Structural homology between the Rap30 DNA-binding domain and linker histone H5: Implications for preinitiation complex assembly

Groft, Caroline M.; Uljon, Sacha N.; Wang, Rong; Werner, M.D.

doi:10.1073/pnas.95.16.9117

Cited by 66 publications

(84 citation statements)

References 50 publications

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“…The winged-helix domains of hRAP30c and hTFIIE␤m can participate in nonspecific DNA binding, although they do not appear to use the same surface regions for these interactions (17,38). In the case of hRAP30c, the DNA interaction sites as judged by NMR are qualitatively similar to those observed by x-ray crystallography for sequence-specific DNA recognition by HNF-3␥ (33).…”

Section: Resultssupporting

confidence: 65%

“…Winged-helix proteins in the pol II transcription initiation complex also include the Cterminal domain of the RAP30 subunit of human TFIIF (hRAP30c) (17) and the middle domain of the ␤ subunit of human TFIIE (hTFIIE␤m) (38). Our hRAP74cc crystal structure provides a third example of a winged-helix motif involved in transcription initiation by pol II.…”

Section: Resultsmentioning

confidence: 99%

“…Mammalian RAP30 can be divided functionally into three regions: (i) the N-terminal region, which is responsible for binding to the N terminus of RAP74 (15); (ii) the middle, putative polymerase binding region (16); and (iii) a C-terminal domain, which resembles a winged-helix DNA-binding protein (17). Inspection of the amino acid sequences of mammalian RAP74 also reveals three functional regions, including (i) the N-terminal globular region, which is responsible for binding to the N terminus of RAP30 (15), (ii) a divergent, highly charged central region lacking hydrophobic residues (18), and (iii) a conserved Cterminal region.…”

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confidence: 99%

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Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF

Kamada

Angelis

Roeder

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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The x-ray structure of a C-terminal fragment of the RAP74 subunit of human transcription factor (TF) IIF has been determined at 1.02-Å resolution. The ␣͞␤ structure is strikingly similar to the globular domain of linker histone H5 and the DNA-binding domain of hepatocyte nuclear factor 3␥ (HNF-3␥), making it a winged-helix protein. The surface electrostatic properties of this compact domain differ significantly from those of bona fide winged-helix transcription factors (HNF-3␥ and RFX1) and from the winged-helix domains found within the RAP30 subunit of TFIIF and the ␤ subunit of TFIIE. RAP74 has been shown to interact with the TFIIF-associated C-terminal domain phosphatase FCP1, and a putative phosphatase binding site has been identified within the RAP74 wingedhelix domain.T ranscription of class II nuclear genes in eukaryotes requires a complex assembly of proteins composed of a multisubunit RNA polymerase II (pol II) and general transcription factors (TFIIs), which are required for assembly of the preinitiation complex (PIC) on promoter DNA and initiation of transcription (1). In the most general case, PIC assembly begins with the TATA box-binding protein (TBP) subunit of TFIID recognizing the TATA element, followed by coordinated accretion of TFIIB, the nonphosphorylated form of pol II plus TFIIF, TFIIE, and TFIIH. Transcription initiation is followed by phosphorylation of the C-terminal domain (CTD) of the largest subunit of pol II, which in turn facilitates promoter clearance and productive elongation. After elongation and termination of pre-mRNA synthesis, a phosphatase recycles pol II to its nonphosphorylated form, allowing the enzyme and the requisite TFIIs to initiate the next round of transcription.Mammalian TFIIF is an ␣␤ hetero-oligomer of RAP74 and RAP30 subunits (RNA polymerase II-associating proteins; 58 kDa and 28 kDa, respectively) (2), which binds to pol II in solution and facilitates delivery of the polymerase to the TFIID-TFIIB-DNA complex on the promoter. TFIIF was originally identified on the basis of physical association with pol II, and its requirement for promoter-specific transcription initiation by this large multisubunit enzyme. Within the PIC, TFIIF stabilizes binding of pol II to TFIID and TFIIB at the promoter (3-5). Moreover, TFIIF is required for entry of TFIIE and TFIIH into the PIC, for subsequent open complex formation catalyzed by the DNA helicase subunit of TFIIH (5-7), and for synthesis of the first phosphodiester bond of nascent transcripts (8-10). It is also possible that TFIIF acts as a scaffold for binding of TFIIH to the growing PIC and͞or that TFIIF actively participates in formation of the open complex. Photocrosslinking experiments suggest that TFIIF interacts with promoter DNA to induce a dramatic conformational change that results in wrapping of DNA around pol II and the class II general transcription factors within the PIC (11-14).Biochemical properties of TFIIF have been attributed to distinct polypeptide chain segments of each of subunit. Mammalian RAP30 can b...

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Section: Resultssupporting

confidence: 65%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF

Kamada

Angelis

Roeder

et al. 2001

Proc. Natl. Acad. Sci. U.S.A.

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“…S6). The yTAF1 arm 1 also shows close similarity to the Rap30 DNA binding wHTH domain (22) (Z score of 4.3 and rmsd in 65 Cα atom positions of 2.8 Å) (Fig. S6).…”

Section: Resultsmentioning

confidence: 99%

“…Substitution of evolutionary conserved yTAF1 Phe493, His494, Phe480 residues, and yTAF7 Phe186 with Ala (Fig. 3D) permitted stable yTAF1/7 formation but completely abolished binding to H3K27me3 (19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35) peptide (Table S2). Other targeted mutations disrupted stable yTAF1/7 complex formation (Table S2).…”

Section: Resultsmentioning

confidence: 99%

Structural and functional insight into TAF1–TAF7, a subcomplex of transcription factor II D

Bhattacharya

Lou

Hwang

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Transcription factor II D (TFIID) is a multiprotein complex that nucleates formation of the basal transcription machinery. TATA binding protein-associated factors 1 and 7 (TAF1 and TAF7), two subunits of TFIID, are integral to the regulation of eukaryotic transcription initiation and play key roles in preinitiation complex (PIC) assembly. Current models suggest that TAF7 acts as a dissociable inhibitor of TAF1 histone acetyltransferase activity and that this event ensures appropriate assembly of the RNA polymerase IImediated PIC before transcriptional initiation. Here, we report the 3D structure of a complex of yeast TAF1 with TAF7 at 2.9 Å resolution. The structure displays novel architecture and is characterized by a large predominantly hydrophobic heterodimer interface and extensive cofolding of TAF subunits. There are no obvious similarities between TAF1 and known histone acetyltransferases. Instead, the surface of the TAF1-TAF7 complex contains two prominent conserved surface pockets, one of which binds selectively to an inhibitory trimethylated histone H3 mark on Lys27 in a manner that is also regulated by phosphorylation at the neighboring H3 serine. Our findings could point toward novel roles for the TAF1-TAF7 complex in regulation of PIC assembly via reading epigenetic histone marks.initiation complex | protein structure | protein-protein interaction | X-ray crystallography T he general transcription factor II D (TFIID) plays a central role in recognition of the core promoter element and mediates accurate transcription initiation by RNA Polymerase (Pol) II for a large class of genes. TFIID nucleates the formation of the preinitiation complex (PIC) at the transcriptional start site by recruiting other general transcription factors (TFII-A, -B, -E, -F, and -H), along with RNA Pol II. TFIID is assembled in a stepwise manner, with a symmetric TFIID core complex recruited first, followed by further recruitment of additional TATA binding protein (TBP)-associated factors (TAFs) to form the complete asymmetric holo-TFIID complex (1). This megadalton-sized multiprotein assembly, comprised of TBP and 13 evolutionary conserved TAFs (2), is organized into a trilobed structure (3) and undergoes striking rearrangements upon binding to TFIIA and DNA (4). TAF subunits serve multiple functions within the TFIID holocomplex. In addition to TBP, TAF1, TAF2, TAF6, and TAF9 are also involved in recognition of DNA initiator and promoter elements. Moreover, TFIID can behave as an epigenetic effector, capable of recognizing posttranslational histone modifications associated with activated transcription. Eukaryotic TAF1 contains a double bromodomain that recognizes acetylated histones, and TAF3 contains a plant homeo domain (PHD) that binds to histone H3 methylated at lysine 4 (5, 6). In addition to roles in basal transcription, TFIID is also associated with diseases. Overexpression of TAF1, which acts as a specific coactivator of androgen receptor, is related to the progression of human prostate cancer (7). Additionally, altera...

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Strukturelle Grundlage der Transkription: 10 Jahre nach dem Chemie‐Nobelpreis

Hantsche

Cramer

2016

Angewandte Chemie

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In allen lebenden Zellen bildet die Transkription den ersten Schritt der Expression genetischer Information. Ihrer Regulation unterliegen Zelldifferenzierung, Morphogenese sowie Antworten auf Umweltveränderungen. Während der Transkription verwendet das Enzym RNA‐Polymerase DNA als Vorlage, um eine komplementäre RNA‐Kopie von einem Gen herzustellen. Wir beschreiben die Entwicklungen in unserem strukturellen Verständnis der Transkription in Eukaryoten, die in den letzten 10 Jahren nach der Verleihung des Nobelpreises für Chemie an Roger Kornberg im Jahr 2006 erzielt wurden. Eine Aufklärung der Transkriptionsinitiation und ‐elongation zeichnet sich ab, wohingegen die Mechanismen der Transkriptionsregulation weitgehend unverstanden bleiben. In diesem Feld wurden strukturbiologische Hybridmethoden entwickelt, die verschiedene Techniken zur Bestimmung der dreidimensionalen Architektur von großen und transienten makromolekularen Komplexen kombinieren.

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Structural homology between the Rap30 DNA-binding domain and linker histone H5: Implications for preinitiation complex assembly

Abstract: The

Cited by 66 publications

References 50 publications

Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF

Crystal structure of the C-terminal domain of the RAP74 subunit of human transcription factor IIF

Structural and functional insight into TAF1–TAF7, a subcomplex of transcription factor II D

Strukturelle Grundlage der Transkription: 10 Jahre nach dem Chemie‐Nobelpreis

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