The Structure of the TFIIH p34 Subunit Reveals a Von Willebrand Factor A Like Fold

Schmitt, Dominik; Kuper, Jochen; Elias, Agnes; Kisker, Caroline

doi:10.1371/journal.pone.0102389

Cited by 10 publications

(9 citation statements)

References 56 publications

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“…Both p34/Tfb4 and p44/Ssl1 have an N-terminal VWA domain and a C-terminal Zn RING motif (Kellenberger et al, 2005; Schmitt et al, 2014; Whittaker and Hynes, 2002). The C-terminal RING motif of p44 interacts with the VWA domain of p34 (Fribourg et al, 2001; Kellenberger et al, 2005; Schmitt et al, 2014), and the VWA domain of p44 interacts with p34 (Iyer et al, 1996).…”

Section: Resultsmentioning

confidence: 99%

Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH

et al. 2015

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Summary TFIIH is essential for both RNA polymerase II transcription and DNA repair, and mutations in TFIIH can result in human disease. Here, we determine the molecular architecture of human and yeast TFIIH by an integrative approach using chemical crosslinking/mass spectrometry (CXMS) data, biochemical analyses, and previously published electron microscopy maps. We identified four new conserved “topological regions” that function as hubs for TFIIH assembly and more than 35 conserved topological features within TFIIH, illuminating a network of interactions involved in TFIIH assembly and regulation of its activities. We show that one of these conserved regions, the p62/Tfb1 Anchor region, directly interacts with the DNA helicase subunit XPD/Rad3 in native TFIIH and is required for the integrity and function of TFIIH. We also reveal the structural basis for defects in patients with Xeroderma pigmentosum and Trichothiodystrophy, with mutations found at the interface between the p62 Anchor region and the XPD subunit.

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Section: Resultsmentioning

confidence: 99%

Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH

et al. 2015

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“…Although divergent in sequence, the Tfb4 and Ssl1 subunits have similar domain organizations with N-terminal von Willebrand factor A (VWA) domains and C-terminal Ring fingers (39,40) (Fig. 2 and 3).…”

Section: Resultsmentioning

confidence: 99%

Function of Conserved Topological Regions within the Saccharomyces cerevisiae Basal Transcription Factor TFIIH

Warfield

Luo

Ranish

et al. 2016

Molecular and Cellular Biology

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bTFIIH is a 10-subunit RNA polymerase II basal transcription factor with a dual role in DNA repair. TFIIH contains three enzymatic functions and over 30 conserved subdomains and topological regions. We systematically tested the function of these regions in three TFIIH core module subunits, i.e., Ssl1, Tfb4, and Tfb2, in the DNA translocase subunit Ssl2, and in the kinase module subunit Tfb3. Our results are consistent with previously predicted roles for the Tfb2 Hub, Ssl2 Lock, and Tfb3 Latch regions, with mutations in these elements typically having severe defects in TFIIH subunit association. We also found unexpected roles for other domains whose function had not previously been defined. First, the Ssl1-Tfb4 Ring domains are important for TFIIH assembly. Second, the Tfb2 Hub and HEAT domains have an unexpected role in association with Tfb3. Third, the Tfb3 Ring domain is important for association with many other TFIIH subunits. Fourth, a partial deletion of the Ssl1 N-terminal extension (NTE) domain inhibits TFIIH function without affecting subunit association. Finally, we used site-specific cross-linking to localize the Tfb3-binding surface on the Rad3 Arch domain. Our cross-linking results suggest that Tfb3 and Rad3 have an unusual interface, with Tfb3 binding on two opposite faces of the Arch. TFIIH is a conserved 10-subunit complex that plays essential roles in both RNA polymerase II (Pol II) transcription and nucleotide excision repair (NER) (1-3). TFIIH and TFIIE are the last basal factors to join the transcription preinitiation complex (PIC) (4). In transcription, TFIIH functions in DNA unwinding, transcription start site (TSS) scanning, promoter escape, and Pol II C-terminal domain (CTD) phosphorylation. During NER, TFIIH promotes the DNA unwinding of an asymmetric region around the site of DNA lesions as an early step in excision and replacement of damaged DNA (5, 6). Mutations in three TFIIH subunits, XPD, XPB, and p8, cause human diseases associated with defects in DNA repair and transcription (1).TFIIH has three enzymatic activities that are essential for these functions. First, the Rad3/XPD (yeast/human) subunit is an ATPdependent DNA helicase that participates in DNA unwinding during NER. While this enzymatic activity is dispensable for transcription, Rad3/XPD is required for transcription as it plays an essential structural role in stabilizing the TFIIH complex (7-10). Second, Ssl2/XPB is an ATP-dependent double-stranded DNA translocase with roles in transcription and DNA repair. Ssl2 promotes formation of the Pol II open complex by reeling downstream promoter DNA into the Pol II active site, leading to DNA unwinding (11, 12). In budding yeast, Pol II transcription initiates downstream from the site of PIC formation (13), and Ssl2 function drives the scanning of downstream promoter DNA for an appropriate TSS (14). In the human transcription system, XPB activity has been implicated in promoter escape and the release of Pol II from contacts with promoter DNA and other PIC components (15, 16). Ssl2...

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“…The amino acid sequence of human P52 was aligned with that of human transportin 4, initially with the PROMALS3D multiple sequences and structure alignment server 84 , and then adjusted manually. The human p44 VWA domain was modelled using the X-ray structure of the p34 subunit of the TFIIH complex from the eukaryotic thermophilic fungus Chaetomium thermophilum (PDB: 4PN7) 85 .…”

Section: Methodsmentioning

confidence: 99%

Near-atomic resolution visualization of human transcription promoter opening

Cheng

Fang

et al. 2016

Nature

274

364

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In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA–RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB.

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The Structure of the TFIIH p34 Subunit Reveals a Von Willebrand Factor A Like Fold

Cited by 10 publications

References 56 publications

Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH

Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH

Function of Conserved Topological Regions within the Saccharomyces cerevisiae Basal Transcription Factor TFIIH

Near-atomic resolution visualization of human transcription promoter opening

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