title: Structural mechanisms of DNA binding and unwinding in bacterial RecQ helicases.
abstract: RecQ helicases unwind remarkably diverse DNA structures as key components of many cellular processes. How RecQ enzymes accommodate different substrates in a unified mechanism that couples ATP hydrolysis to DNA unwinding is unknown. Here, the X-ray crystal structure of the Cronobacter sakazakii RecQ catalytic core domain bound to duplex DNA with a 3' single-stranded extension identifies two DNA-dependent conformational rearrangements: a winged-helix domain pivots ∼90° to close onto duplex DNA, and a conserved aromatic-rich loop is remodeled to bind ssDNA. These changes coincide with a restructuring of the RecQ ATPase active site that positions catalytic residues for ATP hydrolysis. Complex formation also induces a tight bend in the DNA and melts a portion of the duplex. This bending, coupled with translocation, could provide RecQ with a mechanism for unwinding duplex and other DNA structures.
authors.affiliation: Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706; and.
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Manthei
authors.affiliation: Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706; and.
authors.forename: Morgan C
authors.initials: MC
authors.lastname: Hill
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Jordan E
authors.initials: JE
authors.lastname: Burke
authors.affiliation: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706.
authors.forename: Samuel E
authors.initials: SE
authors.lastname: Butcher
authors.affiliation: Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706; and jlkeck@wisc.edu.
authors.forename: James L
authors.initials: JL
authors.lastname: Keck
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry; D016880:Anisotropy; D001419:Bacteria / Q000201:enzymology*; D001665:Binding Sites; D002384:Catalysis; D020134:Catalytic Domain; D059126:Cronobacter / Q000201:enzymology*; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004252:DNA Mutational Analysis; D004277:DNA, Single-Stranded / Q000737:chemistry; D004926:Escherichia coli / Q000201:enzymology; D016680:Genome, Bacterial; D006868:Hydrolysis; D011485:Protein Binding; D053484:RecQ Helicases / Q000737:chemistry*
chemical_list: D004277:DNA, Single-Stranded; D000255:Adenosine Triphosphate; D004247:DNA; C506724:RecQ protein, E coli; D053484:RecQ Helicases
keywords: DNA bending; RecQ; aromatic-rich loop; helicase; mechanism
references.citation: J Mol Biol. 1999 Jul 2;290(1):137-48
references.pmid: 10388562
references.citation: Nucleic Acids Res. 1997 Apr 15;25(8):1537-47
references.pmid: 9092659
references.citation: Nucleic Acids Res. 2005;33(22):6982-91
references.pmid: 16340008
references.citation: J Med Genet. 2006 Feb;43(2):148-52
references.pmid: 15964893
references.citation: J Mol Biol. 2006 May 12;358(4):1071-80
references.pmid: 16530788
references.citation: Cell. 2006 Dec 29;127(7):1349-60
references.pmid: 17190599
references.citation: Annu Rev Biochem. 2007;76:23-50
references.pmid: 17506634
references.citation: Nat Struct Mol Biol. 2007 Jul;14(7):647-52
references.pmid: 17558417
references.citation: Science. 2007 Jul 27;317(5837):513-6
references.pmid: 17656723
references.citation: J Biol Chem. 2008 Jun 27;283(26):17766-76
references.pmid: 18448429
references.citation: Mutat Res. 2008 Aug 25;643(1-2):20-8
references.pmid: 18582477
references.citation: EMBO J. 2008 Aug 20;27(16):2222-9
references.pmid: 18668125
references.citation: EMBO J. 2008 Dec 3;27(23):3209-19
references.pmid: 19008861
references.citation: Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1039-44
references.pmid: 19151156
references.citation: Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):521-8
references.pmid: 20080715
references.citation: Structure. 2010 Feb 10;18(2):177-87
references.pmid: 20159463
references.citation: Curr Opin Struct Biol. 2010 Feb;20(1):121-7
references.pmid: 20061135
references.citation: Biophys Chem. 2010 Jul;149(3):67-77
references.pmid: 20392558
references.citation: Curr Opin Struct Biol. 2010 Jun;20(3):313-24
references.pmid: 20456941
references.citation: Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1373-8
references.pmid: 24379377
references.citation: Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1465-75
references.pmid: 24816114
references.citation: Annu Rev Biochem. 2014;83:519-52
references.pmid: 24606147
references.citation: Protein Sci. 2014 Nov;23(11):1498-507
references.pmid: 25131811
references.citation: Proc Natl Acad Sci U S A. 1999 Oct 12;96(21):11717-22
references.pmid: 10518516
references.citation: J Biochem. 1999 Dec;126(6):986-90
references.pmid: 10578047
references.citation: Curr Opin Struct Biol. 2000 Feb;10(1):110-6
references.pmid: 10679470
references.citation: Nucleic Acids Res. 2001 Apr 15;29(8):1765-71
references.pmid: 11292849
references.citation: J Biol Chem. 2001 Feb 2;276(5):3024-30
references.pmid: 11110789
references.citation: Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8381-7
references.pmid: 11459979
references.citation: Nat Struct Biol. 1997 Jun;4(6):463-7
references.pmid: 9187654
references.citation: Cell. 1997 Aug 22;90(4):635-47
references.pmid: 9288744
references.citation: Trends Biochem Sci. 1997 Nov;22(11):417-8
references.pmid: 9397680
references.citation: Structure. 1998 Jan 15;6(1):89-100
references.pmid: 9493270
references.citation: J Biol Chem. 1998 Oct 16;273(42):27587-92
references.pmid: 9765292
references.citation: Cell. 1999 Apr 2;97(1):75-84
references.pmid: 10199404
references.citation: J Biol Chem. 1999 Apr 30;274(18):12797-802
references.pmid: 10212265
references.citation: Nat Genet. 1999 May;22(1):82-4
references.pmid: 10319867
references.citation: EMBO J. 2003 Oct 1;22(19):4910-21
references.pmid: 14517231
references.citation: Hum Mol Genet. 2003 Nov 1;12(21):2837-44
references.pmid: 12952869
references.citation: Medicine (Baltimore). 1993 Nov;72(6):393-406
references.pmid: 8231788
references.citation: Science. 1996 Apr 12;272(5259):258-62
references.pmid: 8602509
references.citation: Nature. 1996 Nov 28;384(6607):379-83
references.pmid: 8934527
references.citation: Nucleic Acids Res. 1999 Aug 15;27(16):3310-7
references.pmid: 10454638