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Escherichia coli K-12 substr. MG1655 Polypeptide: ATP-dependent helicase



Gene: dinG Accession Numbers: EG11357 (EcoCyc), b0799, ECK0788

Synonyms: rarB

Regulation Summary Diagram: ?

Summary:
DinG exhibits ATP-dependent DNA helicase activity that may play a role in DNA repair and replication. DinG ATPase activity is increased in the presence of single-stranded DNA. The helicase activity is supported by either ATP or dATP, and helicase activity exhibits a requirement for divalent cation that is satisfied by Mg2+, Ca2+, or Mn2+, but not by Zn2+ [Voloshin03].

DinG is active on D-loops in vitro [Voloshin07] and on on R-loops (unique DNA/RNA duplexes that form when an RNA transcript binds to DNA behind the site of transcription) in vitro and in vivo [Voloshin07, Boubakri10]. Inversion of highly transcribed rRNA operons renders dinG essential for growth in rich medium. DinG facilitates progression of replication forks through inverted rRNA operons [Boubakri10].

DinG contains a redox-active [4Fe-4S] cluster with a midpoint redox potential of -390 mV (pH 8.0). Reduction of the iron-sulfur cluster reversibly inactivates helicase activity in vitro [Ren09a]. DNA bound DinG has a reduction potential of 80mV. DNA binding shifts the redox potential of the DinG [4Fe-4S] cluster toward oxidation [Grodick14]. The [4Fe-4S] cluster is involved in DNA charge transfer [Genereux10] - which may be used by DinG to search for for R-loops to repair [Grodick14]. DinG preferentially redistributes onto DNA strands where charge transfer is inhibited by single base mismatches. DinG and Endonuclease III use DNA mediated charge transfer to localise to regions of DNA damage [Grodick14].

DinG is monomeric [Voloshin03]. DinG contains one [4Fe-4S] cluster per monomer; 4 conserved cysteine residues (Cys120, Cys194, Cys199 and Cys205) are essential for cluster binding [Ren09a]. The DinG iron-sulfur cluster is reversibly modified by nitric oxide with concomitant loss of helicase activity [Ren09a]

A dinG mutant is viable and somewhat UV-sensitive, compared to wild type. DinG overproduction causes some UV sensitivity [Voloshin03]. Overexpression of dinG, dinI, or LexA suppresses the cold sensitivity of a dinD mutant [Yasuda96].

Transcription of dinG is induced by nalidixic acid [Van01a] or mitomycin [Lewis92]. Transcription is regulated by LexA via an atypical binding site [Lewis92, Lewis92a].

Citations: [Courcelle01]

Locations: cytosol

Map Position: [832,293 -> 834,443] (17.94 centisomes)
Length: 2151 bp / 716 aa

Molecular Weight of Polypeptide: 81.44 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0002732 , CGSC:31247 , EchoBASE:EB1332 , EcoGene:EG11357 , EcoliWiki:b0799 , Mint:MINT-8393557 , OU-Microarray:b0799 , PortEco:dinG , Pride:P27296 , Protein Model Portal:P27296 , RefSeq:NP_415320 , RegulonDB:EG11357 , SMR:P27296 , String:511145.b0799 , UniProt:P27296

Relationship Links: InterPro:IN-FAMILY:IPR006555 , InterPro:IN-FAMILY:IPR010614 , InterPro:IN-FAMILY:IPR011545 , InterPro:IN-FAMILY:IPR014001 , InterPro:IN-FAMILY:IPR014013 , InterPro:IN-FAMILY:IPR027417 , Pfam:IN-FAMILY:PF00270 , Pfam:IN-FAMILY:PF06733 , Pfam:IN-FAMILY:PF13307 , Prosite:IN-FAMILY:PS51193 , Smart:IN-FAMILY:SM00487 , Smart:IN-FAMILY:SM00491

In Paralogous Gene Group: 202 (2 members)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006200 - ATP catabolic process Inferred from experiment [Voloshin03]
GO:0006281 - DNA repair Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Grodick14]
GO:0009432 - SOS response Inferred from experiment [Lewis92]
GO:0032508 - DNA duplex unwinding Inferred from experiment [Voloshin03]
GO:0006139 - nucleobase-containing compound metabolic process Inferred by computational analysis [GOA01a]
GO:0006310 - DNA recombination Inferred by computational analysis [UniProtGOA11a]
GO:0006974 - cellular response to DNA damage stimulus Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003678 - DNA helicase activity Inferred from experiment [Voloshin03]
GO:0004003 - ATP-dependent DNA helicase activity Inferred from experiment Inferred by computational analysis [GOA01a, Voloshin03]
GO:0005515 - protein binding Inferred from experiment [Cheng12]
GO:0016887 - ATPase activity Inferred from experiment [Voloshin03]
GO:0033680 - ATP-dependent DNA/RNA helicase activity Inferred from experiment [Voloshin07]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Ren09a]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0004386 - helicase activity Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008026 - ATP-dependent helicase activity Inferred by computational analysis [GOA01a]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by curator Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes SOS response
information transfer DNA related DNA repair
information transfer DNA related
regulation type of regulation DNA structure level bent DNA or supercoiling, inversion

Essentiality data for dinG knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Credits:
Last-Curated ? 19-May-2014 by Mackie A , Macquarie University


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 17 -> 294
[UniProt09]
UniProt: Helicase ATP-binding;
Nucleotide-Phosphate-Binding-Region 54 -> 61
[UniProt10a]
UniProt: ATP; Non-Experimental Qualifier: probable;
Mutagenesis-Variant 120
[Ren09a, UniProt12a]
Alternate sequence: C → S; UniProt: Abolishes iron-sulfur-binding.
Metal-Binding-Site 120
[UniProt12a]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 194
[Ren09a, UniProt12a]
Alternate sequence: C → S; UniProt: Abolishes iron-sulfur-binding.
Metal-Binding-Site 194
[UniProt12a]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 199
[Ren09a, UniProt12a]
Alternate sequence: C → S; UniProt: Abolishes iron-sulfur-binding.
Metal-Binding-Site 199
[UniProt12a]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 205
[Ren09a, UniProt12a]
Alternate sequence: C → S; UniProt: Abolishes iron-sulfur-binding.
Metal-Binding-Site 205
[UniProt12a]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity.
Protein-Segment 248 -> 251
[UniProt10]
UniProt: DEGH box; Sequence Annotation Type: short sequence motif;
Sequence-Conflict 513
[Lewis92a, UniProt10]
Alternate sequence: N → H; UniProt: (in Ref. 2; AAA23685);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0799 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11357; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Boubakri10: Boubakri H, de Septenville AL, Viguera E, Michel B (2010). "The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo." EMBO J 29(1);145-57. PMID: 19851282

Cheng12: Cheng Z, Caillet A, Ren B, Ding H (2012). "Stimulation of Escherichia coli DNA damage inducible DNA helicase DinG by the single-stranded DNA binding protein SSB." FEBS Lett 586(21);3825-30. PMID: 23036643

Courcelle01: Courcelle J, Khodursky A, Peter B, Brown PO, Hanawalt PC (2001). "Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli." Genetics 158(1);41-64. PMID: 11333217

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Genereux10: Genereux JC, Barton JK (2010). "Mechanisms for DNA charge transport." Chem Rev 110(3);1642-62. PMID: 20214403

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Grodick14: Grodick MA, Segal HM, Zwang TJ, Barton JK (2014). "DNA-Mediated Signaling by Proteins with 4Fe-4S Clusters Is Necessary for Genomic Integrity." J Am Chem Soc 136(17);6470-8. PMID: 24738733

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Lewis92: Lewis LK, Jenkins ME, Mount DW (1992). "Isolation of DNA damage-inducible promoters in Escherichia coli: regulation of polB (dinA), dinG, and dinH by LexA repressor." J Bacteriol 174(10);3377-85. PMID: 1577702

Lewis92a: Lewis LK, Mount DW (1992). "Interaction of LexA repressor with the asymmetric dinG operator and complete nucleotide sequence of the gene." J Bacteriol 174(15);5110-6. PMID: 1629168

Ren09a: Ren B, Duan X, Ding H (2009). "Redox control of the DNA damage-inducible protein DinG helicase activity via its iron-sulfur cluster." J Biol Chem 284(8);4829-35. PMID: 19074432

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-11 released on 2012-11-26 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Van01a: Van Dyk TK, DeRose EJ, Gonye GE (2001). "LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains." J Bacteriol 183(19);5496-505. PMID: 11544210

Voloshin03: Voloshin ON, Vanevski F, Khil PP, Camerini-Otero RD (2003). "Characterization of the DNA damage-inducible helicase DinG from Escherichia coli." J Biol Chem 278(30):28284-93. PMID: 12748189

Voloshin07: Voloshin ON, Camerini-Otero RD (2007). "The DinG protein from Escherichia coli is a structure-specific helicase." J Biol Chem 282(25);18437-47. PMID: 17416902

Yasuda96: Yasuda T, Nagata T, Ohmori H (1996). "Multicopy suppressors of the cold-sensitive phenotype of the pcsA68 (dinD68) mutation in Escherichia coli." J Bacteriol 178(13);3854-9. PMID: 8682790


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, biocyc14.