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J. Biol. Chem., Vol. 278, Issue 48, 48267-48274, November 28, 2003

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An Extended Winged Helix Domain in General Transcription Factor E/IIE^*

Anton Meinhart, Jascha Blobel, and Patrick Cramer

From the Institute of Biochemistry, Gene Center, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany

Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. Here we define a conserved and functionally essential N-terminal domain in TFE, the archaeal homolog of the large TFIIE subunit . X-ray crystallography shows that this TFE domain adopts a winged helix-turn-helix (winged helix) fold, extended by specific -helices at the N and C termini. Although the winged helix fold is often found in DNA-binding proteins, we show that TFE is not a typical DNA-binding winged helix protein, because its putative DNA-binding face shows a negatively charged groove and an unusually long wing, and because the domain lacks DNA-binding activity in vitro. The groove and a conserved hydrophobic surface patch on the additional N-terminal -helix may, however, allow for interactions with other general transcription factors and RNA polymerase. Homology modeling shows that the TFE domain is conserved in TFIIE, including the potential functional surfaces.

Received for publication, July 21, 2003 , and in revised form, September 4, 2003.

The atomic coordinates and structure factors (code 1Q1H) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported by the research grant CR117-2/1 of the Deutsche Forschungsgemeinschaft (to P. C.), by the EMBO Young Investigator Programme, and by the Fonds der Chemischen Industrie. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

To whom correspondence should be addressed. Tel.: 49-89-2180-76953; Fax: 49-89-2180-76999; E-mail: cramer{at}LMB.uni-muenchen.de.

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