Crystal Structure of the FeS Cluster–Containing Nucleotide Excision Repair Helicase XPD

Abstract

DNA damage recognition by the nucleotide excision repair pathway requires an initial step identifying helical distortions in the DNA and a proofreading step verifying the presence of a lesion. This proofreading step is accomplished in eukaryotes by the TFIIH complex. The critical damage recognition component of TFIIH is the XPD protein, a DNA helicase that unwinds DNA and identifies the damage. Here, we describe the crystal structure of an archaeal XPD protein with high sequence identity to the human XPD protein that reveals how the structural helicase framework is combined with additional elements for strand separation and DNA scanning. Two RecA-like helicase domains are complemented by a 4Fe4S cluster domain, which has been implicated in damage recognition, and an α-helical domain. The first helicase domain together with the helical and 4Fe4S-cluster–containing domains form a central hole with a diameter sufficient in size to allow passage of a single stranded DNA. Based on our results, we suggest a model of how DNA is bound to the XPD protein, and can rationalize several of the mutations in the human XPD gene that lead to one of three severe diseases, xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy.

Effect of mutations in XPD(ERCC2) on pregnancy and prenatal development in mothers of patients with trichothiodystrophy or xeroderma pigmentosum

“…15,21 Our XP and TTD patients had XPD mutations that are similar to those previously published. 1,5,[8][9][10][11] All of our XP and TTD patients were compound heterozygotes for two different XPD mutations. Many XP patients had the common p.R683W mutation combined with other mutations.…”

“…There are several reasons why we believe that the prediction by Moslehi et al 19 that mutations in the C-terminal region of XPD [8][9][10] cause pre-eclampsia may not be correct. There is a complex genotype-phenotype relationship between the location of mutations in the human XPD gene and the presence or absence of clinical features of XP or TTD.…”

“…There is a complex genotype-phenotype relationship between the location of mutations in the human XPD gene and the presence or absence of clinical features of XP or TTD. Mutations are spread out along the 761 amino-acid structure of XPD in both disorders 1,5,[8][9][10][11] The mutations may affect nucleotide-excision repair and/or transcription to different extents. 2,3 In addition, some mutations are found in both XP and TTD patients.…”

Phenotype-specific adverse effects of XPD mutations on human prenatal development implicate impairment of TFIIH-mediated functions in placenta

“…(a) Changes in the amino acid sequences resulting from mutations associated with gestational complications mapped as red spheres to the T. acidophlium XPD crystal structure. 43 The DNA present in the model was generated by superposition of the T. acidophilum XPD helicase domains with the helicase domains of the co-crystal structure of the Hel308 complex 58 and is shown to provide general orientation of functional regions. A gross schematic of the region occupied by the C-terminal motif is indicated by red coloring of the amino acids at the T. acidophilum XPD C-terminus and the box outlined in red dashes that follows.…”

“…All XP and TTD cases with specified mutations in the XPD gene and information on preeclampsia were included in the analysis. T-Coffee, 39 Promals3D, 40 NCBI BLAST, and TM-Align 41 were used for generating structure-based multiple sequence alignments and mapping of the mutations in the XPD gene to the available XPD crystal structures (PDB IDs: 3CRV, 42 2VSF, 43 and 2VL7 44 ). PyMOL and Jalview 45 were used for depiction of mapped XPD mutations and sequence alignments, respectively.…”