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Solution structure of the DNA-binding domain of the TyrR protein of Haemophilus influenzae

¹ Department of Molecular Pharmacology, Stanford University, Stanford, California 94305–5174, USA
² Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907–1153, USA

Reprint requests to: Dr. Oleg Jardetzky, Department of Molecular Pharmacology, Stanford University, Stanford, California 94305–5174, USA; e-mail: jardetzky{at}stanford.edu; fax: (650) 723-2253.

The TyrR protein of Haemophilus influenzae is a 36-kD transcription factor whose major function is to control the expression of genes important in the biosynthesis and transport of aromatic amino acids. Using ¹H and ¹⁵N NMR spectroscopy, we have determined the 3D solution structure of the TyrR C-terminal DNA-binding domain (DBD) containing residues from 258 to 318 (TyrR[258–318]). The NMR results show that this segment of TyrR consists of a potential hinge helix at its N terminus (residues 263–270) as well as three well-defined -helices extending from residues 277–289 (HR-2), 293–300 (HR-1), and 304–314 (HR). Helix HR-1 and HR fold in a typical helix–turn–helix (HTH) motif. The three helices and the hinge helix are tightly bound together by hydrophobic interaction and hydrogen bonds. Several hydrophilic residues whose side chains may directly interact with DNA are identified. A hydrophobic patch that may be part of the interaction surface between the domains of TyrR protein is also observed. Comparisons with the structures of other HTH DNA-binding proteins reveal that in terms of the spatial orientation of the three helices, this protein most closely resembles the cap family.

Keywords: TyrR; protein structure; NMR; DNA-binding domain; helix-turn-helix motif

Abbreviations: 2D and 3D, two- and three-dimensional • DBD, DNA-binding domain • DQF-COSY, double quantum-filtered correlation spectroscopy • DSS, 2,2-dimethyl-2-silapentane-5-sulfonic acid • E. coli, Escherichia coli • RMSD, root mean square deviation • gHSQC, gradient heteronuclear single-quantum coherence • HTH, helix-turn-helix structural motif • TyrR, tyrosine repressor • TyrR(258-318), residues 258-318 of TyrR • NOESY, nuclear Overhauser enhancement spectroscopy • NMR, nuclear magnetic resonance • TOCSY, total correlation spectroscopy

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