUNCTION AS A SSB PROTEIN, AND SUBUNIT.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=19515845; DOI=10.1074/jbc.m109.010454;
RA Norais C.A., Chitteni-Pattu S., Wood E.A., Inman R.B., Cox M.M.;
RT "DdrB protein, an alternative Deinococcus radiodurans SSB induced by
RT ionizing radiation.";
RL J. Biol. Chem. 284:21402-21411(2009).
RN [4]
RP FUNCTION, INTERACTION WITH SSB, MASS SPECTROMETRY, SSDNA-BINDING, AND
RP DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=20451472; DOI=10.1016/j.dnarep.2010.04.006;
RA Xu G., Lu H., Wang L., Chen H., Xu Z., Hu Y., Tian B., Hua Y.;
RT "DdrB stimulates single-stranded DNA annealing and facilitates RecA-
RT independent DNA repair in Deinococcus radiodurans.";
RL DNA Repair 9:805-812(2010).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=23951213; DOI=10.1371/journal.pone.0071651;
RA Lockhart J.S., DeVeaux L.C.;
RT "The essential role of the Deinococcus radiodurans ssb gene in cell
RT survival and radiation tolerance.";
RL PLoS ONE 8:E71651-E71651(2013).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-144 IN COMPLEX WITH SSDNA,
RP SUBUNIT, AND MUTAGENESIS OF GLU-51; ARG-64; TRP-66; ARG-83; ARG-85; LYS-94;
RP LYS-102; LYS-108; ARG-132 AND LYS-135.
RC STRAIN=ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB
RC 9279 / R1 / VKM B-1422;
RX PubMed=23975200; DOI=10.1093/nar/gkt759;
RA Sugiman-Marangos S.N., Peel J.K., Weiss Y.M., Ghirlando R., Junop M.S.;
RT "Crystal structure of the DdrB/ssDNA complex from Deinococcus radiodurans
RT reveals a DNA binding surface involving higher-order oligomeric states.";
RL Nucleic Acids Res. 41:9934-9944(2013).
CC -!- FUNCTION: ssDNA-binding protein that contributes to the ionizing
CC radiation resistance of D.radiodurans. Plays a role in DNA repair and
CC genome reconstitution in a RecA-independent process. Required for
CC recovery from severe genomic fragmentation as a result of exposure to
CC severe levels of ionizing radiation. Binds ssDNA but not dsDNA.
CC Stimulates annealing of complementary ssDNA. Does not complement an ssb
CC disruption. {ECO:0000269|PubMed:15454524, ECO:0000269|PubMed:19515845,
CC ECO:0000269|PubMed:20451472, ECO:0000269|PubMed:23951213}.
CC -!- SUBUNIT: Homopentamer arranged in a ring-structure; DNA binds between
CC subunits and along the top of the ring. The pentamers self-associate to
CC coat ssDNA in higher-ordered structures; oligomerization facilitates
CC the assembly of extended nucleoprotein complexes. Self-assembly does
CC not however require ssDNA-binding. Interacts with SSB.
CC {ECO:0000269|PubMed:19515845, ECO:0000269|PubMed:20451472,
CC ECO:0000269|PubMed:23975200}.
CC -!- INDUCTION: Induced to high levels following extreme ionizing radiation
CC exposure. Also highly induced in response to desiccation stress.
CC {ECO:0000269|PubMed:15454524}.
CC -!- DOMAIN: Contains a novel ssDNA-binding fold, which is structurally and
CC topologically distinct from the OB-fold universally found in standard
CC SSB proteins. The disordered C-terminus of DdrB may mediate
CC interactions with other proteins important for DNA damage recovery (By
CC similarity). {ECO:0000250}.
CC -!- MASS SPECTROMETRY: Mass=25236.7; Method=SELDI; Note=Tagged N-terminally
CC with 6 His residues.; Evidence={ECO:0000269|PubMed:20451472};
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene show a normal growth
CC rate, do not exhibit a decrease in the efficiency of natural
CC transformation, but display a reduced capacity to survive ionizing
CC radiation when exposed at doses superior to 2.5 kGy. DNA repair
CC following irradiations is slower. Cannot be complemented by ssb. A
CC double recA-ddrB disruption shows no signs of DNA repair 24 hours after
CC irradiation. {ECO:0000269|PubMed:15454524, ECO:0000269|PubMed:20451472,
CC ECO:0000269|PubMed:23951213}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAF09667.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AE000513; AAF09667.1; ALT_INIT; Genomic_DNA.
DR EMBL; BK006794; DAA06535.1; -; Genomic_DNA.
DR PIR; D75563; D75563.
DR RefSeq; NP_293796.1; NC_001263.1.
DR RefSeq; WP_027480237.1; NC_001263.1.
DR PDB; 4HQB; X-ray; 2.30 A; A/B/C/D/E=1-144.
DR PDB; 4NOE; X-ray; 2.20 A; A/B/C/D/E=1-144.
DR PDBsum; 4HQB; -.
DR PDBsum; 4NOE; -.
DR AlphaFoldDB; Q9RY80; -.
DR SMR; Q9RY80; -.
DR STRING; 243230.DR_0070; -.
DR EnsemblBacteria; AAF09667; AAF09667; DR_0070.
DR KEGG; dra:DR_0070; -.
DR PATRIC; fig|243230.17.peg.233; -.
DR eggNOG; ENOG50337A5; Bacteria.
DR HOGENOM; CLU_129192_0_0_0; -.
DR OrthoDB; 1680534at2; -.
DR Proteomes; UP000002524; Chromosome I.
DR GO; GO:0003697; F:single-stranded DNA binding; IDA:UniProtKB.
DR GO; GO:0071465; P:cellular response to desiccation; IEP:UniProtKB.
DR GO; GO:0071480; P:cellular response to gamma radiation; IEP:UniProtKB.
DR GO; GO:0006281; P:DNA repair; IMP:UniProtKB.
DR GO; GO:0045002; P:double-strand break repair via single-strand annealing; IDA:CACAO.
DR InterPro; IPR024305; ssDNA-bd_DdrB-like.
DR Pfam; PF12747; DdrB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA damage; DNA repair; DNA-binding; Reference proteome;
KW Stress response.
FT CHAIN 1..188
FT /note="Single-stranded DNA-binding protein DdrB"
FT /id="PRO_0000394491"
FT REGION 140..188
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 51
FT /note="E->A: Forms pentamers but not higher-ordered
FT structures; binds ssDNA normally."
FT /evidence="ECO:0000269|PubMed:23975200"
FT MUTAGEN 64
FT /note="R->A: Reduced ssDNA-binding."
FT /evidence="ECO:0000269|PubMed:23975200"
FT MUTAGEN 66
FT /note="W->A: Reduced ssDNA-binding."
FT /evidence="ECO:0000269|PubMed:23975200"
FT MUTAGEN 83
FT /note="R->A: Forms pentamers but not higher-ordered
FT structures, reduced ssDNA-binding."
FT /evidence="ECO:0000269|PubMed:23975200"
FT MUTAGEN 85
FT /note="R->A: Reduced ssDNA-binding."
FT /evidence="ECO:0000269|PubMed:23975200"
FT MUTAGEN 94
FT /note="K->A: Reduced ssDNA-binding."
FT /evidence="ECO:0000269|PubMed:23975200"
FT MUTAGEN 102
FT /note="K->A: Reduced ssDNA-binding."
FT /evidence="ECO:0000269|PubMed:23975200"
FT MUTAGEN 108
FT /note="K->A: Reduced ssDNA-binding."
FT /evidence="ECO:0000269|PubMed:23975200"
FT MUTAGEN 132
FT /note="R->A: Reduced ssDNA-binding."
FT /evidence="ECO:0000269|PubMed:23975200"
FT MUTAGEN 135
FT /note="K->A: Reduced ssDNA-binding."
FT /evidence="ECO:0000269|PubMed:23975200"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:4NOE"
FT STRAND 13..20
FT /evidence="ECO:0007829|PDB:4NOE"
FT HELIX 21..23
FT /evidence="ECO:0007829|PDB:4NOE"
FT HELIX 24..33
FT /evidence="ECO:0007829|PDB:4NOE"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:4NOE"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:4NOE"
FT HELIX 58..61
FT /evidence="ECO:0007829|PDB:4NOE"
FT STRAND 64..66
FT /evidence="ECO:0007829|PDB:4NOE"
FT TURN 69..71
FT /evidence="ECO:0007829|PDB:4HQB"
FT STRAND 74..77
FT /evidence="ECO:0007829|PDB:4NOE"
FT STRAND 80..87
FT /evidence="ECO:0007829|PDB:4NOE"
FT STRAND 90..92
FT /evidence="ECO:0007829|PDB:4HQB"
FT STRAND 93..97
FT /evidence="ECO:0007829|PDB:4NOE"
FT STRAND 100..106
FT /evidence="ECO:0007829|PDB:4NOE"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:4NOE"
FT HELIX 120..122
FT /evidence="ECO:0007829|PDB:4NOE"
FT STRAND 124..131
FT /evidence="ECO:0007829|PDB:4NOE"
FT HELIX 138..140
FT /evidence="ECO:0007829|PDB:4NOE"
SQ SEQUENCE 188 AA; 20830 MW; 997F38C92EB9AE06 CRC64;
MLQIEFITDL GARVTVNVEH ESRLLDVQRH YGRLGWTSGE IPSGGYQFPI ENEADFDWSL
IGARKWKSPE GEELVIHRGH AYRRRELEAV DSRKLKLPAA IKYSRGAKVS DPQHVREKAD
GDIEYVSLAI FRGGKRQERY AVPGGAAGNG QGRPAPQGQP AQARPQATAA RPAARPPVQP
GQEEETPF
