title: Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.
abstract: The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. How XPC detects structurally diverse lesions embedded within normal DNA is unknown. Here we present a crystal structure that captures the yeast XPC orthologue (Rad4) on a single register of undamaged DNA. The structure shows that a disulphide-tethered Rad4 flips out normal nucleotides and adopts a conformation similar to that seen with damaged DNA. Contrary to many DNA repair enzymes that can directly reject non-target sites as structural misfits, our results suggest that Rad4/XPC uses a kinetic gating mechanism whereby lesion selectivity arises from the kinetic competition between DNA opening and the residence time of Rad4/XPC per site. This mechanism is further supported by measurements of Rad4-induced lesion-opening times using temperature-jump perturbation spectroscopy. Kinetic gating may be a general mechanism used by site-specific DNA-binding proteins to minimize time-consuming interrogations of non-target sites.
authors.affiliation: Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA.
authors.forename: Xuejing
authors.initials: X
authors.lastname: Chen
authors.affiliation: Department of Physics, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA.
authors.forename: Yogambigai
authors.initials: Y
authors.lastname: Velmurugu
authors.affiliation: Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA.
authors.forename: Guanqun
authors.initials: G
authors.lastname: Zheng
authors.affiliation: Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA.
authors.forename: Beomseok
authors.initials: B
authors.lastname: Park
authors.affiliation: Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA.
authors.forename: Yoonjung
authors.initials: Y
authors.lastname: Shim
authors.affiliation: Structural Biology Center, Biosciences Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439, USA.
authors.forename: Youngchang
authors.initials: Y
authors.lastname: Kim
authors.affiliation: Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, USA.
authors.forename: Lili
authors.initials: L
authors.lastname: Liu
authors.affiliation: Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine and University of Pittsburgh Cancer Institute, University of Pittsburgh, 5117 Centre Avenue, Pittsburgh, Pennsylvania 15213, USA.
authors.forename: Bennett
authors.initials: B
authors.lastname: Van Houten
authors.affiliation: Department of Chemistry, Institute for Biophysical Dynamics, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637, USA.
authors.forename: Chuan
authors.initials: C
authors.lastname: He
authors.affiliation: 1] Department of Physics, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA [2] Department of Bioengineering, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA.
authors.forename: Anjum
authors.initials: A
authors.lastname: Ansari
authors.affiliation: Department of Chemistry, University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607, USA.
authors.forename: Jung-Hyun
authors.initials: JH
authors.lastname: Min
mesh_terms: D001703:Biophysics; D003460:Crystallization; D004247:DNA / Q000378:metabolism*; D004249:DNA Damage / Q000502:physiology*; D004260:DNA Repair / Q000502:physiology*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D005453:Fluorescence; D007700:Kinetics; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D012441:Saccharomyces cerevisiae / Q000378:metabolism / Q000502:physiology*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry* / Q000378:metabolism; D013057:Spectrum Analysis; D013696:Temperature
chemical_list: D004268:DNA-Binding Proteins; D046912:Multiprotein Complexes; C490846:RAD23 protein, S cerevisiae; C493797:Rad4 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D004247:DNA