Structural basis for translocation by AddAB helicase–nuclease and its arrest at χ sites

A dual-function helicase–nuclease, typified by RecBCD in Escherichia coli , acts on free DNA ends during bacterial double-stranded break repair until it reaches a χ sequence at which it pauses before continuing with modified enzymatic properties; here several crystal structures of the related AddAB...

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Published in:	Nature (London) Vol. 508; no. 7496; pp. 416 - 419
Main Authors:	Krajewski, Wojciech W., Fu, Xin, Wilkinson, Martin, Cronin, Nora B., Dillingham, Mark S., Wigley, Dale B.
Format:	Journal Article
Language:	English
Published:	London Nature Publishing Group UK 17.04.2014 Nature Publishing Group
Subjects:	631/337/1427/2190 631/337/149 631/535/1266 Adenosine Triphosphate - analogs & derivatives Adenosine Triphosphate - metabolism Bacillus subtilis - enzymology Bacterial Proteins - chemistry Bacterial Proteins - metabolism Binding Sites Binding sites (Biochemistry) Crystallography, X-Ray DNA - chemistry DNA - genetics DNA - metabolism DNA Helicases - chemistry DNA Helicases - metabolism Exodeoxyribonucleases - chemistry Exodeoxyribonucleases - metabolism Genetic research Helicases Humanities and Social Sciences letter Models, Molecular Molecular Conformation multidisciplinary Proteins Recombination, Genetic - genetics Science Structure Structure-Activity Relationship Translocation (Genetics) United States
ISSN:	0028-0836, 1476-4687, 1476-4687
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Abstract	A dual-function helicase–nuclease, typified by RecBCD in Escherichia coli , acts on free DNA ends during bacterial double-stranded break repair until it reaches a χ sequence at which it pauses before continuing with modified enzymatic properties; here several crystal structures of the related AddAB enzyme from Bacillus subtilis bound to χ-containing DNA are presented, offering insight into χ recognition and its effect on DNA translocation. Taming a rampant nuclease In bacterial double-stranded DNA break repair, the free ends are initially acted upon by a dual function helicase/nuclease, typified by the RecBCD enzyme of Escherichia coli . As RecBCD unwinds DNA, it eventually encounters a polar octameric sequence known as Chi (χ), which causes attenuation and a change in specificity of the nuclease activity. Dale Wigley and colleagues have now solved several structures of AddAB, a related enzyme from Bacillus subtilis , bound to χ-containing DNA. These structures offer insight into the translocation process, the recognition of χ, and the pausing that occurs when χ is recognized. In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence χ (Chi) 1 , 2 and is catalysed by either an AddAB- or RecBCD-type helicase–nuclease (reviewed in refs 3 , 4 ). These enzyme complexes unwind and digest the DNA duplex from the broken end until they encounter a χ sequence 5 , whereupon they produce a 3′ single-stranded DNA tail onto which they initiate loading of the RecA protein 6 . Consequently, regulation of the AddAB/RecBCD complex by χ is a key control point in DNA repair and other processes involving genetic recombination. Here we report crystal structures of Bacillus subtilis AddAB in complex with different χ-containing DNA substrates either with or without a non-hydrolysable ATP analogue. Comparison of these structures suggests a mechanism for DNA translocation and unwinding, suggests how the enzyme binds specifically to χ sequences, and explains how χ recognition leads to the arrest of AddAB (and RecBCD) translocation that is observed in single-molecule experiments 7 , 8 , 9 .
AbstractList	In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence χ (Chi) and is catalysed by either an AddAB- or RecBCD-type helicase-nuclease (reviewed in refs 3, 4). These enzyme complexes unwind and digest the DNA duplex from the broken end until they encounter a χ sequence, whereupon they produce a 3' single-stranded DNA tail onto which they initiate loading of the RecA protein. Consequently, regulation of the AddAB/RecBCD complex by χ is a key control point in DNA repair and other processes involving genetic recombination. Here we report crystal structures of Bacillus subtilis AddAB in complex with different χ-containing DNA substrates either with or without a non-hydrolysable ATP analogue. Comparison of these structures suggests a mechanism for DNA translocation and unwinding, suggests how the enzyme binds specifically to χ sequences, and explains how χ recognition leads to the arrest of AddAB (and RecBCD) translocation that is observed in single-molecule experiments.In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence χ (Chi) and is catalysed by either an AddAB- or RecBCD-type helicase-nuclease (reviewed in refs 3, 4). These enzyme complexes unwind and digest the DNA duplex from the broken end until they encounter a χ sequence, whereupon they produce a 3' single-stranded DNA tail onto which they initiate loading of the RecA protein. Consequently, regulation of the AddAB/RecBCD complex by χ is a key control point in DNA repair and other processes involving genetic recombination. Here we report crystal structures of Bacillus subtilis AddAB in complex with different χ-containing DNA substrates either with or without a non-hydrolysable ATP analogue. Comparison of these structures suggests a mechanism for DNA translocation and unwinding, suggests how the enzyme binds specifically to χ sequences, and explains how χ recognition leads to the arrest of AddAB (and RecBCD) translocation that is observed in single-molecule experiments. In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence χ (Chi) (1,2) and is catalysed by either an AddAB- or RecBCD-type helicase-nuclease (reviewed in refs 3, 4). These enzyme complexes unwind and digest the DNA duplex from the broken end until they encounter a χ sequence (5), whereupon they produce a 3' single-stranded DNA tail onto which they initiate loading of the RecA protein (6). Consequently, regulation of the AddAB/ RecBCD complex by χ is a key control point in DNA repair and other processes involving genetic recombination. Here we report crystal structures of Bacillus subtilis AddAB in complex with different χ-containing DNA substrates either with or without a non-hydrolysable ATP analogue. Comparison of these structures suggests a mechanism for DNA translocation and unwinding, suggests how the enzyme binds specifically to χ sequences, and explains how χ recognition leads to the arrest of AddAB (and RecBCD) translocation that is observed in single-molecule experiments (7-9). In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence Chi1,2 and is catalysed by either an AddAB or RecBCD-type helicase-nuclease (reviewed in refs 3, 4). These enzyme complexes unwind and digest the DNA duplex from the broken end until they encounter a Chi sequence5 whereupon they produce a 3′-single-stranded DNA tail onto which they initiate loading of the RecA protein6. Consequently, regulation of the AddAB/RecBCD complex by Chi is a key control point in DNA repair and other processes involving genetic recombination. Here, we report crystal structures of AddAB in complex with different Chi-containing DNA substrates either with or without a nonhydrolysable ATP analogue. Comparison of these structures suggests a mechanism for DNA translocation and unwinding, how the enzyme binds specifically to Chi sequences, and explains how Chi recognition leads to the arrest of AddAB (and RecBCD) translocation that is observed in single molecule experiments7-9. In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence χ (Chi) and is catalysed by either an AddAB- or RecBCD-type helicase-nuclease (reviewed in refs 3, 4). These enzyme complexes unwind and digest the DNA duplex from the broken end until they encounter a χ sequence, whereupon they produce a 3' single-stranded DNA tail onto which they initiate loading of the RecA protein. Consequently, regulation of the AddAB/RecBCD complex by χ is a key control point in DNA repair and other processes involving genetic recombination. Here we report crystal structures of Bacillus subtilis AddAB in complex with different χ-containing DNA substrates either with or without a non-hydrolysable ATP analogue. Comparison of these structures suggests a mechanism for DNA translocation and unwinding, suggests how the enzyme binds specifically to χ sequences, and explains how χ recognition leads to the arrest of AddAB (and RecBCD) translocation that is observed in single-molecule experiments. A dual-function helicase–nuclease, typified by RecBCD in Escherichia coli , acts on free DNA ends during bacterial double-stranded break repair until it reaches a χ sequence at which it pauses before continuing with modified enzymatic properties; here several crystal structures of the related AddAB enzyme from Bacillus subtilis bound to χ-containing DNA are presented, offering insight into χ recognition and its effect on DNA translocation. Taming a rampant nuclease In bacterial double-stranded DNA break repair, the free ends are initially acted upon by a dual function helicase/nuclease, typified by the RecBCD enzyme of Escherichia coli . As RecBCD unwinds DNA, it eventually encounters a polar octameric sequence known as Chi (χ), which causes attenuation and a change in specificity of the nuclease activity. Dale Wigley and colleagues have now solved several structures of AddAB, a related enzyme from Bacillus subtilis , bound to χ-containing DNA. These structures offer insight into the translocation process, the recognition of χ, and the pausing that occurs when χ is recognized. In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence χ (Chi) 1 , 2 and is catalysed by either an AddAB- or RecBCD-type helicase–nuclease (reviewed in refs 3 , 4 ). These enzyme complexes unwind and digest the DNA duplex from the broken end until they encounter a χ sequence 5 , whereupon they produce a 3′ single-stranded DNA tail onto which they initiate loading of the RecA protein 6 . Consequently, regulation of the AddAB/RecBCD complex by χ is a key control point in DNA repair and other processes involving genetic recombination. Here we report crystal structures of Bacillus subtilis AddAB in complex with different χ-containing DNA substrates either with or without a non-hydrolysable ATP analogue. Comparison of these structures suggests a mechanism for DNA translocation and unwinding, suggests how the enzyme binds specifically to χ sequences, and explains how χ recognition leads to the arrest of AddAB (and RecBCD) translocation that is observed in single-molecule experiments 7 , 8 , 9 .
Audience	Academic
Author	Cronin, Nora B. Krajewski, Wojciech W. Wilkinson, Martin Fu, Xin Wigley, Dale B. Dillingham, Mark S.
AuthorAffiliation	2 School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K 1 Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, U.K
AuthorAffiliation_xml	– name: 1 Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, U.K – name: 2 School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, U.K
Author_xml	– sequence: 1 givenname: Wojciech W. surname: Krajewski fullname: Krajewski, Wojciech W. organization: Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK, Present address: CRT Discovery Laboratories, Department of Biological Sciences, Birkbeck, University of London, London WC1E 7HX, UK – sequence: 2 givenname: Xin surname: Fu fullname: Fu, Xin organization: Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK – sequence: 3 givenname: Martin surname: Wilkinson fullname: Wilkinson, Martin organization: Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK – sequence: 4 givenname: Nora B. surname: Cronin fullname: Cronin, Nora B. organization: Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK – sequence: 5 givenname: Mark S. surname: Dillingham fullname: Dillingham, Mark S. organization: School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK – sequence: 6 givenname: Dale B. surname: Wigley fullname: Wigley, Dale B. email: Dale.Wigley@icr.ac.uk organization: Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
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Notes	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Present address: CRT Discovery Laboratories, Department of Biological Sciences, Birkbeck, University of London, London, U.K. Contributions: W.W.K. & D.B.W designed the experiments. W.W.K., X.F., M.W and N.B.C performed the experiments. W.W.K., M.W., M.S.D. and D.B.W. analysed the data and prepared the manuscript.
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Snippet	A dual-function helicase–nuclease, typified by RecBCD in Escherichia coli , acts on free DNA ends during bacterial double-stranded break repair until it... In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence χ... In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence Chi1,2...
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SubjectTerms	631/337/1427/2190 631/337/149 631/535/1266 Adenosine Triphosphate - analogs & derivatives Adenosine Triphosphate - metabolism Bacillus subtilis - enzymology Bacterial Proteins - chemistry Bacterial Proteins - metabolism Binding Sites Binding sites (Biochemistry) Crystallography, X-Ray DNA - chemistry DNA - genetics DNA - metabolism DNA Helicases - chemistry DNA Helicases - metabolism Exodeoxyribonucleases - chemistry Exodeoxyribonucleases - metabolism Genetic research Helicases Humanities and Social Sciences letter Models, Molecular Molecular Conformation multidisciplinary Proteins Recombination, Genetic - genetics Science Structure Structure-Activity Relationship Translocation (Genetics)
Title	Structural basis for translocation by AddAB helicase–nuclease and its arrest at χ sites
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