At the core of nucleotide excision repair

Kuper, Jochen; Kisker, Caroline

doi:10.1016/j.sbi.2023.102605

Cited by 11 publications

(6 citation statements)

References 50 publications

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“…NER consMtutes a mulM-step mulM-protein cascade that can be divided into 4 disMnct phases. The first comprises iniMal lesion recogniMon and also demarks the two entry points of the NER cascade [6][7][8] . In transcripMon coupled repair (TCR) RNA polymerase 2 (RNA pol 2) becomes stalled upon the encounter with a lesion.…”

Section: Mainmentioning

confidence: 99%

“…Initially TFIIH, mainly driven by the XPB translocase, opens the bubble around the lesion. This is aided by the arrival of XPA, enhancing XPBs activity and releasing CAK from TFIIH, thereby activating XPD and initiating phase 3, the lesion verification step 8 . Here the helicase activity of XPD further opens the bubble and when XPD encounters a lesion it becomes stalled, demarking a point of no return.…”

Section: Mainmentioning

confidence: 99%

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Trapped in translocation – Stalling of XPD on a crosslinked DNA substrate

Kuper,

Hove,

Maidl

et al. 2024

Preprint

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The super family 2 (SF2) helicase XPD is a central component of the general transcription factor II H (TFIIH) which is essential for transcription and nucleotide excision DNA repair (NER)1. Within these two processes XPDs helicase function is vital for NER but not for transcription initiation, where XPD only acts as a scaffold for other factors2. We deciphered one of the most enigmatic steps in XPD helicase action: the active separation of dsDNA and its stalling upon approaching an interstrand crosslink, one of the most severe DNA damages in the cell, using cryo EM. Furthermore, the structure clearly shows how dsDNA is separated and reveals a highly unusual involvement of the Arch domain in active dsDNA separation. Combined with mutagenesis and biochemical analyses, we identify distinct functional residues important for helicase activity. Surprisingly, those areas also affect core TFIIH translocase activity, revealing a yet unencountered function of XPD within the TFIIH scaffold. Importantly, our structure provides a basis for XPD damage recognition and further suggests how the NER bubble could be formed, leading to a model for the location of the XPG nuclease relative to the excised damage.

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Section: Mainmentioning

confidence: 99%

Section: Mainmentioning

confidence: 99%

Trapped in translocation – Stalling of XPD on a crosslinked DNA substrate

Kuper,

Hove,

Maidl

et al. 2024

Preprint

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“…In GG-NER, the 6−4PP lesion is recognized by the xeroderma pigmentosum C protein (XPC) ( 7 , 40 ), while for CPD, recognition first employs the UV-damaged DNA-binding protein complex UV-DDB followed by hand-off to XPC ( 20 , 41 , 42 ). XPC that is bound to the damaged duplex recruits TFIIH, whose XPB translocase opens the DNA by translocating along the double-stranded DNA (dsDNA) in the 3′ to 5′ direction; its XPD helicase searches for the lesion by tracking along the damaged single-stranded DNA (ssDNA) in the 5′ to 3′ direction, in concert with XPA, RPA and XPG, to form a pre-incision complex ( 36 , 38 , 43–46 ). Once XPD is stalled at the lesion site, the XPF-ERCC1 nuclease is recruited and dual incision by XPF-ERCC1 and XPG takes place ( 47 ).…”

Section: Introductionmentioning

confidence: 99%

Differing structures and dynamics of two photolesions portray verification differences by the human XPD helicase

Fu,

Geacintov,

Broyde

2023

Nucleic Acids Research

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Ultraviolet light generates cyclobutane pyrimidine dimer (CPD) and pyrimidine 6−4 pyrimidone (6−4PP) photoproducts that cause skin malignancies if not repaired by nucleotide excision repair (NER). While the faster repair of the more distorting 6–4PPs is attributed mainly to more efficient recognition by XPC, the XPD lesion verification helicase may play a role, as it directly scans the damaged DNA strand. With extensive molecular dynamics simulations of XPD-bound single-strand DNA containing each lesion outside the entry pore of XPD, we elucidate strikingly different verification processes for these two lesions that have very different topologies. The open book-like CPD thymines are sterically blocked from pore entry and preferably entrapped by sensors that are outside the pore; however, the near-perpendicular 6−4PP thymines can enter, accompanied by a displacement of the Arch domain toward the lesion, which is thereby tightly accommodated within the pore. This trapped 6−4PP may inhibit XPD helicase activity to foster lesion verification by locking the Arch to other domains. Furthermore, the movement of the Arch domain, only in the case of 6−4PP, may trigger signaling to the XPG nuclease for subsequent lesion incision by fostering direct contact between the Arch domain and XPG, and thereby facilitating repair of 6−4PP.

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“…NER constitutes a multistep multiprotein cascade that can be divided into four distinct phases. The first phase comprises initial lesion recognition and demarks the two possible entry points of the NER cascade [4][5][6] . At one entry point, transcription-coupled repair (TC-NER), RNA polymerase II (RNA Pol II) becomes stalled upon encountering a lesion.…”

mentioning

confidence: 99%

“…Initially, TFIIH, mainly driven by the XPB translocase, opens a bubble around the lesion. This is aided by the arrival of XPA, enhancing XPB activity and releasing CAK from TFIIH, thereby activating XPD and initiating phase 3, the lesion verification step 6 . Here, the helicase activity of XPD further opens the bubble and, when XPD encounters a lesion, it stalls, enabling the maturation of the preincision complex.…”

mentioning

confidence: 99%

XPD stalled on cross-linked DNA provides insight into damage verification

Kuper,

Hove,

Maidl

et al. 2024

Nat Struct Mol Biol

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The superfamily 2 helicase XPD is a central component of the general transcription factor II H (TFIIH), which is essential for transcription and nucleotide excision DNA repair (NER). Within these two processes, the helicase function of XPD is vital for NER but not for transcription initiation, where XPD acts only as a scaffold for other factors. Using cryo-EM, we deciphered one of the most enigmatic steps in XPD helicase action: the active separation of double-stranded DNA (dsDNA) and its stalling upon approaching a DNA interstrand cross-link, a highly toxic form of DNA damage. The structure shows how dsDNA is separated and reveals a highly unusual involvement of the Arch domain in active dsDNA separation. Combined with mutagenesis and biochemical analyses, we identified distinct functional regions important for helicase activity. Surprisingly, those areas also affect core TFIIH translocase activity, revealing a yet unencountered function of XPD within the TFIIH scaffold. In summary, our data provide a universal basis for NER bubble formation, XPD damage verification and XPG incision.

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At the core of nucleotide excision repair

Cited by 11 publications

References 50 publications

Trapped in translocation – Stalling of XPD on a crosslinked DNA substrate

Trapped in translocation – Stalling of XPD on a crosslinked DNA substrate

Differing structures and dynamics of two photolesions portray verification differences by the human XPD helicase

XPD stalled on cross-linked DNA provides insight into damage verification

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