{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T10:16:59Z","timestamp":1779185819948,"version":"3.51.4"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2020,8,21]],"date-time":"2020-08-21T00:00:00Z","timestamp":1597968000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Spanish Ministry of Science","award":["BFU2017-87397-P"],"award-info":[{"award-number":["BFU2017-87397-P"]}]},{"name":"Spanish Ministry of Science","award":["BFU2013-48374-P"],"award-info":[{"award-number":["BFU2013-48374-P"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Nucleotide excision repair (NER) is an essential pathway to remove bulky lesions affecting one strand of DNA. Defects in components of this repair system are at the ground of genetic diseases such as xeroderma pigmentosum (XP) and Cockayne syndrome (CS). The XP complementation group G (XPG) endonuclease cleaves the damaged DNA strand on the 3\u2032 side of the lesion coordinated with DNA re-synthesis. Here, we determined crystal structures of the XPG nuclease domain in the absence and presence of DNA. The overall fold exhibits similarities to other flap endonucleases but XPG harbors a dynamic helical arch that is uniquely oriented and defines a gateway. DNA binding through a helix-2-turn-helix motif, assisted by one flanking \u03b1-helix on each side, shows high plasticity, which is likely relevant for DNA scanning. A positively-charged canyon defined by the hydrophobic wedge and \u03b2-pin motifs provides an additional DNA-binding surface. Mutational analysis identifies helical arch residues that play critical roles in XPG function. A model for XPG participation in NER is proposed. Our structures and biochemical data represent a valuable tool to understand the atomic ground of XP and CS, and constitute a starting point for potential therapeutic applications.<\/jats:p>","DOI":"10.1093\/nar\/gkaa688","type":"journal-article","created":{"date-parts":[[2020,8,6]],"date-time":"2020-08-06T19:46:33Z","timestamp":1596743193000},"page":"9943-9958","source":"Crossref","is-referenced-by-count":26,"title":["The crystal structure of human XPG, the xeroderma pigmentosum group G endonuclease, provides insight into nucleotide excision DNA repair"],"prefix":"10.1093","volume":"48","author":[{"given":"Roc\u00edo","family":"Gonz\u00e1lez-Corrochano","sequence":"first","affiliation":[{"name":"Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Federico M","family":"Ruiz","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas\u00a0M\u00a0I","family":"Taylor","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sonia","family":"Huecas","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Srdja","family":"Drakulic","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mercedes","family":"Sp\u00ednola-Amilibia","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5097-731X","authenticated-orcid":false,"given":"Carlos","family":"Fern\u00e1ndez-Tornero","sequence":"additional","affiliation":[{"name":"Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,8,21]]},"reference":[{"key":"2020092420050457600_B1","doi-asserted-by":"crossref","first-page":"1071","DOI":"10.1038\/nature08467","article-title":"The DNA-damage response in human biology and disease","volume":"461","author":"Jackson","year":"2009","journal-title":"Nature"},{"key":"2020092420050457600_B2","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1016\/j.biochi.2003.10.014","article-title":"The XPG story","volume":"85","author":"Clarkson","year":"2003","journal-title":"Biochimie"},{"key":"2020092420050457600_B3","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1016\/j.biochi.2003.09.010","article-title":"DNA repair-deficient diseases, xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy","volume":"85","author":"Lehmann","year":"2003","journal-title":"Biochimie"},{"key":"2020092420050457600_B4","doi-asserted-by":"crossref","first-page":"8949","DOI":"10.1038\/sj.onc.1206096","article-title":"Subpathways of nucleotide excision repair and their regulation","volume":"21","author":"Hanawalt","year":"2002","journal-title":"Oncogene"},{"key":"2020092420050457600_B5","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.dnarep.2015.09.003","article-title":"Nucleotide excision repair in humans","volume":"36","author":"Spivak","year":"2015","journal-title":"DNA Repair (Amst.)"},{"key":"2020092420050457600_B6","doi-asserted-by":"crossref","first-page":"8285","DOI":"10.1074\/jbc.271.14.8285","article-title":"Reaction mechanism of human DNA repair excision nuclease","volume":"271","author":"Mu","year":"1996","journal-title":"J. Biol. Chem."},{"key":"2020092420050457600_B7","doi-asserted-by":"crossref","first-page":"811","DOI":"10.1016\/S0092-8674(00)80155-5","article-title":"Xeroderma pigmentosum group F caused by a defect in a structure-specific DNA repair endonuclease","volume":"86","author":"Sijbers","year":"1996","journal-title":"Cell"},{"key":"2020092420050457600_B8","doi-asserted-by":"crossref","first-page":"2885","DOI":"10.1038\/s41467-019-10745-5","article-title":"Structural basis of TFIIH activation for nucleotide excision repair","volume":"10","author":"Kokic","year":"2019","journal-title":"Nat. Commun."},{"key":"2020092420050457600_B9","doi-asserted-by":"crossref","first-page":"6559","DOI":"10.1093\/emboj\/16.21.6559","article-title":"Mechanism of open complex and dual incision formation by human nucleotide excision repair factors","volume":"16","author":"Evans","year":"1997","journal-title":"EMBO J."},{"key":"2020092420050457600_B10","doi-asserted-by":"crossref","first-page":"a012609","DOI":"10.1101\/cshperspect.a012609","article-title":"Nucleotide excision repair in eukaryotes","volume":"5","author":"Scharer","year":"2013","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"2020092420050457600_B11","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1038\/emboj.2009.49","article-title":"Coordination of dual incision and repair synthesis in human nucleotide excision repair","volume":"28","author":"Staresincic","year":"2009","journal-title":"EMBO J."},{"key":"2020092420050457600_B12","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1016\/j.molcel.2010.02.009","article-title":"Three DNA polymerases, recruited by different mechanisms, carry out NER repair synthesis in human cells","volume":"37","author":"Ogi","year":"2010","journal-title":"Mol. Cell"},{"key":"2020092420050457600_B13","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1042\/BST0380433","article-title":"Substrate recognition and catalysis by flap endonucleases and related enzymes","volume":"38","author":"Tomlinson","year":"2010","journal-title":"Biochem. Soc. Trans."},{"key":"2020092420050457600_B14","doi-asserted-by":"crossref","first-page":"7030","DOI":"10.1074\/jbc.M412228200","article-title":"The spacer region of XPG mediates recruitment to nucleotide excision repair complexes and determines substrate specificity","volume":"280","author":"Dunand-Sauthier","year":"2005","journal-title":"J. Biol. Chem."},{"key":"2020092420050457600_B15","doi-asserted-by":"crossref","first-page":"24522","DOI":"10.1074\/jbc.272.39.24522","article-title":"The DNA repair endonuclease XPG binds to proliferating cell nuclear antigen (PCNA) and shares sequence elements with the PCNA-binding regions of FEN-1 and cyclin-dependent kinase inhibitor p21","volume":"272","author":"Gary","year":"1997","journal-title":"J. Biol. Chem."},{"key":"2020092420050457600_B16","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1038\/nrm.2016.177","article-title":"Control of structure-specific endonucleases to maintain genome stability","volume":"18","author":"Dehe","year":"2017","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2020092420050457600_B17","doi-asserted-by":"crossref","first-page":"3664","DOI":"10.1073\/pnas.89.8.3664","article-title":"Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5\u2032 and the 6th phosphodiester bond 3\u2032 to the photodimer","volume":"89","author":"Huang","year":"1992","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020092420050457600_B18","doi-asserted-by":"crossref","first-page":"7177","DOI":"10.1074\/jbc.271.12.7177","article-title":"Analysis of incision sites produced by human cell extracts and purified proteins during nucleotide excision repair of a 1,3-intrastrand d(GpTpG)-cisplatin adduct","volume":"271","author":"Moggs","year":"1996","journal-title":"J. Biol. Chem."},{"key":"2020092420050457600_B19","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1093\/emboj\/16.3.625","article-title":"Open complex formation around a lesion during nucleotide excision repair provides a structure for cleavage by human XPG protein","volume":"16","author":"Evans","year":"1997","journal-title":"EMBO J."},{"key":"2020092420050457600_B20","doi-asserted-by":"crossref","first-page":"432","DOI":"10.1038\/371432a0","article-title":"XPG endonuclease makes the 3\u2032 incision in human DNA nucleotide excision repair","volume":"371","author":"O\u2019Donovan","year":"1994","journal-title":"Nature"},{"key":"2020092420050457600_B21","doi-asserted-by":"crossref","first-page":"e12256","DOI":"10.7554\/eLife.12256","article-title":"Human Holliday junction resolvase GEN1 uses a chromodomain for efficient DNA recognition and cleavage","volume":"4","author":"Lee","year":"2015","journal-title":"Elife"},{"key":"2020092420050457600_B22","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1016\/j.cell.2011.03.005","article-title":"Structures of human exonuclease 1 DNA complexes suggest a unified mechanism for nuclease family","volume":"145","author":"Orans","year":"2011","journal-title":"Cell"},{"key":"2020092420050457600_B23","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1016\/j.cell.2011.03.004","article-title":"Human flap endonuclease structures, DNA double-base flipping, and a unified understanding of the FEN1 superfamily","volume":"145","author":"Tsutakawa","year":"2011","journal-title":"Cell"},{"key":"2020092420050457600_B24","doi-asserted-by":"crossref","first-page":"4507","DOI":"10.1093\/nar\/gks051","article-title":"Flap endonucleases pass 5\u2032-flaps through a flexible arch using a disorder-thread-order mechanism to confer specificity for free 5\u2032-ends","volume":"40","author":"Patel","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"2020092420050457600_B25","doi-asserted-by":"crossref","first-page":"10762","DOI":"10.1093\/nar\/gku729","article-title":"Crystal structure of the catalytic core of Rad2: insights into the mechanism of substrate binding","volume":"42","author":"Mietus","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2020092420050457600_B26","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1006\/jmbi.1993.1012","article-title":"Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin","volume":"229","author":"Van\u00a0Duyne","year":"1993","journal-title":"J. Mol. Biol."},{"key":"2020092420050457600_B27","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1107\/S0907444909047337","article-title":"Xds","volume":"66","author":"Kabsch","year":"2010","journal-title":"Acta Crystallogr. D. Biol. Crystallogr."},{"key":"2020092420050457600_B28","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1107\/S0021889807021206","article-title":"Phaser crystallographic software","volume":"40","author":"McCoy","year":"2007","journal-title":"J. Appl. Crystallogr."},{"key":"2020092420050457600_B29","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1107\/S0907444910007493","article-title":"Features and development of Coot","volume":"66","author":"Emsley","year":"2010","journal-title":"Acta Crystallogr. D. Biol. Crystallogr."},{"key":"2020092420050457600_B30","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1107\/S0907444909052925","article-title":"PHENIX: a comprehensive Python-based system for macromolecular structure solution","volume":"66","author":"Adams","year":"2010","journal-title":"Acta Crystallogr. D. Biol. Crystallogr."},{"key":"2020092420050457600_B31","doi-asserted-by":"crossref","first-page":"2184","DOI":"10.1107\/S0907444904023510","article-title":"REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use","volume":"60","author":"Vagin","year":"2004","journal-title":"Acta Crystallogr. D. Biol. Crystallogr."},{"key":"2020092420050457600_B32","doi-asserted-by":"crossref","first-page":"W375","DOI":"10.1093\/nar\/gkm216","article-title":"MolProbity: all-atom contacts and structure validation for proteins and nucleic acids","volume":"35","author":"Davis","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2020092420050457600_B33","doi-asserted-by":"crossref","first-page":"16030","DOI":"10.1074\/jbc.272.25.16030","article-title":"The non-catalytic function of XPG protein during dual incision in human nucleotide excision repair","volume":"272","author":"Wakasugi","year":"1997","journal-title":"J. Biol. Chem."},{"key":"2020092420050457600_B34","doi-asserted-by":"crossref","first-page":"19500","DOI":"10.1074\/jbc.M213155200","article-title":"Structural determinants for substrate binding and catalysis by the structure-specific endonuclease XPG","volume":"278","author":"Hohl","year":"2003","journal-title":"J. Biol. Chem."},{"key":"2020092420050457600_B35","doi-asserted-by":"crossref","first-page":"6010","DOI":"10.1073\/pnas.1704845114","article-title":"Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I","volume":"114","author":"Shi","year":"2017","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020092420050457600_B36","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1073\/pnas.96.1.38","article-title":"Mutagenesis of conserved lysine residues in bacteriophage T5 5\u2032-3\u2032 exonuclease suggests separate mechanisms of endo-and exonucleolytic cleavage","volume":"96","author":"Garforth","year":"1999","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020092420050457600_B37","doi-asserted-by":"crossref","first-page":"31713","DOI":"10.1074\/jbc.M703209200","article-title":"Crystal structure of bacteriophage T4 5\u2032 nuclease in complex with a branched DNA reveals how flap endonuclease-1 family nucleases bind their substrates","volume":"282","author":"Devos","year":"2007","journal-title":"J. Biol. Chem."},{"key":"2020092420050457600_B38","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1038\/nsmb.3241","article-title":"Direct observation of DNA threading in flap endonuclease complexes","volume":"23","author":"AlMalki","year":"2016","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2020092420050457600_B39","doi-asserted-by":"crossref","first-page":"111","DOI":"10.3389\/fgene.2019.00111","article-title":"Identification of a ERCC5 c.2333T&gt;C (L778P) variant in two Tunisian siblings with mild xeroderma pigmentosum phenotype","volume":"10","author":"Chikhaoui","year":"2019","journal-title":"Front Genet"},{"key":"2020092420050457600_B40","doi-asserted-by":"crossref","first-page":"1841","DOI":"10.1038\/jid.2013.54","article-title":"Characterization of three XPG-defective patients identifies three missense mutations that impair repair and transcription","volume":"133","author":"Schafer","year":"2013","journal-title":"J. Invest. Dermatol."},{"key":"2020092420050457600_B41","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1203\/00006450-200103000-00016","article-title":"Xeroderma pigmentosum group G with severe neurological involvement and features of Cockayne syndrome in infancy","volume":"49","author":"Zafeiriou","year":"2001","journal-title":"Pediatr. Res."},{"key":"2020092420050457600_B42","doi-asserted-by":"crossref","first-page":"W314","DOI":"10.1093\/nar\/gku411","article-title":"DUET: a server for predicting effects of mutations on protein stability using an integrated computational approach","volume":"42","author":"Pires","year":"2014","journal-title":"Nucleic. Acids. Res."},{"key":"2020092420050457600_B43","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1046\/j.0022-202x.2001.01673.x","article-title":"The founding members of xeroderma pigmentosum group G produce XPG protein with severely impaired endonuclease activity","volume":"118","author":"Lalle","year":"2002","journal-title":"J. Invest. Dermatol."},{"key":"2020092420050457600_B44","doi-asserted-by":"crossref","first-page":"972","DOI":"10.1046\/j.1523-1747.2002.01782.x","article-title":"Relationship of neurologic degeneration to genotype in three xeroderma pigmentosum group G patients","volume":"118","author":"Emmert","year":"2002","journal-title":"J. Invest. Dermatol."},{"key":"2020092420050457600_B45","doi-asserted-by":"crossref","first-page":"E1236","DOI":"10.1073\/pnas.1519444113","article-title":"Deep phenotyping of 89 xeroderma pigmentosum patients reveals unexpected heterogeneity dependent on the precise molecular defect","volume":"113","author":"Fassihi","year":"2016","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020092420050457600_B46","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1111\/j.1600-0625.2012.01446.x","article-title":"Xeroderma pigmentosum complementation group G patient with a novel homozygous missense mutation and no neurological abnormalities","volume":"21","author":"Moriwaki","year":"2012","journal-title":"Exp. Dermatol."},{"key":"2020092420050457600_B47","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1093\/hmg\/3.6.963","article-title":"Mutations that disable the DNA repair gene XPG in a xeroderma pigmentosum group G patient","volume":"3","author":"Nouspikel","year":"1994","journal-title":"Hum. Mol. Genet."},{"key":"2020092420050457600_B48","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1002\/humu.22259","article-title":"Novel XPG (ERCC5) mutations affect DNA repair and cell survival after ultraviolet but not oxidative stress","volume":"34","author":"Soltys","year":"2013","journal-title":"Hum. Mutat."},{"key":"2020092420050457600_B49","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/S0092-8674(03)01036-5","article-title":"Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair","volume":"116","author":"Chapados","year":"2004","journal-title":"Cell"},{"key":"2020092420050457600_B50","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1158\/1535-7163.MCT-07-0192","article-title":"Predicting cisplatin and trabectedin drug sensitivity in ovarian and colon cancers","volume":"7","author":"Stevens","year":"2008","journal-title":"Mol. Cancer Ther."},{"key":"2020092420050457600_B51","doi-asserted-by":"crossref","first-page":"14127","DOI":"10.1073\/pnas.1921311117","article-title":"Human XPG nuclease structure, assembly, and activities with insights for neurodegeneration and cancer from pathogenic mutations","volume":"117","author":"Tsutakawa","year":"2020","journal-title":"Proc. Natl. Acad. Sci. U.S.A."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/17\/9943\/33787167\/gkaa688.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/17\/9943\/33787167\/gkaa688.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,25]],"date-time":"2020-09-25T00:07:39Z","timestamp":1600992459000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/17\/9943\/5895332"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,8,21]]},"references-count":51,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2020,8,21]]},"published-print":{"date-parts":[[2020,9,25]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkaa688","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,9,25]]},"published":{"date-parts":[[2020,8,21]]}}}