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Structural studies have shown XPD bound to its single-stranded DNA substrate, but molecular and dynamic characterization of how XPD translocates on undamaged DNA and how it stalls to verify lesions remains poorly understood. Here, we have performed extensive all-atom MD simulations of human XPD bound to undamaged and damaged ssDNA, containing a mutagenic pyrimidine (6\u22124) pyrimidone UV photoproduct (6\u22124PP), near the XPD pore entrance. We characterize how XPD responds to the presence of the DNA lesion, delineating the atomistic-scale mechanism that it utilizes to discriminate between damaged and undamaged nucleotides. We identify key amino acid residues, including FeS residues R112, R196, H135, K128, Arch residues E377 and R380, and ATPase lobe 1 residues 215\u2212221, that are involved in damage verification and show how movements of Arch and ATPase lobe 1 domains relative to the FeS domain modulate these interactions. These structural and dynamic molecular depictions of XPD helicase activity with unmodified DNA and its inhibition by the lesion elucidate how the lesion is verified by inducing XPD stalling.<\/jats:p>","DOI":"10.1093\/nar\/gkac496","type":"journal-article","created":{"date-parts":[[2022,6,17]],"date-time":"2022-06-17T09:55:10Z","timestamp":1655459710000},"page":"6837-6853","source":"Crossref","is-referenced-by-count":20,"title":["Mechanism of lesion verification by the human XPD helicase in nucleotide excision repair"],"prefix":"10.1093","volume":"50","author":[{"given":"Iwen","family":"Fu","sequence":"first","affiliation":[{"name":"Department of Biology, New York University , 100 Washington Square East, New York, NY\u00a010003, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Mu","sequence":"additional","affiliation":[{"name":"Department of Biology, New York University , 100 Washington Square East, New York, NY\u00a010003, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas E","family":"Geacintov","sequence":"additional","affiliation":[{"name":"Department of Chemistry, New York University , 100 Washington Square East, New York, NY\u00a010003, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3802-7511","authenticated-orcid":false,"given":"Suse","family":"Broyde","sequence":"additional","affiliation":[{"name":"Department of Biology, New York University , 100 Washington Square East, New York, NY\u00a010003, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,6,17]]},"reference":[{"key":"2022070723594090800_B1","doi-asserted-by":"crossref","first-page":"102972","DOI":"10.1016\/j.dnarep.2020.102972","article-title":"Envisioning how the prototypic molecular machine TFIIH functions in transcription initiation and DNA repair","volume":"96","author":"Tsutakawa","year":"2020","journal-title":"DNA Rep. 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Engl."},{"key":"2022070723594090800_B7","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1038\/nrm3822","article-title":"Understanding nucleotide excision repair and its roles in cancer and ageing","volume":"15","author":"Marteijn","year":"2014","journal-title":"Nat. Rev. Mol. Cell. Biol."},{"key":"2022070723594090800_B8","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1002\/em.22087","article-title":"Mechanisms of DNA damage, repair, and mutagenesis","volume":"58","author":"Chatterjee","year":"2017","journal-title":"Environ. Mol. 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