title: CPD damage recognition by transcribing RNA polymerase II.
abstract: Cells use transcription-coupled repair (TCR) to efficiently eliminate DNA lesions such as ultraviolet light-induced cyclobutane pyrimidine dimers (CPDs). Here we present the structure-based mechanism for the first step in eukaryotic TCR, CPD-induced stalling of RNA polymerase (Pol) II. A CPD in the transcribed strand slowly passes a translocation barrier and enters the polymerase active site. The CPD 5'-thymine then directs uridine misincorporation into messenger RNA, which blocks translocation. Artificial replacement of the uridine by adenosine enables CPD bypass; thus, Pol II stalling requires CPD-directed misincorporation. In the stalled complex, the lesion is inaccessible, and the polymerase conformation is unchanged. This is consistent with nonallosteric recruitment of repair factors and excision of a lesion-containing DNA fragment in the presence of Pol II.
authors.affiliation: Munich Center for Integrated Protein Science CiPS, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Brueckner
authors.forename: Ulrich
authors.initials: U
authors.lastname: Hennecke
authors.forename: Thomas
authors.initials: T
authors.lastname: Carell
authors.forename: Patrick
authors.initials: P
authors.lastname: Cramer
mesh_terms: D001665:Binding Sites; D004249:DNA Damage; D004260:DNA Repair; D008957:Models, Genetic; D011487:Protein Conformation; D011740:Pyrimidine Dimers / Q000378:metabolism*; D012319:RNA Polymerase II / Q000737:chemistry / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology / Q000235:genetics*; D013698:Templates, Genetic; D014158:Transcription, Genetic; D014529:Uridine / Q000378:metabolism; D014544:Uridine Triphosphate / Q000378:metabolism
chemical_list: D011740:Pyrimidine Dimers; D012333:RNA, Messenger; D012319:RNA Polymerase II; D014544:Uridine Triphosphate; D014529:Uridine