scholarly journals The crystal structure of human XPG, the xeroderma pigmentosum group G endonuclease, provides insight into nucleotide excision DNA repair

2020 ◽  
Vol 48 (17) ◽  
pp. 9943-9958
Author(s):  
Rocío González-Corrochano ◽  
Federico M Ruiz ◽  
Nicholas M I Taylor ◽  
Sonia Huecas ◽  
Srdja Drakulic ◽  
...  
Keyword(s):  
Dna Binding ◽  
Xeroderma Pigmentosum ◽  
Mutational Analysis ◽  
Excision Repair ◽  
Genetic Diseases ◽  
Complementation Group ◽  
Repair System ◽  
High Plasticity ◽  
Starting Point ◽  
Nucleotide Excision

Abstract Nucleotide excision repair (NER) is an essential pathway to remove bulky lesions affecting one strand of DNA. Defects in components of this repair system are at the ground of genetic diseases such as xeroderma pigmentosum (XP) and Cockayne syndrome (CS). The XP complementation group G (XPG) endonuclease cleaves the damaged DNA strand on the 3′ side of the lesion coordinated with DNA re-synthesis. Here, we determined crystal structures of the XPG nuclease domain in the absence and presence of DNA. The overall fold exhibits similarities to other flap endonucleases but XPG harbors a dynamic helical arch that is uniquely oriented and defines a gateway. DNA binding through a helix-2-turn-helix motif, assisted by one flanking α-helix on each side, shows high plasticity, which is likely relevant for DNA scanning. A positively-charged canyon defined by the hydrophobic wedge and β-pin motifs provides an additional DNA-binding surface. Mutational analysis identifies helical arch residues that play critical roles in XPG function. A model for XPG participation in NER is proposed. Our structures and biochemical data represent a valuable tool to understand the atomic ground of XP and CS, and constitute a starting point for potential therapeutic applications.

The XPD helicase: XPanDing archaeal XPD structures to get a grip on human DNA repair

2010 ◽  
Vol 391 (7) ◽  
Author(s):  
Stefanie C. Wolski ◽  
Jochen Kuper ◽  
Caroline Kisker
Keyword(s):  
Transcription Initiation ◽  
Xeroderma Pigmentosum ◽  
Excision Repair ◽  
Complementation Group ◽  
Iron Sulfur Cluster ◽  
Sulfur Cluster ◽  
Iron Sulfur ◽  
Nucleotide Excision ◽  
Xpd Helicase ◽  
Group D

Abstract Xeroderma pigmentosum complementation group D protein (XPD) is an iron-sulfur cluster containing 5′-3′ helicase and, in humans, part of the transcription factor TFIIH. TFIIH is involved in nucleotide excision repair as well as in transcription initiation. Recently, three different groups have reported the structures of archaeal XPDs. All structures revealed a four-domain organization with two RecA-like domains, an Arch domain and an iron-sulfur cluster domain. It was possible to rationalize several of the mutations in the human XPD gene that lead to one of the three severe diseases xeroderma pigmentosum, Cockayne syndrome and trichothiodystrophy. The different structures are compared and disease-related mutations are discussed.

scholarly journals In Silico Drug Repurposing by Structural Alteration after Induced Fit: Discovery of a Candidate Agent for Recovery of Nucleotide Excision Repair in Xeroderma Pigmentosum Group D Mutant (R683W)

Biomedicines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 249
Author(s):  
Yutaka Takaoka ◽  
Mika Ohta ◽  
Satoshi Tateishi ◽  
Aki Sugano ◽  
Eiji Nakano ◽  
...  
Keyword(s):  
Nucleotide Excision Repair ◽  
In Silico ◽  
Xeroderma Pigmentosum ◽  
Excision Repair ◽  
Drug Repurposing ◽  
Complementation Group ◽  
Drug Candidate ◽  
Induced Fit ◽  
Nucleotide Excision ◽  
Group D

Xeroderma pigmentosum complementation group D (XPD) is a UV-sensitive syndrome and a rare incurable genetic disease which is caused by the genetic mutation of the excision repair cross-complementation group 2 gene (ERCC2). Patients who harbor only XPD R683W mutant protein develop severe photosensitivity and progressive neurological symptoms. Cultured cells derived from patients with XPD (XPD R683W cells) demonstrate a reduced nucleotide excision repair (NER) ability. We hope to ameliorate clinical symptoms if we can identify candidate agents that would aid recovery of the cells’ NER ability. To investigate such candidates, we created in silico methods of drug repurposing (in silico DR), a strategy that utilizes the recovery of ATP-binding in the XPD R683W protein after the induced fit. We chose 4E1RCat and aprepitant as the candidates for our in silico DR, and evaluated them by using the UV-induced unscheduled DNA synthesis (UDS) assay to verify the recovery of NER in XPD R683W cells. UDS values of the cells improved about 1.4–1.7 times after 4E1RCat treatment compared with solvent-only controls; aprepitant showed no positive effect. In this study, therefore, we succeeded in finding the candidate agent 4E1RCat for XPD R683W. We also demonstrated that our in silico DR method is a cost-effective approach for drug candidate discovery.

scholarly journals Case Report: Identification of a Heterozygous XPA c.553C>T Mutation Causing Neurological Impairment in a Case of Xeroderma Pigmentosum Complementation Group A

2021 ◽  
Vol 12 ◽  
Author(s):  
Juan Antonio García-Carmona ◽  
Matthew J. Yousefzadeh ◽  
Fernando Alarcón-Soldevilla ◽  
Eva Fages-Caravaca ◽  
Tra L. Kieu ◽  
...  
Keyword(s):  
Xeroderma Pigmentosum ◽  
Excision Repair ◽  
Neurological Impairment ◽  
Complementation Group ◽  
Dermal Fibroblasts ◽  
Novel Mutations ◽  
Recessive Mutations ◽  
Whole Exome ◽  
Nucleotide Excision ◽  
Group A

We aimed to determine if an adolescent patient presenting with neurological impairment has xeroderma pigmentosum (XP). For this purpose, whole-exome sequencing was performed to assess mutations in XP genes. Dermal fibroblasts were established from a skin biopsy and XPA expression determined by immunoblotting. Nucleotide excision repair (NER) capacity was measured by detection of unscheduled DNA synthesis (UDS) in UVC-irradiated patient fibroblasts. Genetic analysis revealed two recessive mutations in XPA, one known c.682C>T, p.Arg228Ter, and the other c.553C>T, p.Gln185Ter, only two cases were reported. XPA protein was virtually undetectable in lysates from patient-derived fibroblast. The patient had significantly lower UV-induced UDS (3.03 ± 1.95%, p < 0.0001) compared with healthy controls (C5RO = 100 ± 12.2; C1UMN = 118 ± 5.87), indicating significant NER impairment. In conclusion, measurement of NER capacity is beneficial for the diagnosis of XP and in understanding the functional impact of novel mutations in XP genes. Our findings highlight the importance of neurologists considering XP in their differential diagnosis when evaluating patients with atypical neurodegeneration.

scholarly journals Relationship of the Xeroderma Pigmentosum Group E DNA Repair Defect to the Chromatin and DNA Binding Proteins UV-DDB and Replication Protein A

1998 ◽  
Vol 18 (6) ◽  
pp. 3182-3190 ◽  
Author(s):  
Vesna RapićOtrin ◽  
Isao Kuraoka ◽  
Tiziana Nardo ◽  
Mary McLenigan ◽  
A. P. M. Eker ◽  
...  
Keyword(s):  
Dna Binding ◽  
Nucleotide Excision Repair ◽  
Xeroderma Pigmentosum ◽  
Excision Repair ◽  
Protein A ◽  
Replication Protein A ◽  
Replication Protein ◽  
Cell Extracts ◽  
Nucleotide Excision ◽  
Repair Defect

ABSTRACT Cells from complementation groups A through G of the heritable sun-sensitive disorder xeroderma pigmentosum (XP) show defects in nucleotide excision repair of damaged DNA. Proteins representing groups A, B, C, D, F, and G are subunits of the core recognition and incision machinery of repair. XP group E (XP-E) is the mildest form of the disorder, and cells generally show about 50% of the normal repair level. We investigated two protein factors previously implicated in the XP-E defect, UV-damaged DNA binding protein (UV-DDB) and replication protein A (RPA). Three newly identified XP-E cell lines (XP23PV, XP25PV, and a line formerly classified as an XP variant) were defective in UV-DDB binding activity but had levels of RPA in the normal range. The XP-E cell extracts did not display a significant nucleotide excision repair defect in vitro, with either UV-irradiated DNA or a uniquely placed cisplatin lesion used as a substrate. Purified UV-DDB protein did not stimulate repair of naked DNA by DDB− XP-E cell extracts, but microinjection of the protein into DDB−XP-E cells could partially correct the repair defect. RPA stimulated repair in normal, XP-E, or complemented extracts from other XP groups, and so the effect of RPA was not specific for XP-E cell extracts. These data strengthen the connection between XP-E and UV-DDB. Coupled with previous results, the findings suggest that UV-DDB has a role in the repair of DNA in chromatin.

scholarly journals Xeroderma Pigmentosum Complementation Group E Protein (XPE/DDB2): Purification of Various Complexes of XPE and Analyses of Their Damaged DNA Binding and Putative DNA Repair Properties

2005 ◽  
Vol 25 (22) ◽  
pp. 9784-9792 ◽  
Author(s):  
Gülnihal Kulaksız ◽  
Joyce T. Reardon ◽  
Aziz Sancar
Keyword(s):  
Dna Binding ◽  
Nucleotide Excision Repair ◽  
Xeroderma Pigmentosum ◽  
Cellular Response ◽  
Excision Repair ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Small Subunit ◽  
Nucleotide Excision ◽  
Damaged Dna

ABSTRACT Xeroderma pigmentosum is characterized by increased sensitivity of the affected individuals to sunlight and light-induced skin cancers and, in some cases, to neurological abnormalities. The disease is caused by a mutation in genes XPA through XPG and the XP variant (XPV) gene. The proteins encoded by the XPA, -B, -C, -D, -F, and -G genes are required for nucleotide excision repair, and the XPV gene encodes DNA polymerase eta, which carries out translesion DNA synthesis. In contrast, the mechanism by which the XPE gene product prevents sunlight-induced cancers is not known. The gene (XPE/DDB2) encodes the small subunit of a heterodimeric DNA binding protein with high affinity to UV-damaged DNA (UV-damaged DNA binding protein [UV-DDB]). The DDB2 protein exists in at least four forms in the cell: monomeric DDB2, DDB1-DDB2 heterodimer (UV-DDB), and as a protein associated with both the Cullin 4A (CUL4A) complex and the COP9 signalosome. To better define the role of DDB2 in the cellular response to DNA damage, we purified all four forms of DDB2 and analyzed their DNA binding properties and their effects on mammalian nucleotide excision repair. We find that DDB2 has an intrinsic damaged DNA binding activity and that under our assay conditions neither DDB2 nor complexes that contain DDB2 (UV-DDB, CUL4A, and COP9) participate in nucleotide excision repair carried out by the six-factor human excision nuclease.

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