Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

Handle URI:
http://hdl.handle.net/10754/622951
Title:
Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1
Authors:
Rashid, Fahad; Harris, Paul D.; Zaher, Manal S.; Sobhy, Mohamed Abdelmaboud; Joudeh, Luay I; Yan, Chunli; Piwonski, Hubert Marek ( 0000-0001-8666-3945 ) ; Tsutakawa, Susan E; Ivanov, Ivaylo; Tainer, John A; Habuchi, Satoshi ( 0000-0002-6663-2807 ) ; Hamdan, Samir ( 0000-0001-5192-1852 )
Abstract:
Human flap endonuclease 1 (FEN1) and related structure-specific 5'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually 'locks' protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Rashid F, Harris PD, Zaher MS, Sobhy MA, Joudeh LI, et al. (2017) Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. eLife 6. Available: http://dx.doi.org/10.7554/elife.21884.
Publisher:
eLife Sciences Organisation, Ltd.
Journal:
eLife
Issue Date:
23-Feb-2017
DOI:
10.7554/elife.21884
Type:
Article
ISSN:
2050-084X
Sponsors:
The research reported here was supported by King Abdullah University of Science and Technology through core funding to S.M.H. and a Competitive Research Award (CRG3) to S.M.H. and J.A.T, as well as National Science Foundation CAREER award MCB-1149521 and National Institute of Health grant R01GM110387 to I.I. J.A.T. also acknowledges support of a Robert A. Welch Chemistry Chair, the Cancer Prevention and Research Institute of Texas, and the University of Texas System Science and Technology Acquisition and Retention STARs program. Computational resources were provided in part by a National Science Foundation XSEDE allocation CHE110042 and through an allocation at NERSC supported by the U.S. Department of Energy Office of Science contract DE-AC02-05CH11231. The authors declare no competing financial interests.
Additional Links:
https://elifesciences.org/content/6/e21884
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorRashid, Fahaden
dc.contributor.authorHarris, Paul D.en
dc.contributor.authorZaher, Manal S.en
dc.contributor.authorSobhy, Mohamed Abdelmabouden
dc.contributor.authorJoudeh, Luay Ien
dc.contributor.authorYan, Chunlien
dc.contributor.authorPiwonski, Hubert Mareken
dc.contributor.authorTsutakawa, Susan Een
dc.contributor.authorIvanov, Ivayloen
dc.contributor.authorTainer, John Aen
dc.contributor.authorHabuchi, Satoshien
dc.contributor.authorHamdan, Samiren
dc.date.accessioned2017-02-28T12:11:06Z-
dc.date.available2017-02-28T12:11:06Z-
dc.date.issued2017-02-23en
dc.identifier.citationRashid F, Harris PD, Zaher MS, Sobhy MA, Joudeh LI, et al. (2017) Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1. eLife 6. Available: http://dx.doi.org/10.7554/elife.21884.en
dc.identifier.issn2050-084Xen
dc.identifier.doi10.7554/elife.21884en
dc.identifier.urihttp://hdl.handle.net/10754/622951-
dc.description.abstractHuman flap endonuclease 1 (FEN1) and related structure-specific 5'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually 'locks' protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.en
dc.description.sponsorshipThe research reported here was supported by King Abdullah University of Science and Technology through core funding to S.M.H. and a Competitive Research Award (CRG3) to S.M.H. and J.A.T, as well as National Science Foundation CAREER award MCB-1149521 and National Institute of Health grant R01GM110387 to I.I. J.A.T. also acknowledges support of a Robert A. Welch Chemistry Chair, the Cancer Prevention and Research Institute of Texas, and the University of Texas System Science and Technology Acquisition and Retention STARs program. Computational resources were provided in part by a National Science Foundation XSEDE allocation CHE110042 and through an allocation at NERSC supported by the U.S. Department of Energy Office of Science contract DE-AC02-05CH11231. The authors declare no competing financial interests.en
dc.publishereLife Sciences Organisation, Ltd.en
dc.relation.urlhttps://elifesciences.org/content/6/e21884en
dc.rightsArchived with thanks to eLifeen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectBiochemistryen
dc.subjectBiophysicsen
dc.subjectStructural Biologyen
dc.titleSingle-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1en
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journaleLifeen
dc.eprint.versionPost-printen
dc.contributor.institutionDepartment of Chemistry, Georgia State University, Atlanta, United States.en
dc.contributor.institutionLawrence Berkeley National Laboratory, Berkeley, United States.en
kaust.authorRashid, Fahaden
kaust.authorHarris, Paul D.en
kaust.authorZaher, Manal S.en
kaust.authorSobhy, Mohamed Abdelmabouden
kaust.authorJoudeh, Luay Ien
kaust.authorPiwonski, Hubert Mareken
kaust.authorHabuchi, Satoshien
kaust.authorHamdan, Samiren
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