Mechanism of DNA loading by the DNA repair helicase XPD

Constantinescu-Aruxandei, Diana; Petrovic-Stojanovska, Biljana; Penedo, J. Carlos; White, Malcolm F.; Naismith, James H.

doi:10.1093/nar/gkw102

Cited by 39 publications

(36 citation statements)

References 48 publications

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“…In contrast, in eukaryotic NER, XPD is likely present as a single copy in the multisubunit TFIIH complex, as visualized in several electron microscopy studies (52,53). The crystal structure of XPD shows a small (ϳ1 nm diameter) pore in the protein formed by domain 1 together with the arch and iron sulfur (FeS) cluster containing domains through which the ssDNA is believed to thread (10,54). As XPD translocates along the DNA, the arch and FeS cluster domains are believed to act as a "ploughshare" that separates the two ssDNA strands.…”

Section: Uvrb and Xpd Helicase Activities Are Activated By Proteinmentioning

confidence: 99%

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Wirth

Gross

Roth

et al. 2016

Journal of Biological Chemistry

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Nucleotide excision repair is an important and highly conserved DNA repair mechanism with an exceptionally large range of chemically and structurally unrelated targets. Lesion verification is believed to be achieved by the helicases UvrB and XPD in the prokaryotic and eukaryotic processes, respectively. Using single molecule atomic force microscopy analyses, we demonstrate that UvrB and XPD are able to load onto DNA and pursue lesion verification in the absence of the initial lesion detection proteins. Interestingly, our studies show different lesion recognition strategies for the two functionally homologous helicases, as apparent from their distinct DNA strand preferences, which can be rationalized from the different structural features and interactions with other nucleotide excision repair protein factors of the two enzymes. Nucleotide excision repair (NER)4 is an important DNA repair mechanism with a large range of chemically and structurally unrelated targets. Examples range from bulky DNA adducts to interstrand DNA cross-links caused by antitumor drugs (1-3). In humans, NER is the only repair system for the removal of UV irradiation-induced photoproducts such as the intrastrand cross-linking cyclobutane-pyrimidine dimers (CPDs), and dysfunctional NER is responsible for severe diseases, including xeroderma pigmentosum (XP) (1-3).The mechanism of NER is highly conserved between organisms. In bacteria, NER involves the proteins UvrA, UvrB, and UvrC. In the current model of prokaryotic NER, a hetero-tetrameric complex of UvrA and UvrB (UvrA 2 B 2 ) scans the DNA for lesions. When a lesion is encountered, initial lesion sensing by a dimer of UvrA is based on detection of DNA distortion. Conformational changes in the UvrA 2 B 2 complex result in an unwinding and opening of dsDNA around the lesion, providing an unpaired (bubble) region likely required by UvrB to thread onto one of the ssDNA strands. The helicase UvrB is believed to verify the presence of a lesion by insertion of a ␤-hairpin via interactions with residues at the base of the hairpin (2). Upon lesion verification by UvrB, UvrA dissociates from the complex, and ATP re-binding by UvrB results in the formation of the lesion-specific UvrB-DNA complex, which recruits the NER endonuclease UvrC (UvrBC complex). UvrC carries out two incisions on either side of the lesion. The 12-13-nucleotide (nt)-long ssDNA stretch (2) containing the lesion can then be removed together with the endonuclease by the helicase UvrD, and the resulting gap is filled and sealed by DNA polymerase I and ligase.Eukaryotic NER encompasses a total of ϳ30 proteins, including the xeroderma pigmentosum group proteins (XPA-XPG). Repair can either be initiated by a stalled RNA polymerase in transcription-coupled NER or via global genome NER. In global genome NER, upon initial detection of short destabilized DNA structures by the CEN2-XPC-HR23B complex, the ATPase/ helicase XPB, which is part of the 10-subunit transcription factor IIH (TFIIH) complex, then directly interacts with XPC (4) and...

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Section: Uvrb and Xpd Helicase Activities Are Activated By Proteinmentioning

confidence: 99%

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Wirth

Gross

Roth

et al. 2016

Journal of Biological Chemistry

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“…Accordingly, the CAK subcomplex is present during transcription initiation, when the XPD helicase is inactive, and removed during NER, when XPD helicase activity is required 2,18,19,31 . The interactions between MAT1 and XPD observed in our cryo-EM map might be involved in mediating this inhibition, possibly by limiting the conformational freedom of the ARCH domain, which has been implicated in DNA substrate loading by XPD 11 . In the context of the human Pol II-PIC 5 , MAT1 may also be involved in forming contacts between TFIIH and the PIC core (Fig.…”

mentioning

confidence: 93%

“…In our cryo-EM map, an elongated density connects the DRD-like domain of XPB with a region of XPD RecA2 that is inferred to be part of the DNA substrate-binding site on the basis of the structures of archaeal XPD–DNA complexes 11,12 (Fig. 3a).…”

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confidence: 97%

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The cryo-electron microscopy structure of human transcription factor IIH

Greber

Nguyen

Fang

et al. 2017

Nature

114

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Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription1. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair1. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair2, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation1,2. Mutations in the TFIIH subunits XPB, XPD, and p8 lead to severe premature ageing and cancer propensity in the genetic diseases xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy, highlighting the importance of TFIIH for cellular physiology3. Here we present the cryo-electron microscopy structure of human TFIIH at 4.4 Å resolution. The structure reveals the molecular architecture of the TFIIH core complex, the detailed structures of its constituent XPB and XPD ATPases, and how the core and kinase subcomplexes of TFIIH are connected. Additionally, our structure provides insight into the conformational dynamics of TFIIH and the regulation of its activity.

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“…The xeroderma pigmentosum group D proteins are the only characterized SF2 helicases that translocate 5Ј to 3Ј direction along DNA (32,33,45). The iron-sulfur cluster responsible for coupling ATP hydrolysis to 5Ј to 3Ј DNA translocation in the archaeal xeroderma pigmentosum group D protein family member Rad3 (33,46) is not present in the sequence of NPH I. Thus, another feature of NPH I determines 5Ј to 3Ј translocation directionality.…”

Section: Discussionmentioning

confidence: 99%

Nucleoside Triphosphate Phosphohydrolase I (NPH I) Functions as a 5′ to 3′ Translocase in Transcription Termination of Vaccinia Early Genes

Hindman

Gollnick

2016

Journal of Biological Chemistry

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Vaccinia virus early genes are transcribed immediately upon infection. Nucleoside triphosphate phosphohydrolase I (NPH I)is an essential component of the early gene transcription complex. NPH I hydrolyzes ATP to release transcripts during transcription termination. The ATPase activity of NPH I requires single-stranded (ss) DNA as a cofactor; however, the source of this cofactor within the transcription complex is not known. Based on available structures of transcription complexes it has been hypothesized that the ssDNA cofactor is obtained from the unpaired non-template strand within the transcription bubble. In vitro transcription on templates that lack portions of the nontemplate strand within the transcription bubble showed that the upstream portion of the transcription bubble is required for efficient NPH I-mediated transcript release. Complementarity between the template and non-template strands in this region is also required for NPH I-mediated transcript release. This observation complicates locating the source of the ssDNA cofactor within the transcription complex because removal of the nontemplate strand also disrupts transcription bubble reannealing. Prior studies have shown that ssRNA binds to NPH I, but it does not activate ATPase activity. Chimeric transcription templates with RNA in the non-template strand confirm that the source of the ssDNA cofactor for NPH I is the upstream portion of the non-template strand in the transcription bubble. Consistent with this conclusion we also show that isolated NPH I acts as a 5 to 3 translocase on single-stranded DNA.

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Mechanism of DNA loading by the DNA repair helicase XPD

Cited by 39 publications

References 48 publications

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

Conservation and Divergence in Nucleotide Excision Repair Lesion Recognition

The cryo-electron microscopy structure of human transcription factor IIH

Nucleoside Triphosphate Phosphohydrolase I (NPH I) Functions as a 5′ to 3′ Translocase in Transcription Termination of Vaccinia Early Genes

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