Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

Shi, Yuqian; Hellinga, Homme W.; Beese, Lorena S.

doi:10.1073/pnas.1704845114

Title: Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

Journal Article · Mon May 22 00:00:00 EDT 2017 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1704845114· OSTI ID:1373796

Shi, Yuqian ^[1]; Hellinga, Homme W. ^[1]; Beese, Lorena S. ^[1]

Duke Univ. Medical Center, Durham, NC (United States)

Human exonuclease 1 (hExo1) is a member of the RAD2/XPG structure-specific 5'-nuclease superfamily. Its dominant, processive 5'–3' exonuclease and secondary 5'-flap endonuclease activities participate in various DNA repair, recombination, and replication processes. A single active site processes both recessed ends and 5'-flap substrates. By initiating enzyme reactions in crystals, we have trapped hExo1 reaction intermediates that reveal structures of these substrates before and after their exo- and endonucleolytic cleavage, as well as structures of uncleaved, unthreaded, and partially threaded 5' flaps. Their distinctive 5' ends are accommodated by a small, mobile arch in the active site that binds recessed ends at its base and threads 5' flaps through a narrow aperture within its interior. A sequence of successive, interlocking conformational changes guides the two substrate types into a shared reaction mechanism that catalyzes their cleavage by an elaborated variant of the two-metal, in-line hydrolysis mechanism. Coupling of substrate-dependent arch motions to transition-state stabilization suppresses inappropriate or premature cleavage, enhancing processing fidelity. Furthermore, the striking reduction in flap conformational entropy is catalyzed, in part, by arch motions and transient binding interactions between the flap and unprocessed DNA strand. At the end of the observed reaction sequence, hExo1 resets without relinquishing DNA binding, suggesting a structural basis for its processivity.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Institutes of Health (NIH)

Grant/Contract Number:: R01 GM091487; P01 CA092584

OSTI ID:: 1373796

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Vol. 114, Issue 23; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: ENGLISH

Citation Metrics:

Cited by: 27 works

Citation information provided by
Web of Science

References (34)

Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1 Sobhy, Mohamed A.; Joudeh, Luay I.; Huang, Xiaojuan Cell Reports, Vol. 3, Issue 6 https://doi.org/10.1016/j.celrep.2013.05.001	journal	June 2013
The Exonuclease 1 Glu589Lys Gene Polymorphism and Cancer Susceptibility: Evidence Based on a Meta-analysis Bayram, Suleyman Asian Pacific Journal of Cancer Prevention, Vol. 15, Issue 6 https://doi.org/10.7314/APJCP.2014.15.6.2571	journal	March 2014
Structures of Human Exonuclease 1 DNA Complexes Suggest a Unified Mechanism for Nuclease Family Orans, Jillian; McSweeney, Elizabeth A.; Iyer, Ravi R. Cell, Vol. 145, Issue 2 https://doi.org/10.1016/j.cell.2011.03.005	journal	April 2011
Human Flap Endonuclease Structures, DNA Double-Base Flipping, and a Unified Understanding of the FEN1 Superfamily Tsutakawa, Susan E.; Classen, Scott; Chapados, Brian R. Cell, Vol. 145, Issue 2 https://doi.org/10.1016/j.cell.2011.03.004	journal	April 2011
Activities of human exonuclease 1 that promote cleavage of transcribed immunoglobulin switch regions Vallur, A. C.; Maizels, N. Proceedings of the National Academy of Sciences, Vol. 105, Issue 43 https://doi.org/10.1073/pnas.0805327105	journal	October 2008
Mechanism of 5′-Directed Excision in Human Mismatch Repair Genschel, Jochen; Modrich, Paul Molecular Cell, Vol. 12, Issue 5 https://doi.org/10.1016/S1097-2765(03)00428-3	journal	November 2003
Identification of Holliday junction resolvases from humans and yeast Ip, Stephen C. Y.; Rass, Ulrich; Blanco, Miguel G. Nature, Vol. 456, Issue 7220 https://doi.org/10.1038/nature07470	journal	November 2008
Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. Beese, L. S.; Steitz, T. A. The EMBO Journal, Vol. 10, Issue 1 https://doi.org/10.1002/j.1460-2075.1991.tb07917.x	journal	January 1991
RNase H2-Initiated Ribonucleotide Excision Repair Sparks, Justin L.; Chon, Hyongi; Cerritelli, Susana M. Molecular Cell, Vol. 47, Issue 6 https://doi.org/10.1016/j.molcel.2012.06.035	journal	September 2012
Avoidance of ribonucleotide-induced mutations by RNase H2 and Srs2-Exo1 mechanisms Potenski, Catherine J.; Niu, Hengyao; Sung, Patrick Nature, Vol. 511, Issue 7508 https://doi.org/10.1038/nature13292	journal	June 2014
Human exonuclease 1 (EXO1) activity characterization and its function on flap structures Keijzers, Guido; Bohr, Vilhelm A.; Rasmussen, Lene Juel Bioscience Reports, Vol. 35, Issue 3 https://doi.org/10.1042/BSR20150058	journal	June 2015
Single-molecule imaging reveals the mechanism of Exo1 regulation by single-stranded DNA binding proteins Myler, Logan R.; Gallardo, Ignacio F.; Zhou, Yi Proceedings of the National Academy of Sciences, Vol. 113, Issue 9 https://doi.org/10.1073/pnas.1516674113	journal	February 2016
Molecular interactions of human Exo1 with DNA Lee, B. -i. Nucleic Acids Research, Vol. 30, Issue 4 https://doi.org/10.1093/nar/30.4.942	journal	February 2002
Open complex formation around a lesion during nucleotide excision repair provides a structure for cleavage by human XPG protein Evans, E. The EMBO Journal, Vol. 16, Issue 3 https://doi.org/10.1093/emboj/16.3.625	journal	February 1997
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
Human Exonuclease 1 Functionally Complements Its Yeast Homologues in DNA Recombination, RNA Primer Removal, and Mutation Avoidance Qiu, Junzhuan; Qian, Ying; Chen, Victoria Journal of Biological Chemistry, Vol. 274, Issue 25 https://doi.org/10.1074/jbc.274.25.17893	journal	June 1999
Direct observation of DNA threading in flap endonuclease complexes AlMalki, Faizah A.; Flemming, Claudia S.; Zhang, Jing Nature Structural & Molecular Biology, Vol. 23, Issue 7 https://doi.org/10.1038/nsmb.3241	journal	June 2016
Interactions of mutant and wild-type flap endonucleases with oligonucleotide substrates suggest an alternative model of DNA binding Dervan, J. J.; Feng, M.; Patel, D. Proceedings of the National Academy of Sciences, Vol. 99, Issue 13 https://doi.org/10.1073/pnas.082241699	journal	June 2002
Human exonuclease 1 and BLM helicase interact to resect DNA and initiate DNA repair Nimonkar, A. V.; Ozsoy, A. Z.; Genschel, J. Proceedings of the National Academy of Sciences, Vol. 105, Issue 44 https://doi.org/10.1073/pnas.0809380105	journal	October 2008
NMRPipe: A multidimensional spectral processing system based on UNIX pipes Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW. Journal of Biomolecular NMR, Vol. 6, Issue 3 https://doi.org/10.1007/BF00197809	journal	November 1995
A general two-metal-ion mechanism for catalytic RNA. Steitz, T. A.; Steitz, J. A. Proceedings of the National Academy of Sciences, Vol. 90, Issue 14 https://doi.org/10.1073/pnas.90.14.6498	journal	July 1993
Poly(ADP-ribose)-binding promotes Exo1 damage recruitment and suppresses its nuclease activities Cheruiyot, Abigael; Paudyal, Sharad C.; Kim, In-Kwon DNA Repair, Vol. 35 https://doi.org/10.1016/j.dnarep.2015.09.021	journal	November 2015
The Saccharomyces cerevisiae Dna2 can function as a sole nuclease in the processing of Okazaki fragments in DNA replication Levikova, Maryna; Cejka, Petr Nucleic Acids Research, Vol. 43, Issue 16 https://doi.org/10.1093/nar/gkv710	journal	July 2015
Inactivation of Exonuclease 1 in mice results in DNA mismatch repair defects, increased cancer susceptibility, and male and female sterility Wei, K. Genes & Development, Vol. 17, Issue 5 https://doi.org/10.1101/gad.1060603	journal	February 2003
Crystal Structure of a Eukaryotic GEN1 Resolving Enzyme Bound to DNA Liu, Yijin; Freeman, Alasdair D. J.; Déclais, Anne-Cécile Cell Reports, Vol. 13, Issue 11 https://doi.org/10.1016/j.celrep.2015.11.042	journal	December 2015
Human Exonuclease I Is Required for 5′ and 3′ Mismatch Repair Genschel, Jochen; Bazemore, Laura R.; Modrich, Paul Journal of Biological Chemistry, Vol. 277, Issue 15 https://doi.org/10.1074/jbc.M111854200	journal	January 2002
A single cleavage assay for T5 5'->3' exonuclease: Determination of the catalytic parameters for wild-type and mutant proteins Pickering, T. J.; Thorpe, S. J.; Grasby, J. A. Nucleic Acids Research, Vol. 27, Issue 3 https://doi.org/10.1093/nar/27.3.730	journal	February 1999
Speeding molecular recognition by using the folding funnel: The fly-casting mechanism Shoemaker, B. A.; Portman, J. J.; Wolynes, P. G. Proceedings of the National Academy of Sciences, Vol. 97, Issue 16 https://doi.org/10.1073/pnas.160259697	journal	July 2000
The RAD2 Domain of Human Exonuclease 1 Exhibits 5′ to 3′ Exonuclease and Flap Structure-specific Endonuclease Activities Lee, Byung-In; Wilson, David M. Journal of Biological Chemistry, Vol. 274, Issue 53 https://doi.org/10.1074/jbc.274.53.37763	journal	December 1999
The PIN domain of EXO1 recognizes poly(ADP-ribose) in DNA damage response Zhang, Feng; Shi, Jiazhong; Chen, Shih-Hsun Nucleic Acids Research, Vol. 43, Issue 22 https://doi.org/10.1093/nar/gkv939	journal	September 2015
Flap endonucleases pass 5′-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5′-ends Patel, Nikesh; Atack, John M.; Finger, L. David Nucleic Acids Research, Vol. 40, Issue 10 https://doi.org/10.1093/nar/gks051	journal	February 2012
Exo1 plays a major role in DNA end resection in humans and influences double-strand break repair and damage signaling decisions Tomimatsu, Nozomi; Mukherjee, Bipasha; Deland, Katherine DNA Repair, Vol. 11, Issue 4 https://doi.org/10.1016/j.dnarep.2012.01.006	journal	April 2012
Complementary Roles for Exonuclease 1 and Flap Endonuclease 1 in Maintenance of Triplet Repeats Vallur, Aarthy C.; Maizels, Nancy Journal of Biological Chemistry, Vol. 285, Issue 37 https://doi.org/10.1074/jbc.M110.132738	journal	July 2010
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997

Cited By (9)

Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis Hwang, Wonseok; Yoo, Jungmin; Lee, Yuno Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-06750-9	journal	October 2018
Missed cleavage opportunities by FEN1 lead to Okazaki fragment maturation via the long-flap pathway. Zaher, Manal S.; Rashid, Fahad; Song, Bo Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.27567	text	January 2018
DNA duplex recognition activates Exo1 nuclease activity Li, Yuxi; Shen, Jiangchuan; Niu, Hengyao Journal of Biological Chemistry, Vol. 294, Issue 30 https://doi.org/10.1074/jbc.ra119.008549	journal	June 2019
Resolution of the Holliday junction recombination intermediate by human GEN1 at the single-molecule level Sobhy, Mohamed A.; Bralić, Amer; Raducanu, Vlad-Stefan Nucleic Acids Research, Vol. 47, Issue 4 https://doi.org/10.1093/nar/gky1280	journal	December 2018
A conserved loop–wedge motif moderates reaction site search and recognition by FEN1 Thompson, Mark J.; Gotham, Victoria J. B.; Ciani, Barbara Nucleic Acids Research, Vol. 46, Issue 15 https://doi.org/10.1093/nar/gky506	journal	June 2018
Positioning the 5′-flap junction in the active site controls the rate of flap endonuclease-1–catalyzed DNA cleavage Song, Bo; Hamdan, Samir M.; Hingorani, Manju M. Journal of Biological Chemistry, Vol. 293, Issue 13 https://doi.org/10.1074/jbc.ra117.001137	journal	February 2018
Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5′ exonuclease activities Uson, Maria Loressa; Carl, Ayala; Goldgur, Yehuda Nucleic Acids Research, Vol. 46, Issue 8 https://doi.org/10.1093/nar/gky238	journal	April 2018
Missed cleavage opportunities by FEN1 lead to Okazaki fragment maturation via the long-flap pathway Zaher, Manal S.; Rashid, Fahad; Song, Bo Nucleic Acids Research, Vol. 46, Issue 6 https://doi.org/10.1093/nar/gky082	journal	February 2018
Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1 Bennet, Ian A.; Finger, L. David; Baxter, Nicola J. Nucleic Acids Research, Vol. 46, Issue 11 https://doi.org/10.1093/nar/gky293	journal	April 2018

Similar Records

Flap endonucleases pass 5'-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5'-ends

Journal Article · Wed Feb 08 00:00:00 EST 2012 · Nucleic Acids Research · OSTI ID:1373796

Patel, Nikesh; Atack, John M.; Finger, L. David; +6 more

Coordinateendonucleolytic 5' and 3' trimming of terminally blocked blunt DNA double-strand break ends by Artemis nuclease and DNA-dependent protein kinase

Journal Article · Mon Feb 18 00:00:00 EST 2008 · Nucleic Acids Research · OSTI ID:1373796

Povirk, Lawrence; Khan, Imran S; Zhou, Rui-Zhe; +3 more

Crystal structures of [lamda] exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity

Journal Article · Tue Jul 19 00:00:00 EDT 2011 · Proc. Natl. Acad. Sci. USA · OSTI ID:1373796

Zhang, Jinjin; McCabe, Kimberly A.; Bell, Charles E.

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Rad2/XPG superfamily
DNA repair
flap endonuclease
crystallography
exonuclease

Title: Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I

Citation Formats

References (34)

Cited By (9)

Similar Records

Related Subjects