RADD_ECOLI
ID RADD_ECOLI Reviewed; 586 AA.
AC P33919; P36926; P36927; P76449; Q2MAQ7;
DT 01-FEB-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 149.
DE RecName: Full=Putative DNA repair helicase RadD {ECO:0000303|PubMed:25425430};
DE EC=3.6.4.12 {ECO:0000305|PubMed:25425430, ECO:0000305|PubMed:25484163};
GN Name=radD {ECO:0000303|PubMed:25425430}; Synonyms=yejH, yejI, yejJ;
GN OrderedLocusNames=b2184, JW2172;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 1-403.
RC STRAIN=K12 / BHB2600;
RA Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K.,
RA Church G.M.;
RT "Automated multiplex sequencing of the E.coli genome.";
RL Submitted (OCT-1993) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP DISRUPTION PHENOTYPE.
RC STRAIN=K12 / MG1655 / e14;
RX PubMed=25049088; DOI=10.1128/jb.01589-14;
RA Byrne R.T., Chen S.H., Wood E.A., Cabot E.L., Cox M.M.;
RT "Escherichia coli genes and pathways involved in surviving extreme exposure
RT to ionizing radiation.";
RL J. Bacteriol. 196:3534-3545(2014).
RN [5]
RP FUNCTION, DOMAIN, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF LYS-37; CYS-437
RP AND 356-TYR--GLY-586.
RC STRAIN=K12 / MG1655 / e14;
RX PubMed=25425430; DOI=10.1111/mmi.12885;
RA Chen S.H., Byrne R.T., Wood E.A., Cox M.M.;
RT "Escherichia coli radD (yejH) gene: a novel function involved in radiation
RT resistance and double-strand break repair.";
RL Mol. Microbiol. 95:754-768(2015).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=25484163; DOI=10.1111/mmi.12899;
RA Cooper D.L., Boyle D.C., Lovett S.T.;
RT "Genetic analysis of Escherichia coli RadA: functional motifs and genetic
RT interactions.";
RL Mol. Microbiol. 95:769-779(2015).
RN [7]
RP ATPASE ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, INTERACTION WITH SSB,
RP SUBUNIT, SSDNA-BINDING, AND MUTAGENESIS OF LYS-37.
RC STRAIN=K12 / MG1655 (DE3);
RX PubMed=27519413; DOI=10.1074/jbc.m116.736223;
RA Chen S.H., Byrne-Nash R.T., Cox M.M.;
RT "Escherichia coli RadD Protein Functionally Interacts with the Single-
RT stranded DNA-binding Protein.";
RL J. Biol. Chem. 291:20779-20786(2016).
RN [8]
RP FUNCTION, DISRUPTION PHENOTYPE, AND DNA-BINDING.
RC STRAIN=K12;
RX PubMed=31665437; DOI=10.1093/nar/gkz960;
RA Romero Z.J., Armstrong T.J., Henrikus S.S., Chen S.H., Glass D.J.,
RA Ferrazzoli A.E., Wood E.A., Chitteni-Pattu S., van Oijen A.M., Lovett S.T.,
RA Robinson A., Cox M.M.;
RT "Frequent template switching in postreplication gaps: suppression of
RT deleterious consequences by the Escherichia coli Uup and RadD proteins.";
RL Nucleic Acids Res. 48:212-230(2020).
RN [9] {ECO:0007744|PDB:6JDE}
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) IN COMPLEX WITH ZINC, COFACTOR,
RP SUBUNIT, AND DOMAIN.
RC STRAIN=K12;
RX PubMed=31035307; DOI=10.1002/prot.25704;
RA Kuang X., Tang Q., Liu Y.P., Yan X.X., Xu W.;
RT "Crystal structure of a novel ATPase RadD from Escherichia coli.";
RL Proteins 87:791-795(2019).
CC -!- FUNCTION: RadD contains helicase motifs, suggesting it may be a
CC helicase, although that activity has not been observed (Probable). In
CC combination with RadA is important in repair of double-strand DNA
CC breaks (DSB) (PubMed:25425430, PubMed:25484163). Has DNA-independent
CC ATPase activity that is stimulated by single-stranded DNA-binding
CC protein SSB. ATPase is stimulated by a peptide with the last 10
CC residues of SSB, but not when the peptide's last Phe residue is
CC missing. Binds ssDNA; binding is slightly better in the presence of
CC nucleotides (PubMed:27519413). May be involved in resolution of
CC branched DNA intermediates that result from template switching in
CC postreplication gaps. Binds to DNA structures with 3 branches that
CC resemble replication forks (PubMed:31665437).
CC {ECO:0000269|PubMed:25425430, ECO:0000269|PubMed:25484163,
CC ECO:0000269|PubMed:27519413, ECO:0000269|PubMed:31665437,
CC ECO:0000305|PubMed:25425430, ECO:0000305|PubMed:25484163,
CC ECO:0000305|PubMed:27519413}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.12;
CC Evidence={ECO:0000305|PubMed:25425430, ECO:0000305|PubMed:25484163};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:31035307, ECO:0007744|PDB:6JDE};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.85 uM for ATP {ECO:0000269|PubMed:27519413};
CC KM=0.63 uM for ATP in the presence of SSB
CC {ECO:0000269|PubMed:27519413};
CC KM=0.40 uM for ATP in the presence of last 10 residues of SSB
CC {ECO:0000269|PubMed:27519413};
CC Note=ATPase activity in the presence of KCl in the absence of any
CC nucleic acid substrate. {ECO:0000269|PubMed:27519413};
CC pH dependence:
CC Optimum pH is >7.5. {ECO:0000269|PubMed:27519413};
CC -!- SUBUNIT: Monomer (PubMed:31035307, PubMed:27519413). Interacts with
CC single-stranded DNA-binding protein SSB (PubMed:27519413).
CC {ECO:0000269|PubMed:27519413, ECO:0000269|PubMed:31035307}.
CC -!- DOMAIN: The C-terminal domain (residues 356-586) is required to
CC alleviate the deleterious effects of UV or ciprofloxacin (CFX)
CC treatment in a double radA-radD mutant; its effect on ionising
CC irradiation (IR) survival in the single radD mutant were not reported
CC (PubMed:25425430). Crystals have 4 domains; helicase ATP-binding
CC (residues 7-185), helicase C-terminal (residues 187-365), a zinc finger
CC domain (residues 376-425) and the C-terminal domain (429-574)
CC (PubMed:31035307). {ECO:0000269|PubMed:25425430,
CC ECO:0000269|PubMed:31035307}.
CC -!- DISRUPTION PHENOTYPE: 100- to 10000-fold decrease in survival after IR
CC (PubMed:25049088, PubMed:25425430). Double radA-radD deletions have
CC nearly 10(6)-fold lower survival upon IR, and the double mutant is more
CC severely affected by UV radiation than either of the single mutants
CC alone (up to 100 J/m(2)). The single mutation is more sensitive to
CC dsDNA breaks induced by CFX, the double radA-radD mutant is inviable
CC upon CFX treatment; the SOS response is slightly induced in the single
CC and more induced in the double mutant. No effect on RecA-mediated
CC conjugational DNA recombination (PubMed:25425430). In another study
CC double radA-radD deletions are sensitive to CFX but not to UV (up to 40
CC J/m(2)) or azidothymidine (AZT) (PubMed:25484163). Deletion of radD
CC leads to an increase in DNA crossing over, DNA repeat deletion and DNA
CC repeat expansion; double uup-radD deletion increases the phenotypes.
CC Single radD deletion has no effect on cell growth or filamentation,
CC double uup-radD deletions are filamentous and lack defined nucleoids.
CC Single deletion is more sensitive to CFX (PubMed:31665437).
CC {ECO:0000269|PubMed:25049088, ECO:0000269|PubMed:25425430,
CC ECO:0000269|PubMed:25484163, ECO:0000269|PubMed:31665437}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA16381.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U00096; AAC75245.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76649.1; -; Genomic_DNA.
DR EMBL; U00008; AAA16381.1; ALT_FRAME; Genomic_DNA.
DR PIR; G64987; G64987.
DR RefSeq; NP_416689.1; NC_000913.3.
DR RefSeq; WP_000578061.1; NZ_LN832404.1.
DR PDB; 6JDE; X-ray; 2.80 A; A/B=1-586.
DR PDB; 7R7J; X-ray; 2.03 A; A/B=1-586.
DR PDBsum; 6JDE; -.
DR PDBsum; 7R7J; -.
DR AlphaFoldDB; P33919; -.
DR SMR; P33919; -.
DR BioGRID; 4259416; 278.
DR BioGRID; 849903; 1.
DR IntAct; P33919; 5.
DR STRING; 511145.b2184; -.
DR PaxDb; P33919; -.
DR PRIDE; P33919; -.
DR EnsemblBacteria; AAC75245; AAC75245; b2184.
DR EnsemblBacteria; BAE76649; BAE76649; BAE76649.
DR GeneID; 945529; -.
DR KEGG; ecj:JW2172; -.
DR KEGG; eco:b2184; -.
DR PATRIC; fig|1411691.4.peg.52; -.
DR EchoBASE; EB1979; -.
DR eggNOG; COG1061; Bacteria.
DR HOGENOM; CLU_014765_1_0_6; -.
DR InParanoid; P33919; -.
DR OMA; WIYQYHY; -.
DR PhylomeDB; P33919; -.
DR BioCyc; EcoCyc:EG12045-MON; -.
DR BioCyc; MetaCyc:EG12045-MON; -.
DR PRO; PR:P33919; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:EcoCyc.
DR GO; GO:0003678; F:DNA helicase activity; IEA:UniProtKB-EC.
DR GO; GO:0003697; F:single-stranded DNA binding; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; ISM:EcoCyc.
DR GO; GO:0051301; P:cell division; IMP:EcoCyc.
DR GO; GO:0006302; P:double-strand break repair; IMP:EcoCyc.
DR GO; GO:0006301; P:postreplication repair; IMP:EcoCyc.
DR GO; GO:0010212; P:response to ionizing radiation; IMP:EcoCyc.
DR GO; GO:0009410; P:response to xenobiotic stimulus; IMP:EcoCyc.
DR GO; GO:0006412; P:translation; IEA:InterPro.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR006935; Helicase/UvrB_N.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR001650; Helicase_C.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR011332; Ribosomal_zn-bd.
DR Pfam; PF00271; Helicase_C; 1.
DR Pfam; PF04851; ResIII; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR SUPFAM; SSF57829; SSF57829; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; DNA damage; DNA repair; DNA-binding; Helicase;
KW Hydrolase; Metal-binding; Nucleotide-binding; Reference proteome; Zinc.
FT CHAIN 1..586
FT /note="Putative DNA repair helicase RadD"
FT /id="PRO_0000169164"
FT DOMAIN 18..171
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00541,
FT ECO:0000303|PubMed:31035307"
FT DOMAIN 241..386
FT /note="Helicase C-terminal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00542,
FT ECO:0000303|PubMed:31035307"
FT REGION 376..425
FT /note="Zinc finger domain"
FT /evidence="ECO:0000303|PubMed:31035307"
FT REGION 429..574
FT /note="C-terminal domain"
FT /evidence="ECO:0000303|PubMed:31035307"
FT BINDING 384
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:31035307,
FT ECO:0007744|PDB:6JDE"
FT BINDING 387
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:31035307,
FT ECO:0007744|PDB:6JDE"
FT BINDING 411
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:31035307,
FT ECO:0007744|PDB:6JDE"
FT BINDING 425
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:31035307,
FT ECO:0007744|PDB:6JDE"
FT MUTAGEN 37
FT /note="K->R: Partially complements a radD deletion mutant
FT for survival of ionizing radiation (possible loss of ATPase
FT activity), increases sensitivity to UV of a double radA-
FT radD deletion. Has a dominant negative effect on survival
FT of UV in the presence of wild-type enzyme or ciprofloxacin
FT survival. Has no ATPase activity, does not bind ssDNA."
FT /evidence="ECO:0000269|PubMed:25425430,
FT ECO:0000269|PubMed:27519413"
FT MUTAGEN 356..586
FT /note="Missing: Does not complement sensitivity of a double
FT radA-radD deletion to dsDNA breaks."
FT /evidence="ECO:0000269|PubMed:25425430"
FT MUTAGEN 437
FT /note="C->A: Does not complement sensitivity of a double
FT radA-radD deletion to dsDNA breaks."
FT /evidence="ECO:0000269|PubMed:25425430"
FT HELIX 7..22
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 38..47
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 49..58
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 59..70
FT /evidence="ECO:0007829|PDB:6JDE"
FT TURN 71..73
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 77..80
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 91..96
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 97..101
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 104..106
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 111..116
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 119..122
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 128..140
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 145..149
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 153..155
FT /evidence="ECO:0007829|PDB:6JDE"
FT TURN 156..158
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 159..165
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 168..170
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 177..184
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 187..192
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 224..233
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 238..248
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 249..251
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 253..258
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 262..270
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 276..280
FT /evidence="ECO:0007829|PDB:6JDE"
FT TURN 286..288
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 289..295
FT /evidence="ECO:0007829|PDB:6JDE"
FT TURN 296..299
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 302..310
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 319..324
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 331..338
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 339..341
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 351..355
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 378..383
FT /evidence="ECO:0007829|PDB:6JDE"
FT TURN 385..387
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 390..397
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 399..401
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 403..406
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 413..416
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 422..424
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 428..431
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 458..466
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 471..486
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 489..498
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 503..509
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 513..522
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 524..527
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 528..530
FT /evidence="ECO:0007829|PDB:6JDE"
FT HELIX 540..545
FT /evidence="ECO:0007829|PDB:6JDE"
FT TURN 546..548
FT /evidence="ECO:0007829|PDB:6JDE"
FT STRAND 554..571
FT /evidence="ECO:0007829|PDB:6JDE"
SQ SEQUENCE 586 AA; 66413 MW; 2D173250F83333DF CRC64;
MIFTLRPYQQ EAVDATLNHF RRHKTPAVIV LPTGAGKSLV IAELARLARG RVLVLAHVKE
LVAQNHAKYQ ALGLEADIFA AGLKRKESHG KVVFGSVQSV ARNLDAFQGE FSLLIVDECH
RIGDDEESQY QQILTHLTKV NPHLRLLGLT ATPFRLGKGW IYQFHYHGMV RGDEKALFRD
CIYELPLRYM IKHGYLTPPE RLDMPVVQYD FSRLQAQSNG LFSEADLNRE LKKQQRITPH
IISQIMEFAA TRKGVMIFAA TVEHAKEIVG LLPAEDAALI TGDTPGAERD VLIENFKAQR
FRYLVNVAVL TTGFDAPHVD LIAILRPTES VSLYQQIVGR GLRLAPGKTD CLILDYAGNP
HDLYAPEVGT PKGKSDNVPV QVFCPACGFA NTFWGKTTAD GTLIEHFGRR CQGWFEDDDG
HREQCDFRFR FKNCPQCNAE NDIAARRCRE CDTVLVDPDD MLKAALRLKD ALVLRCSGMS
LQHGHDEKGE WLKITYYDED GADVSERFRL QTPAQRTAFE QLFIRPHTRT PGIPLRWITA
ADILAQQALL RHPDFVVARM KGQYWQVREK VFDYEGRFRL AHELRG
