Structure of the human transcription factor TFIIF revealed by limited proteolysis with trypsin

Cai, Yong; Mitsuyasu, Hiromichi; Zhang, Chun; Oshiro, Satoru; Kitajima, Shigetaka

doi:10.1016/s0014-5793(98)01068-0

Cited by 10 publications

(3 citation statements)

References 33 publications

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“…Both subunits also contain a C-terminal winged helix (WH) domain 97,98 . The WH domains are connected to the dimerization module by a charged region in TFIIFα and a linker region in TFIIFβ 31,32, 99 . In contrast to a canonical WH domain, the TFIIFα WH domain contains an extra α-helix between helices H2 and H3 (REF.…”

Section: Rpb4-rpb7mentioning

confidence: 99%

Structural basis of transcription initiation by RNA polymerase II

Sainsbury

Bernecky

Cramer

2015

Nat Rev Mol Cell Biol

355

343

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Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter.

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Section: Rpb4-rpb7mentioning

confidence: 99%

Structural basis of transcription initiation by RNA polymerase II

Sainsbury

Bernecky

Cramer

2015

Nat Rev Mol Cell Biol

355

343

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“…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. The RAP74 N-terminal segment (1-217) is involved in PIC assembly and stimulates elongation, and residues 1-172 suffice for delivery of pol II to a preformed complex of TBP, TFIIB, RAP30, and the adenovirus major late promoter (19).…”

mentioning

confidence: 99%

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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“…This suggests a structural organization of TFIIF that, in agreement with predictions based on sequence analysis, consists of globular domains connected by disordered segments. The central region of Tfg1, the largest yeast TFIIF subunit, is highly charged and hypersensitive to proteolysis, which also suggests a poorly ordered structure94. Interestingly, this part of TFIIF is expected to be largely exposed in the RNAP II–TFIIF complex, and TFIIF has been shown to play a critical role in promoting association of Mediator with polymerase and the PIC (ref.…”

Section: Core Machinery: Hinges and Wobbling Partsmentioning

confidence: 99%

Malleable machines take shape in eukaryotic transcriptional regulation

et al. 2008

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Transcriptional control requires the spatially and temporally coordinated action of many macromolecular complexes. Chromosomal proteins, transcription factors, co-activators and components of the general transcription machinery, including RNA polymerases, often use structurally or stoichiometrically ill-defined regions for interactions that convey regulatory information in processes ranging from chromatin remodeling to mRNA processing. Determining the functional significance of intrinsically disordered protein regions and developing conceptual models of their action will help to illuminate their key role in transcription regulation. Complexes comprising disordered regions often display short recognition elements embedded in flexible and sequentially variable environments that can lead to structural and functional malleability. This provides versatility to recognize multiple targets having different structures, facilitate conformational rearrangements and physically communicate with many partners in response to environmental changes. All these features expand the capacities of ordered complexes and give rise to efficient regulatory mechanisms.At the critical intersection between signaling pathways and the process of gene expression, transcription regulation controls and influences many cellular and physiological processes, from cell differentiation and development to metabolic responses to environmental stimuli. Transcription regulation depends on communication and interaction between many large multiprotein complexes, which results in transmission of regulatory information to the RNA polymerases that carry out the synthesis of mRNA from a chromosomal DNA template. In eukaryotic organisms, diverse arrays of proteins are involved in every aspect of transcription regulation, from chromatin remodeling to mRNA processing. These include (i) the histones, chromatin and macromolecular complexes that modify chromatin structure and provide access to the DNA, (ii) transcription factors that bind to upstream regulatory sequences, (iii) co-activators that communicate signals to the core transcription machinery and (iv) general Early observations about two decades ago indicated that various components of the transcription machinery, such as the transactivator domains (TADs) of the GCN4 and GAL4 transcription factors and the C-terminal domain (CTD) of RNA polymerase II (RNAP II), cannot be characterized by a well-defined three-dimensional structure, and that their functions may even be independent of their actual sequences1. These domains were envisaged to act as charged 'blobs' or 'noodles' that would allow recognition of interacting partners of variable architectures and form nontraditional assemblages. Although this scenario has been refined subsequently2, it has been recognized only recently that structurally ill-defined proteins and protein segments, termed intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs), are abundant in eukaryotic proteomes. For example, >50% of proteins are p...

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Structure of the human transcription factor TFIIF revealed by limited proteolysis with trypsin

Cited by 10 publications

References 33 publications

Structural basis of transcription initiation by RNA polymerase II

Structural basis of transcription initiation by RNA polymerase II

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

Malleable machines take shape in eukaryotic transcriptional regulation

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