The Archaeal XPB Protein is a ssDNA-Dependent ATPase with a Novel Partner

Richards, Jodi D.; Cubeddu, Liza; Roberts, J. A. Fraser; Liu, Huanting; White, Malcolm F.

doi:10.1016/j.jmb.2007.12.019

Cited by 31 publications

(37 citation statements)

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“…Bax1 and XPB were shown previously to interact physically in vitro (16), and bioinformatic analyses have suggested that Bax1 might be a DNA endonuclease (18). This prediction was confirmed recently for Bax1 from Thermoplasma acidophilum (19).…”

mentioning

confidence: 58%

“…However, A. fulgidus XPB was crystallized in the absence of its cognate Bax1 partner, and it is therefore possible that the unusual structure observed by Fan et al (17) was due to unusual conformational flexibility induced by the absence of the Bax1 subunit. It has been noted previously that XPB from S. solfataricus is heat-labile and prone to aggregation in the absence of its Bax1 partner (16). A definitive answer to this question will require further analysis of the conformational flexibility of XPB in the presence and absence of Bax1.…”

Section: Discussionmentioning

confidence: 97%

“…The N-terminal polyhistidine tag was removed from the XPB protein by cleavage with TEV protease prior to gel filtration. XPB and Bax1 copurified on each column as a complex with an apparent stoichiometry of 1:1, as shown previously (16,19). Mutated variants with inactivated XPB or Bax1 were prepared as described under "Experimental Procedures" and purified as for the wild type protein complex.…”

Section: Cloning Expression and Purification Of The Xpb-bax1mentioning

confidence: 99%

“…The crystal structure of archaeal XPD provided a molecular explanation for the effects of mutations causing xeroderma pigmentosum, trichothiodystrophy, and Cockayne's syndrome (9,14,15). Archaeal XPB on its own is an ssDNA-dependent ATPase in vitro, with weak helicase activity under some conditions (16,17). A crystal structure of the core of XPB from Archaeoglobus fulgidus revealed the presence of two canonical motor domains and two accessory domains named the thumb (Thm) domain and damage recognition domain (DRD) with putative roles in DNA damage detection (17).…”

mentioning

confidence: 99%

“…Genes encoding archaeal XPB are usually found next to a gene encoding a protein of unknown function named Bax1 (16). Bax1 and XPB were shown previously to interact physically in vitro (16), and bioinformatic analyses have suggested that Bax1 might be a DNA endonuclease (18).…”

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confidence: 99%

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The XBP-Bax1 Helicase-Nuclease Complex Unwinds and Cleaves DNA

Rouillon

White

2010

Journal of Biological Chemistry

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XPB helicase is an integral part of transcription factor TFIIH, required for both transcription initiation and nucleotide excision repair (NER). Along with the XPD helicase, XPB plays a crucial but only partly understood role in defining and extending the DNA repair bubble around lesions in NER. Archaea encode clear homologues of XPB and XPD, and structural studies of these proteins have yielded key insights relevant to the eukaryal system. Here we show that archaeal XPB functions with a structure-specific nuclease, Bax1, as a helicase-nuclease machine that unwinds and cleaves model NER substrates. DNA bubbles are extended by XPB and cleaved by Bax1 at a position equivalent to that cut by the XPG nuclease in eukaryal NER. The helicase activity of archaeal XPB is dependent on the conserved Thumb domain, which may act as the helix breaker. The N-terminal damage recognition domain of XPB is shown to be crucial for XPB-Bax1 activity and may be unique to the archaea. These findings have implications for the role of XPB in both archaeal and eukaryal NER and for the evolution of the NER pathway. XPB is shown to be a very limited helicase that can act on small DNA bubbles and open a defined region of the DNA duplex. The specialized functions of the accessory domains of XPB are now more clearly delineated. This is also the first direct demonstration of a repair function for archaeal XPB and suggests strongly that the role of XPB in transcription occurred later in evolution than that in repair.The superfamily 2 helicase XPB (Rad25 in Saccharomyces cerevisiae) is an essential component of transcription factor TFIIH. The ATPase activity of XPB is required for both nucleotide excision repair (NER) 2 and transcription initiation from RNA polymerase II promoters (1, 2). The NER pathway is a highly flexible system that is required for the detection and removal of a wide variety of bulky and helix-distorting lesions, including photoproducts. Mutations in the xpb or xpd genes in humans can cause the serious genetic diseases xeroderma pigmentosum, trichothiodystrophy, and Cockayne's syndrome, due to defects in both transcription and repair (reviewed in Ref.3). Examples of xpb mutations in humans are much more rare than those seen in the xpd gene, probably due to the crucial role of the XPB protein in basal transcription (4).Although the ATPase activities of both proteins are required for NER (5), the respective roles of the XPB and XPD helicase components of TFIIH are still a matter of debate. XPD is the more robust helicase (6), and it has been suggested to bind 5Ј of the DNA lesion and translocate in a 5Ј to 3Ј direction toward the damage site, potentially acting as a sensor or proofreader of DNA damage for the NER pathway either by jamming directly on DNA lesions (7) or perhaps through damage sensing by its iron-sulfur cluster binding domain (8, 9). However, little direct evidence exists in support of these possibilities at present, and indeed it is not yet clear whether XPD or XPB binds first at repair sites or whether they bi...

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confidence: 58%

Section: Discussionmentioning

confidence: 97%

Section: Cloning Expression and Purification Of The Xpb-bax1mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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The XBP-Bax1 Helicase-Nuclease Complex Unwinds and Cleaves DNA

Rouillon

White

2010

Journal of Biological Chemistry

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Cerebro‐oculo‐facio‐skeletal syndrome caused by the homozygous pathogenic variant Gly47Arg in ERCC2

Heuvel

Rust

Marquardt

2020

American J of Med Genetics Pt A

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DNA damage repair is a pivotal mechanism in life. The nucleotide excision repair pathway protects the cells against DNA damage and involves XPD, an ATP dependent helicase that is part of the multisubunit protein complex TFIIH. XPD is encoded by the excision repair cross‐complementation group 2 gene (ERCC2). Only three patients with cerebro‐oculo‐facio‐skeletal syndrome (COFS), caused by mutations in ERCC2, have been published so far. This report describes a boy with the homozygous amino acid change p.Gly47Arg in XPD. He presented with profound microcephaly, psychomotor retardation, failure to thrive, cutaneous photosensitivity, a bilateral hearing deficit and optic atrophy, thrombocytopenia, and recurrent episodes of pneumonia. We report the first homozygous occurrence of the pathogenic variant Gly47Arg in the ERCC2 gene. Occurring homozygous, this variant was associated with COFS syndrome, leading to early death of the patient at the age of 21 months.

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The Family Sulfolobaceae

Albers¹,

Siebers²

2014

The Prokaryotes

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The Archaeal XPB Protein is a ssDNA-Dependent ATPase with a Novel Partner

Cited by 31 publications

References 40 publications

The XBP-Bax1 Helicase-Nuclease Complex Unwinds and Cleaves DNA

The XBP-Bax1 Helicase-Nuclease Complex Unwinds and Cleaves DNA

Cerebro‐oculo‐facio‐skeletal syndrome caused by the homozygous pathogenic variant Gly47Arg in ERCC2

The Family Sulfolobaceae

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