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      Recognition of Damaged DNA for Nucleotide Excision Repair: A Correlated Motion Mechanism with a Mismatched cis-syn Thymine Dimer Lesion

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          Abstract

          Mammalian global genomic nucleotide excision repair requires lesion recognition by XPC, whose detailed binding mechanism remains to be elucidated. Here we have delineated the dynamic molecular pathway and energetics of lesion-specific and productive binding by the Rad4/yeast XPC lesion recognition factor, as it forms the open complex [Min, J. H., and Pavletich, N. P. (2007) Nature 449, 570–575; Chen, X., et al. (2015) Nat. Commun. 6, 5849] that is required for excision. We investigated extensively a cis-syn cyclobutane pyrimidine dimer in mismatched duplex DNA, using high-level computational approaches. Our results delineate a preferred correlated motion mechanism, which provides for the first time an atomistic description of the sequence of events as Rad4 productively binds to the damaged DNA.

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          The Protein Data Bank.

          H M Berman, J Westbrook, Z. Feng … (2000)
          The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
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            Mechanism of open complex and dual incision formation by human nucleotide excision repair factors.

            J Egly, Robin Wood, Cathryn Evans … (1997)
            During nucleotide excision repair in human cells, a damaged DNA strand is cleaved by two endonucleases, XPG on the 3' side of the lesion and ERCC1-XPF on the 5' side. These structure-specific enzymes act at junctions between duplex and single-stranded DNA. ATP-dependent formation of an open DNA structure of approximately 25 nt around the adduct precedes this dual incision. We investigated the mechanism of open complex formation and find that mutations in XPB or XPD, the DNA helicase subunits of the transcription and repair factor TFIIH, can completely prevent opening and dual incision in cell-free extracts. A deficiency in XPC protein also prevents opening. The absence of RPA, XPA or XPG activities leads to an intermediate level of strand separation. In contrast, XPF or ERCC1-defective extracts open normally and generate a 3' incision, but fail to form the 5' incision. This same repair defect was observed in extracts from human xeroderma pigmentosum cells with an alteration in the C-terminal domain of XPB, suggesting that XPB has an additional role in facilitating 5' incision by ERCC1-XPF nuclease. These data support a mechanism in which TFIIH-associated helicase activity and XPC protein catalyze initial formation of the key open intermediate, with full extension to the cleavage sites promoted by the other core nucleotide excision repair factors. Opening is followed by dual incision, with the 3' cleavage made first.
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              A history of TFIIH: two decades of molecular biology on a pivotal transcription/repair factor.

              Frédéric Coin, Jean-Marc Egly (2011)
              The TFIIH multiprotein complex is organized into a 7-subunit core associated with a 3-subunit CDK-activating kinase module (CAK). Three enzymatic subunits are present in TFIIH, two ATP-dependent DNA helicases: XPB and XPD, and the kinase Cdk7. Mutations in three of the subunits, XPB, XPD and TTDA, lead to three distinct genetic disorders: xeroderma pigmentosum (XP), Cockayne syndrome (CS) and trichothiodystrophy (TTD) predisposing patients not only to cancer and ageing but also to developmental and neurological defects. These heterogeneous phenotypes originate from the dual role of TFIIH in transcription and DNA repair. For twenty years, many molecular studies have been conducted with the aim to unveil the role of TFIIH in DNA repair and transcription as well as the origin of the phenotypes of patients. This review intends to give a non-exhaustive survey of the most prominent discoveries on the molecular functioning of TFIIH. Copyright © 2011 Elsevier B.V. All rights reserved.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Biochemistry
                Journal ID (iso-abbrev): Biochemistry
                Journal ID (publisher-id): bi
                Journal ID (coden): bichaw
                Title: Biochemistry
                Publisher: American Chemical Society
                ISSN (Print): 0006-2960
                ISSN (Electronic): 1520-4995
                Publication date (Electronic): 13 August 2015
                Publication date (Print): 01 September 2015
                Publication date PMC-release: 13 August 2016
                Volume: 54
                Issue: 34
                Pages: 5263-5267
                Affiliations
                [1] †Department of Biology and ‡Department of Chemistry, New York University , New York, New York 10003, United States
                [§ ]NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China
                Author notes
                [* ]Phone: +1 212 998 8231. Fax: +1 212 995 4015. E-mail: broyde@ 123456nyu.edu .
                [* ]Phone: +1 212 998 7882. E-mail: yz22@ 123456nyu.edu .
                Article
                DOI: 10.1021/acs.biochem.5b00840
                PMC ID: 4748833
                PubMed ID: 26270861
                SO-VID: a5fbc4d6-d6f2-48ca-847c-49b365cc81d4
                Copyright © Copyright © 2015 American Chemical Society
                License:

                This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

                History
                Date received : 24 July 2015
                Date revision received : 12 August 2015
                Categories
                Subject: Accelerated Publication
                Custom metadata
                document-id-old-9 bi5b00840
                document-id-new-14 bi-2015-008405
                ccc-price

                ScienceOpen disciplines: Biochemistry
                Data availability:
                ScienceOpen disciplines: Biochemistry

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