Kinetic gating mechanism of DNA damage recognition by Rad4/XPC.

Xuejing Chen,Jung-Hyun Min,Anjum Ansari,Youngchang Kim,Yogambigai Velmurugu,Yoonjung Shim,Chuan He,Guanqun Zheng,Beomseok Park,Bennett Van Houten,Lili Liu

doi:10.1038/ncomms6849

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.

Highlights

The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors
Once bound to a lesion, XPC recruits the multi-subunit transcription factor IIH (TFIIH) that verifies the lesion[3], which coordinates the assembly of nucleotide excision repair (NER) factors, causing excision of a lesion-containing single-stranded DNA and repair synthesis that restores the duplex[2]
DNA lesions that XPC recognizes include a wide variety of intra-strand crosslinks and helix-distorting adducts, which are formed by ultraviolet light (UV), air and water pollutants, and toxins[2]

Summary

Introduction

The xeroderma pigmentosum C (XPC) complex initiates nucleotide excision repair by recognizing DNA lesions before recruiting downstream factors. 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. Correspondence and requests for materials should be addressed to A.A. Control and maintenance of the genome is initiated by proteins that recognize and assemble at specific target sites on DNA. These proteins can single out a small number of target sites from a vast excess of closely related non-target sites. XPC can recognize artificially destabilized DNA such as 2- to 3-base-pair (bp) mismatch bubble (refs 8,12 and this study), such mismatches fail the verification step by TFIIH and are not excised by NER

Methods

Results

Conclusion