Functional domains of the Xenopus laevis 5S gene promoter.

Pieler, Tomas; Oei, Shiao Li; Hamm, Jörg; Engelke, U; Erdmann, Volker A.

doi:10.1002/j.1460-2075.1985.tb04144.x

Cited by 58 publications

(45 citation statements)

References 32 publications

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“…Together, fingers 1-2-3 bind within an 11-bp region located between positions ϩ81 and ϩ91 of the ICR, specifying the DNA sequence GGANGGNNGNN (noncoding strand) and NNNNCCNNNNG (coding strand). The structure agrees well with the earlier identification of the Pol III promoter element box C that was derived from site-directed mutagenesis of the 5S rRNA gene (8). The local details of finger conformation and DNA contacts, seen in a recent NMR structure of fingers 1-2-3 bound to 15 bp of DNA (20,21), closely match our x-ray structure of the longer fragment.…”

Section: Resultssupporting

confidence: 87%

“…The two flanking fingers, 4 and 6, straddle the neighboring minor grooves and appear to serve primarily as spacer elements in DNA recognition. In this way the six-finger protein binds in a precise manner to the separated IE and box C sequences (8). program CURVES (28) shows that there are three localized bends (29) of 16.7°, 24.4°, and 18.4°at base pairs ϩ70, ϩ85, and ϩ90.…”

Section: Resultsmentioning

confidence: 99%

“…Finger 5 binds to bases in the major groove at the IE element, positions ϩ70 to ϩ73, 7 bp upstream of box C. A standard major-groove finger interaction is supplemented by contacts between Leu-148 (Ϫ1) and the base of T74Ј, Ser-150 (ϩ2) and phosphate-74Ј, and Lys-153 and phosphate-73Ј. The DNA sequence specified by finger 5 is GGNNN (noncoding strand) and NNNAT (coding strand), the consensus IE sequence (8).…”

Section: Resultsmentioning

confidence: 99%

“…Prior methylation of certain guanine bases or ethylation of several phosphates interferes with the binding of TFIIIA (10,34). Site-directed mutagenesis of base pairs within the ICR decreases transcriptional activity (8,35) or lowers TFIIIA binding (36,37). Some amino acid mutations in TFIIIA linkers (38)(39)(40) or zinc fingers (41) decrease TFIIIA binding to the ICR.…”

Section: Resultsmentioning

confidence: 99%

“…This site lies within the 5S rRNA coding sequence itself. It is effectively a tripartite promoter (8) containing separated ''box A,'' ''intermediate element'' (IE), and ''box C'' sequences ( Fig. 1 A).…”

mentioning

confidence: 99%

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Differing roles for zinc fingers in DNA recognition: Structure of a six-finger transcription factor IIIA complex

Nolte

Conlin

Harrison

et al. 1998

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

233

185

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The crystal structure of the six NH 2 -terminal zinc fingers of Xenopus laevis transcription factor IIIA (TFIIIA) bound with 31 bp of the 5S rRNA gene promoter has been determined at 3.1 Å resolution. Individual zinc fingers are positioned differently in the major groove and across the minor groove of DNA to span the entire length of the duplex. These results show how TFIIIA can recognize several separated DNA sequences by using fewer fingers than necessary for continuous winding in the major groove.TFIIIA is an essential component of the RNA polymerase III (Pol III) transcription initiation complex for 5S rRNA in Xenopus laevis oocytes (1-3). TFIIIA also participates in the nuclear export (4) and storage of 5S rRNA, with which it forms a stable cytoplasmic 7S particle (5). The DNA-binding site for a single TFIIIA protein extends over 55 bp of the 5S rRNA gene promoter (6, 7). This site lies within the 5S rRNA coding sequence itself. It is effectively a tripartite promoter (8) containing separated ''box A,'' ''intermediate element'' (IE), and ''box C'' sequences ( Fig. 1 A). Similar regulatory elements exist in tRNA gene promoters. Mapping the details of this extensive protein-DNA interaction using chemical, biochemical, and genetic techniques has continued for almost 20 years (1-3, 9, 10). The discovery of nine zinc fingers in TFIIIA (11,12) led to the notion of a transcription factor with repeated modules in its DNA-binding domain (Fig. 1B).Our present knowledge of how zinc fingers bind specifically to DNA comes largely from several x-ray structures (13)(14)(15)(16)(17)(18). In all of these protein-DNA complexes, there are contiguous zinc finger interactions with base pairs in the major groove. In Zif268, for example, three fingers recognize successive, overlapping base pair quartets in the major groove, covering a total of 10 bp. In the DNA complex of a five-finger segment from Gli, the first finger lies outside the major groove and makes no DNA contacts. The remaining fingers wrap in the major groove rather like those of Zif268. An extension of this mode of binding is not sufficient to explain the size of the TFIIIA-binding site, however (see, for example, models proposed in refs. 9 and 10). The NH 2 -terminal six zinc fingers of TFIIIA bound in a complex with 31 bp of the 5S rRNA gene has been reconstituted (19) and crystallized. We report here the structure of the complex at 3.1 Å resolution (Table 1) and describe how its zinc fingers interact with DNA in different ways. An NMR structure of fingers 1-2-3 bound to DNA has recently been published (20, 21). MATERIALS AND METHODSProtein and DNA Oligonucleotides. Recombinant TFIIIA (amino acid residues 1-190) was produced from plasmid pRSET B (Invitrogen) in Escherichia coli BL21(DE3). After sonication the protein was extracted in 7 M urea from cell pellets and purified on Bio-Rex 70 (Bio-Rad) and heparin Sepharose columns. Synthetic oligonucleotides were purified by MonoQ (Pharmacia) chromatography in 7 M urea. Thymines were replaced by 5-iododeoxyurac...

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Section: Resultssupporting

confidence: 87%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

See 3 more Smart Citations

Differing roles for zinc fingers in DNA recognition: Structure of a six-finger transcription factor IIIA complex

Nolte

Conlin

Harrison

et al. 1998

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

233

185

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Transkription in Eukaryonten – die Rolle von Transkriptionskomplexen und ihren Komponenten

Wingender

Seifart²

1987

Angew. Chem.

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DaO DNA in RNA trdnskribiert wird, ist eine alte Erkenntnis und als solche Teil des ,,Zentralen Dogmas" der molekularen Genetik. Wie dieser ProzeR jedoch auf die einzelnen Gene hingelenkt wird, ist bei hoheren Zellen (Eukaryonten) immer noch nicht vollig verstanden. Die RNA-Polymerasen bedurfen offensichtlich zur Gen-Erkennung einer ganzen Reihe helfender Faktoren (Transkriptionsfaktoren). Diese bilden am Gen zusammen mit dem Enzym einen Transkriptionskomplex. Der Aufbau dieser Komplexe beginnt klar zu werden, und am groBten ist das Wissen iiber die Steuerung der RNA-Polymerase 111, die fur die Synthese bestimmter kleiner RNA-Molekule zustandig ist. Wie sehr die Erkenntnisse, die an diesern System gewonnen wurden, Modellcharakter haben, erweist sich besonders deutlich in einer Reihe neuester Arbeiten. Ein besonders gut untersuchtes Protein (TFIIIA), das ein positiver Regulator fur die Expression ribosomaler 5s-RNA ist, hat Struktureigenschaften, die bisher bei DNA-bindenden Proteinen unbekannt waren. Es zeigt sich immer mehr, daR die ,,Architektur" von TFIII A nicht die einer exotischen Kuriositat ist, sondern wahrscheinlich als Beispiel fur einen generellen Bauplan gesehen werden muO.

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Transcription in Eukaryotes—The Role of Transcription Complexes and Their Components

Wingender¹,

Seifart²

1987

Angew. Chem. Int. Ed. Engl.

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The fact that DNA is transcribed into RNA has long been known and has become part of the "central dogma" of molecular genetics. The mechanisms responsible for controlling this process at the individual genes of higher cells (eukaryotes), however, are still not completely understood. RNA polymerases apparently require a number of auxiliary factors (transcription factors) for gene recognition. These factors combine with the enzyme at the gene to form a transcription complex. The structures of these complexes are starting to become clearer; most is known about the control of RNA polymerase 111, the enzyme responsible for the synthesis of certain small RNA molecules. The model character of the results obtained with this system is clearly underlined by a series of recent publications. TFIII A is an especially intensively studied protein, which is a positive regulator for the expression of ribosomal 5s RNA and possesses structural properties that were previously unknown in DNA-binding proteins. It is becoming increasingly evident that the "architecture" of T F I I I A is not an exotic curiosity but probably exemplifies a general structural plan.

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Functional domains of the Xenopus laevis 5S gene promoter.

Cited by 58 publications

References 32 publications

Differing roles for zinc fingers in DNA recognition: Structure of a six-finger transcription factor IIIA complex

Differing roles for zinc fingers in DNA recognition: Structure of a six-finger transcription factor IIIA complex

Transkription in Eukaryonten – die Rolle von Transkriptionskomplexen und ihren Komponenten

Transcription in Eukaryotes—The Role of Transcription Complexes and Their Components

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