DING_ECOLI
ID DING_ECOLI Reviewed; 716 AA.
AC P27296;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 3.
DT 03-AUG-2022, entry version 165.
DE RecName: Full=ATP-dependent DNA helicase DinG {ECO:0000255|HAMAP-Rule:MF_02205, ECO:0000305};
DE EC=3.6.4.12 {ECO:0000255|HAMAP-Rule:MF_02205, ECO:0000269|PubMed:12748189, ECO:0000269|PubMed:17416902};
GN Name=dinG {ECO:0000255|HAMAP-Rule:MF_02205, ECO:0000303|PubMed:1629168};
GN Synonyms=rarB; OrderedLocusNames=b0799, JW0784;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8037924; DOI=10.1266/jjg.69.1;
RA Ohmori H.;
RT "Structural analysis of the rhlE gene of Escherichia coli.";
RL Jpn. J. Genet. 69:1-12(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND INDUCTION.
RX PubMed=1629168; DOI=10.1128/jb.174.15.5110-5116.1992;
RA Lewis L.K., Mount D.W.;
RT "Interaction of LexA repressor with the asymmetric dinG operator and
RT complete nucleotide sequence of the gene.";
RL J. Bacteriol. 174:5110-5116(1992).
RN [3]
RP SEQUENCE REVISION.
RX PubMed=8385320; DOI=10.1093/nar/21.6.1497;
RA Koonin E.V.;
RT "Escherichia coli dinG gene encodes a putative DNA helicase related to a
RT group of eukaryotic helicases including Rad3 protein.";
RL Nucleic Acids Res. 21:1497-1497(1993).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [5]
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 [6]
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 [7]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, SUBUNIT, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=12748189; DOI=10.1074/jbc.m301188200;
RA Voloshin O.N., Vanevski F., Khil P.P., Camerini-Otero R.D.;
RT "Characterization of the DNA damage-inducible helicase DinG from
RT Escherichia coli.";
RL J. Biol. Chem. 278:28284-28293(2003).
RN [8]
RP FUNCTION, AND CATALYTIC ACTIVITY.
RX PubMed=17416902; DOI=10.1074/jbc.m700376200;
RA Voloshin O.N., Camerini-Otero R.D.;
RT "The DinG protein from Escherichia coli is a structure-specific helicase.";
RL J. Biol. Chem. 282:18437-18447(2007).
RN [9]
RP COFACTOR, IRON-SULFUR-BINDING, ACTIVITY REGULATION, AND MUTAGENESIS OF
RP CYS-120; CYS-194; CYS-199 AND CYS-205.
RX PubMed=19074432; DOI=10.1074/jbc.m807943200;
RA Ren B., Duan X., Ding H.;
RT "Redox control of the DNA damage-inducible protein DinG helicase activity
RT via its iron-sulfur cluster.";
RL J. Biol. Chem. 284:4829-4835(2009).
RN [10]
RP FUNCTION.
RX PubMed=24738733; DOI=10.1021/ja501973c;
RA Grodick M.A., Segal H.M., Zwang T.J., Barton J.K.;
RT "DNA-mediated signaling by proteins with 4Fe-4S clusters is necessary for
RT genomic integrity.";
RL J. Am. Chem. Soc. 136:6470-6478(2014).
CC -!- FUNCTION: DNA-dependent ATPase and 5'-3' DNA helicase (PubMed:12748189,
CC PubMed:17416902). Can also unwind DNA-RNA hybrid duplexes. Is active on
CC D-loops and R-loops, and on forked structures (PubMed:17416902). May be
CC involved in recombinational DNA repair and the resumption of
CC replication after DNA damage (PubMed:17416902). The redox cluster is
CC involved in DNA-mediated charge-transport signaling between DNA repair
CC proteins from distinct pathways. DinG cooperates at long-range with
CC endonuclease III, a base excision repair enzyme, using DNA charge
CC transport to redistribute to regions of DNA damage (PubMed:24738733).
CC {ECO:0000269|PubMed:12748189, ECO:0000269|PubMed:17416902,
CC ECO:0000269|PubMed:24738733}.
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:0000255|HAMAP-Rule:MF_02205,
CC ECO:0000269|PubMed:12748189, ECO:0000269|PubMed:17416902};
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02205,
CC ECO:0000269|PubMed:19074432};
CC Note=Binds 1 [4Fe-4S] cluster. The iron-sulfur cluster is essential for
CC protein stability and helicase activity. {ECO:0000269|PubMed:19074432};
CC -!- ACTIVITY REGULATION: ATPase activity is 15-fold stimulated by single-
CC stranded DNA (ssDNA). ATP-dependent DNA helicase activity requires
CC divalent cations (Mg(2+), Ca(2+) or Mn(2+)) but is not detected in the
CC presence of Zn(2+) (PubMed:12748189). Reduction of the [4Fe-4S] cluster
CC reversibly switches off helicase activity. Remains fully active after
CC exposure to 100-fold excess of hydrogen peroxide, but the [4Fe-4S]
CC cluster can be efficiently modified by nitric oxide (NO), forming the
CC DinG-bound dinitrosyl iron complex with the concomitant inactivation of
CC helicase activity (PubMed:19074432). {ECO:0000269|PubMed:12748189,
CC ECO:0000269|PubMed:19074432}.
CC -!- SUBUNIT: Monomer in solution. {ECO:0000269|PubMed:12748189}.
CC -!- INTERACTION:
CC P27296; P0AGE0: ssb; NbExp=2; IntAct=EBI-1114590, EBI-1118620;
CC -!- INDUCTION: DNA damage-inducible. Transcriptionally regulated by LexA.
CC {ECO:0000269|PubMed:1629168}.
CC -!- DISRUPTION PHENOTYPE: Deletion of the gene results in a slight
CC reduction of UV resistance. {ECO:0000269|PubMed:12748189}.
CC -!- SIMILARITY: Belongs to the helicase family. DinG subfamily. Type 1 sub-
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_02205, ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA23685.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; L02123; AAA53655.1; -; Genomic_DNA.
DR EMBL; M81935; AAA23685.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00096; AAC73886.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35465.1; -; Genomic_DNA.
DR PIR; G64816; G64816.
DR RefSeq; NP_415320.1; NC_000913.3.
DR RefSeq; WP_001340191.1; NZ_STEB01000019.1.
DR PDB; 6FWR; X-ray; 2.50 A; A=1-716.
DR PDB; 6FWS; X-ray; 2.50 A; A/B=1-716.
DR PDBsum; 6FWR; -.
DR PDBsum; 6FWS; -.
DR AlphaFoldDB; P27296; -.
DR SMR; P27296; -.
DR BioGRID; 4259964; 118.
DR IntAct; P27296; 22.
DR MINT; P27296; -.
DR STRING; 511145.b0799; -.
DR BindingDB; P27296; -.
DR PaxDb; P27296; -.
DR PRIDE; P27296; -.
DR EnsemblBacteria; AAC73886; AAC73886; b0799.
DR EnsemblBacteria; BAA35465; BAA35465; BAA35465.
DR GeneID; 945431; -.
DR KEGG; ecj:JW0784; -.
DR KEGG; eco:b0799; -.
DR PATRIC; fig|511145.12.peg.826; -.
DR EchoBASE; EB1332; -.
DR eggNOG; COG1199; Bacteria.
DR HOGENOM; CLU_012117_4_1_6; -.
DR InParanoid; P27296; -.
DR OMA; PRRAQNY; -.
DR PhylomeDB; P27296; -.
DR BioCyc; EcoCyc:EG11357-MON; -.
DR BioCyc; MetaCyc:EG11357-MON; -.
DR PRO; PR:P27296; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:EcoliWiki.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003678; F:DNA helicase activity; IDA:EcoCyc.
DR GO; GO:0033677; F:DNA/RNA helicase activity; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0032508; P:DNA duplex unwinding; IDA:EcoCyc.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IBA:GO_Central.
DR GO; GO:0009432; P:SOS response; IEP:EcoCyc.
DR Gene3D; 3.40.50.300; -; 2.
DR HAMAP; MF_02205; DinG_proteobact; 1.
DR InterPro; IPR006555; ATP-dep_Helicase_C.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR010614; DEAD_2.
DR InterPro; IPR045028; DinG/Rad3-like.
DR InterPro; IPR039000; DinG_proteobact.
DR InterPro; IPR014013; Helic_SF1/SF2_ATP-bd_DinG/Rad3.
DR InterPro; IPR006554; Helicase-like_DEXD_c2.
DR InterPro; IPR014001; Helicase_ATP-bd.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR11472; PTHR11472; 1.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF06733; DEAD_2; 1.
DR Pfam; PF13307; Helicase_C_2; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00488; DEXDc2; 1.
DR SMART; SM00491; HELICc2; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR PROSITE; PS51193; HELICASE_ATP_BIND_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; ATP-binding; DNA damage; DNA recombination;
KW DNA repair; DNA-binding; Helicase; Hydrolase; Iron; Iron-sulfur;
KW Metal-binding; Nucleotide-binding; Reference proteome.
FT CHAIN 1..716
FT /note="ATP-dependent DNA helicase DinG"
FT /id="PRO_0000101996"
FT DOMAIN 17..294
FT /note="Helicase ATP-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02205"
FT MOTIF 248..251
FT /note="DEAH box"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02205"
FT BINDING 54..61
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02205"
FT BINDING 120
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02205,
FT ECO:0000305|PubMed:19074432"
FT BINDING 194
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02205,
FT ECO:0000305|PubMed:19074432"
FT BINDING 199
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02205,
FT ECO:0000305|PubMed:19074432"
FT BINDING 205
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02205,
FT ECO:0000305|PubMed:19074432"
FT MUTAGEN 120
FT /note="C->S: Abolishes iron-sulfur-binding."
FT /evidence="ECO:0000269|PubMed:19074432"
FT MUTAGEN 194
FT /note="C->S: Abolishes iron-sulfur-binding."
FT /evidence="ECO:0000269|PubMed:19074432"
FT MUTAGEN 199
FT /note="C->S: Abolishes iron-sulfur-binding."
FT /evidence="ECO:0000269|PubMed:19074432"
FT MUTAGEN 205
FT /note="C->S: Abolishes iron-sulfur-binding."
FT /evidence="ECO:0000269|PubMed:19074432"
FT CONFLICT 513
FT /note="N -> H (in Ref. 2; AAA23685)"
FT /evidence="ECO:0000305"
FT HELIX 5..19
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 29..42
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 50..53
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 60..75
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 78..85
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 86..94
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 96..103
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 115..117
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 121..129
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 137..142
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 150..164
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 172..174
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 181..187
FT /evidence="ECO:0007829|PDB:6FWR"
FT TURN 191..193
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 196..198
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 206..215
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 218..223
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 224..232
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 235..237
FT /evidence="ECO:0007829|PDB:6FWS"
FT HELIX 240..242
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 243..247
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 250..252
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 253..258
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 259..261
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 262..266
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 269..289
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 297..299
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 301..323
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 332..335
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 337..339
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 343..372
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 379..407
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 416..424
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 426..438
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 441..447
FT /evidence="ECO:0007829|PDB:6FWR"
FT TURN 448..451
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 455..460
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 469..475
FT /evidence="ECO:0007829|PDB:6FWR"
FT TURN 479..482
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 484..487
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 494..497
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 498..501
FT /evidence="ECO:0007829|PDB:6FWR"
FT TURN 511..513
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 514..530
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 535..540
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 544..553
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 555..560
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 561..564
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 569..581
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 586..591
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 592..597
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 602..604
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 606..610
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 621..632
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 637..640
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 642..654
FT /evidence="ECO:0007829|PDB:6FWR"
FT STRAND 665..669
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 673..676
FT /evidence="ECO:0007829|PDB:6FWR"
FT HELIX 678..685
FT /evidence="ECO:0007829|PDB:6FWR"
SQ SEQUENCE 716 AA; 81440 MW; 63E6767E8EAA67D2 CRC64;
MALTAALKAQ IAAWYKALQE QIPDFIPRAP QRQMIADVAK TLAGEEGRHL AIEAPTGVGK
TLSYLIPGIA IAREEQKTLV VSTANVALQD QIYSKDLPLL KKIIPDLKFT AAFGRGRYVC
PRNLTALAST EPTQQDLLAF LDDELTPNNQ EEQKRCAKLK GDLDTYKWDG LRDHTDIAID
DDLWRRLSTD KASCLNRNCY YYRECPFFVA RREIQEAEVV VANHALVMAA MESEAVLPDP
KNLLLVLDEG HHLPDVARDA LEMSAEITAP WYRLQLDLFT KLVATCMEQF RPKTIPPLAI
PERLNAHCEE LYELIASLNN ILNLYMPAGQ EAEHRFAMGE LPDEVLEICQ RLAKLTEMLR
GLAELFLNDL SEKTGSHDIV RLHRLILQMN RALGMFEAQS KLWRLASLAQ SSGAPVTKWA
TREEREGQLH LWFHCVGIRV SDQLERLLWR SIPHIIVTSA TLRSLNSFSR LQEMSGLKEK
AGDRFVALDS PFNHCEQGKI VIPRMRVEPS IDNEEQHIAE MAAFFRKQVE SKKHLGMLVL
FASGRAMQRF LDYVTDLRLM LLVQGDQPRY RLVELHRKRV ANGERSVLVG LQSFAEGLDL
KGDLLSQVHI HKIAFPPIDS PVVITEGEWL KSLNRYPFEV QSLPSASFNL IQQVGRLIRS
HGCWGEVVIY DKRLLTKNYG KRLLDALPVF PIEQPEVPEG IVKKKEKTKS PRRRRR
