MetaCyc Enzyme: ATP-dependent DNA helicase

Gene: recQ Accession Numbers: EG10833 (MetaCyc), b3822, ECK3816

Species: Escherichia coli K-12 substr. MG1655

A component of the RecF recombinational pathway, RecQ is a helicase that functions in blocking illegitimate recombination, enhancing topoisomerase activity, initiating SOS signaling and clearing blocked replication forks.

RecQ is an ATP-dependent DNA helicase [Umezu90]. Its activity also depends on magnesium ion and single-strand binding protein (SSB) [Harmon01, Umezu93a]. Its kM for dsDNA is 0.5-0.9 uM (measured in concentration of base pairs), with a kcat of 2.3-2.7 base pairs/s/RecQ monomer and optimal activity at 0.05mM magnesium ion [Harmon01]. Cooperativity of ATP binding suggests a multimeric active form, but ample evidence indicates that RecQ functions as a monomer [Harmon01, Xu03]. Based on fluorescence titration, one RecQ binds per ten nucleotides of substrate DNA, and single-stranded and duplex DNA bind competitively [Dou04]. Fluorescence evaluation has also been used to determine the dependence of DNA unwinding rate on the concentration of RecQ and magnesium ion [Zhang05g].

As it carries out its helicase activity, RecQ also stimulates topoisomerase III, leading to enhanced supercoiling and catenation of covalently closed DNA [Harmon99, Harmon03].

RecQ suppresses illegitimate recombination that occurs via regions of short homology, as well as spontaneous and UV-induced recombination [Ikeda04, Hanada97, Hanada00]. In vitro, RecQ can initiate homologous recombination in the company of RecA and SSB, but also unwinds RecA-formed recombinational junctions, disrupting recombination [Harmon98].

RecQ binds blocked replication forks, specifically binding forks with leading strand gaps more efficiently than those with lagging strand gaps or Holliday junctions. It then unwinds the duplex DNA template and the lagging strand, generating a gap on the lagging strand [Courcelle99, Courcelle03a, Hishida04].

RecQ consists of a large (59 kD) amino-terminal domain that contains its helicase activity and a smaller (9 kD) carboxy-terminal domain that contains its DNA-binding activity [Bernstein03a]. Crystal structures of the catalytic core have been determined to 1.8 Å resolution in the unbound state and to 2.5 Å resolution in the ATP-bound state. The core consists of four subdomains, two of which make up the helicase region, the other two forming zinc-binding motifs [Bernstein03]. This zinc-binding region is required for protein stability and DNA binding, but not for enzymatic activity [Liu04e]. The crystal structure of the carboxy-terminal Helicase-and-RNase-D-C-terminal (HRDC) domain has also been determined, and has a globular fold similar to other DNA binding domains [Bernstein05].

Loss of recQ yields thymineless death and deficiency in the RecF recombination pathway, as well as inhibition of the SOS response [Nakayama85, Hishida04]. A triple mutant lacking the helicases RecQ, HelD and UvrD is deficient in homologous recombination and recombinational DNA repair [Mendonca95].

Citations: [Irino86, Morimatsu14]

Locations: cytosol, bacterial nucleoid

Map Position: [4,003,887 -> 4,005,716]

Molecular Weight of Polypeptide: 68.363 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012483 , CGSC:17959 , DIP:DIP-10656N , EchoBASE:EB0826 , EcoGene:EG10833 , EcoliWiki:b3822 , Mint:MINT-1223947 , ModBase:P15043 , OU-Microarray:b3822 , PortEco:recQ , PR:PRO_000023706 , Protein Model Portal:P15043 , RefSeq:YP_026263 , RegulonDB:EG10833 , SMR:P15043 , String:511145.b3822 , UniProt:P15043

Relationship Links: InterPro:IN-FAMILY:IPR001650 , InterPro:IN-FAMILY:IPR002121 , InterPro:IN-FAMILY:IPR004589 , InterPro:IN-FAMILY:IPR006293 , InterPro:IN-FAMILY:IPR010997 , InterPro:IN-FAMILY:IPR011545 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR014001 , InterPro:IN-FAMILY:IPR018982 , InterPro:IN-FAMILY:IPR027417 , PDB:Structure:1OYW , PDB:Structure:1OYY , PDB:Structure:1WUD , Pfam:IN-FAMILY:PF00270 , Pfam:IN-FAMILY:PF00271 , Pfam:IN-FAMILY:PF00570 , Pfam:IN-FAMILY:PF09382 , Prosite:IN-FAMILY:PS50967 , Prosite:IN-FAMILY:PS51192 , Prosite:IN-FAMILY:PS51194 , Smart:IN-FAMILY:SM00341 , Smart:IN-FAMILY:SM00487 , Smart:IN-FAMILY:SM00490 , Smart:IN-FAMILY:SM00956

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006281 - DNA repair Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Mendonca95]
GO:0006310 - DNA recombination Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Harmon98, Mendonca95]
GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Mendonca95]
GO:0032508 - DNA duplex unwinding Inferred from experiment Inferred by computational analysis [GOA01a, Umezu90, Xu03]
GO:0006260 - DNA replication Inferred by computational analysis [GOA01a]
GO:0009432 - SOS response Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0044237 - cellular metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003677 - DNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Dou04]
GO:0004003 - ATP-dependent DNA helicase activity Inferred from experiment Inferred by computational analysis [GOA01a, Umezu90]
GO:0005515 - protein binding Inferred from experiment [Shereda09]
GO:0008094 - DNA-dependent ATPase activity Inferred from experiment [Umezu90]
GO:0008270 - zinc ion binding Inferred from experiment [Liu04e]
GO:0016887 - ATPase activity Inferred from experiment [Umezu90]
GO:0017116 - single-stranded DNA-dependent ATP-dependent DNA helicase activity Inferred from experiment [Xu03]
GO:0046914 - transition metal ion binding Inferred from experiment [Umezu90]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01a]
GO:0003824 - catalytic activity Inferred by computational analysis [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:0043140 - ATP-dependent 3'-5' DNA helicase activity Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Umezu90]
GO:0017117 - single-stranded DNA-dependent ATP-dependent DNA helicase complex Inferred from experiment [Xu03]
GO:0030894 - replisome Inferred from experiment [Sanchez06a]
GO:0043590 - bacterial nucleoid Inferred from experiment [Sanchez06a]
GO:0005622 - intracellular Inferred by computational analysis [GOA01a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer DNA related DNA recombination
information transfer DNA related DNA repair
information transfer DNA related DNA replication

Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

Enzymatic reaction of: ATP-dependent DNA helicase

a supercoiled duplex DNA + ATP <=> a single stranded DNA + ADP + phosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.

Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

Cofactors or Prosthetic Groups: Mg2+ [Harmon01]

Kinetic Parameters:

Km (μM)
a supercoiled duplex DNA

Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Umezu90, UniProt11]
UniProt: Removed.
Chain 2 -> 609
UniProt: ATP-dependent DNA helicase recQ;
Conserved-Region 34 -> 202
UniProt: Helicase ATP-binding;
Nucleotide-Phosphate-Binding-Region 47 -> 54
UniProt: ATP; Non-Experimental Qualifier: potential;
Protein-Segment 146 -> 149
UniProt: DEAH box; Sequence Annotation Type: short sequence motif.
Conserved-Region 223 -> 371
UniProt: Helicase C-terminal;
Sequence-Conflict 255
[Irino86, Daniels92, UniProt10]
UniProt: (in Ref. 1 and 2);
Sequence-Conflict 503 -> 504
[Irino86, Daniels92, UniProt10]
UniProt: (in Ref. 1 and 2);
Conserved-Region 529 -> 609
UniProt: HRDC;
Sequence-Conflict 600
[Irino86, UniProt10]
UniProt: (in Ref. 1; AAA24517);

Suzanne Paley on Thu Oct 21, 2004:
Position updated based on U00096.2 release of genome
10/20/97 Gene b3822 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10833; confirmed by SwissProt match.


Bernstein03: Bernstein DA, Zittel MC, Keck JL (2003). "High-resolution structure of the E.coli RecQ helicase catalytic core." EMBO J 22(19);4910-21. PMID: 14517231

Bernstein03a: Bernstein DA, Keck JL (2003). "Domain mapping of Escherichia coli RecQ defines the roles of conserved N- and C-terminal regions in the RecQ family." Nucleic Acids Res 31(11);2778-85. PMID: 12771204

Bernstein05: Bernstein DA, Keck JL (2005). "Conferring substrate specificity to DNA helicases: role of the RecQ HRDC domain." Structure 13(8);1173-82. PMID: 16084389

Courcelle03a: Courcelle J, Donaldson JR, Chow KH, Courcelle CT (2003). "DNA damage-induced replication fork regression and processing in Escherichia coli." Science 299(5609);1064-7. PMID: 12543983

Courcelle99: Courcelle J, Hanawalt PC (1999). "RecQ and RecJ process blocked replication forks prior to the resumption of replication in UV-irradiated Escherichia coli." Mol Gen Genet 262(3);543-51. PMID: 10589843

Daniels92: Daniels DL, Plunkett G, Burland V, Blattner FR (1992). "Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes." Science 1992;257(5071);771-8. PMID: 1379743

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

Dou04: Dou SX, Wang PY, Xu HQ, Xi XG (2004). "The DNA binding properties of the Escherichia coli RecQ helicase." J Biol Chem 279(8);6354-63. PMID: 14665634

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

Hanada00: Hanada K, Iwasaki M, Ihashi S, Ikeda H (2000). "UvrA and UvrB suppress illegitimate recombination: synergistic action with RecQ helicase." Proc Natl Acad Sci U S A 97(11);5989-94. PMID: 10811888

Hanada97: Hanada K, Ukita T, Kohno Y, Saito K, Kato J, Ikeda H (1997). "RecQ DNA helicase is a suppressor of illegitimate recombination in Escherichia coli." Proc Natl Acad Sci U S A 94(8);3860-5. PMID: 9108069

Harmon01: Harmon FG, Kowalczykowski SC (2001). "Biochemical characterization of the DNA helicase activity of the escherichia coli RecQ helicase." J Biol Chem 276(1);232-43. PMID: 11024023

Harmon03: Harmon FG, Brockman JP, Kowalczykowski SC (2003). "RecQ helicase stimulates both DNA catenation and changes in DNA topology by topoisomerase III." J Biol Chem 278(43);42668-78. PMID: 12909639

Harmon98: Harmon FG, Kowalczykowski SC (1998). "RecQ helicase, in concert with RecA and SSB proteins, initiates and disrupts DNA recombination." Genes Dev 12(8);1134-44. PMID: 9553043

Harmon99: Harmon FG, DiGate RJ, Kowalczykowski SC (1999). "RecQ helicase and topoisomerase III comprise a novel DNA strand passage function: a conserved mechanism for control of DNA recombination." Mol Cell 3(5);611-20. PMID: 10360177

Hishida04: Hishida T, Han YW, Shibata T, Kubota Y, Ishino Y, Iwasaki H, Shinagawa H (2004). "Role of the Escherichia coli RecQ DNA helicase in SOS signaling and genome stabilization at stalled replication forks." Genes Dev 18(15);1886-97. PMID: 15289460

Ikeda04: Ikeda H, Shiraishi K, Ogata Y (2004). "Illegitimate recombination mediated by double-strand break and end-joining in Escherichia coli." Adv Biophys 38(Complete);3-20. PMID: 15476890

Irino86: Irino N, Nakayama K, Nakayama H (1986). "The recQ gene of Escherichia coli K12: primary structure and evidence for SOS regulation." Mol Gen Genet 205(2);298-304. PMID: 3027506

Liu04e: Liu JL, Rigolet P, Dou SX, Wang PY, Xi XG (2004). "The zinc finger motif of Escherichia coli RecQ is implicated in both DNA binding and protein folding." J Biol Chem 279(41);42794-802. PMID: 15292213

Mendonca95: Mendonca VM, Klepin HD, Matson SW (1995). "DNA helicases in recombination and repair: construction of a delta uvrD delta helD delta recQ mutant deficient in recombination and repair." J Bacteriol 177(5);1326-35. PMID: 7868608

Morimatsu14: Morimatsu K, Kowalczykowski SC (2014). "RecQ helicase and RecJ nuclease provide complementary functions to resect DNA for homologous recombination." Proc Natl Acad Sci U S A 111(48);E5133-42. PMID: 25411316

Nakayama85: Nakayama K, Irino N, Nakayama H (1985). "The recQ gene of Escherichia coli K12: molecular cloning and isolation of insertion mutants." Mol Gen Genet 200(2);266-71. PMID: 2993821

Sanchez06a: Sanchez H, Kidane D, Castillo Cozar M, Graumann PL, Alonso JC (2006). "Recruitment of Bacillus subtilis RecN to DNA double-strand breaks in the absence of DNA end processing." J Bacteriol 188(2);353-60. PMID: 16385024

Shereda09: Shereda RD, Reiter NJ, Butcher SE, Keck JL (2009). "Identification of the SSB binding site on E. coli RecQ reveals a conserved surface for binding SSB's C terminus." J Mol Biol 386(3);612-25. PMID: 19150358

Umezu90: Umezu K, Nakayama K, Nakayama H (1990). "Escherichia coli RecQ protein is a DNA helicase." Proc Natl Acad Sci U S A 87(14);5363-7. PMID: 2164680

Umezu93a: Umezu K, Nakayama H (1993). "RecQ DNA helicase of Escherichia coli. Characterization of the helix-unwinding activity with emphasis on the effect of single-stranded DNA-binding protein." J Mol Biol 230(4);1145-50. PMID: 8387604

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.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

Xu03: Xu HQ, Deprez E, Zhang AH, Tauc P, Ladjimi MM, Brochon JC, Auclair C, Xi XG (2003). "The Escherichia coli RecQ helicase functions as a monomer." J Biol Chem 278(37);34925-33. PMID: 12805371

Zhang05g: Zhang XD, Dou SX, Xie P, Wang PY, Xi XG (2005). "RecQ helicase-catalyzed DNA unwinding detected by fluorescence resonance energy transfer." Acta Biochim Biophys Sin (Shanghai) 37(9);593-600. PMID: 16143813

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 19.0 on Mon Oct 5, 2015, BIOCYC14B.