Three-dimensional structure of the DNA-binding domain of the fructose repressor from Escherichia coli by 1H and 15N NMR

FruR is an Escherichia coli transcriptional regulator that belongs to the LacI DNA-binding protein family. By using 1H and 15N NMR spectroscopy, we have determined the three-dimensional solution structure of the FruR N-terminal DNA-binding domain consisting of 57 amino acid residues. A total of 809...

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Bibliographic Details
Published in:Journal of molecular biology 1997-07, Vol.270 (3), p.496-510
Main Authors: Penin, François, Geourjon, Christophe, Montserret, Roland, Böckmann, Anja, Lesage, Anne, Yang, Yin Shan, Bonod-Bidaud, Christelle, Cortay, Jean-Claude, Nègre, Didier, Cozzone, Alain J., Deléage, Gilbert
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Bacterial Proteins
Bacterial Proteins - chemistry
Bacterial Proteins - genetics
Bacterial Proteins - isolation & purification
Biochemistry, Molecular Biology
DNA-binding domain
DNA-Binding Proteins
DNA-Binding Proteins - chemistry
Escherichia coli
Escherichia coli - chemistry
Escherichia coli Proteins
fru repressor
helix-turn-helix motif
heteronuclear NMR spectroscopy
Lac Repressors
Life Sciences
Magnetic Resonance Spectroscopy
Magnetic Resonance Spectroscopy - methods
Models, Molecular
Molecular Sequence Data
protein structure
Protein Structure, Secondary
Recombinant Fusion Proteins
Repressor Proteins
Repressor Proteins - chemistry
Repressor Proteins - genetics
Repressor Proteins - isolation & purification
Sequence Alignment
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Description
Summary:FruR is an Escherichia coli transcriptional regulator that belongs to the LacI DNA-binding protein family. By using 1H and 15N NMR spectroscopy, we have determined the three-dimensional solution structure of the FruR N-terminal DNA-binding domain consisting of 57 amino acid residues. A total of 809 NMR-derived distances and 54 dihedral angle constraints have been used for molecular modelling with the X-PLOR program. The resulting set of calculated structures presents an average root-mean-square deviation of 0.37 Å at the main-chain level for the first 47 residues. This highly defined N-terminal part of the structure reveals a similar topology for the three α-helices when compared to the 3D structures of LacI and PurR counterparts. The most striking difference lies in the connection between helix II and helix III, in which three additional residues are present in FruR. This connecting segment is well structured and contains a type III turn. Apart from hydrophobic interactions of non-polar residues with the core of the domain, this connecting segment is stabilised by several hydrogen bonds and by the aromatic ring stacking between Tyr19 of helix II and Tyr28 of the turn. The region containing the putative “hinge helix” (helix IV), that has been described in PurR-DNA complex to make specific base contacts in the minor groove of DNA, is unfolded. Examination of hydrogen bonds highlights the importance of homologous residues that seem to be conserved for their ability to fulfil helix N and C-capping roles in the LacI repressor family.
ISSN:0022-2836
1089-8638
DOI:10.1006/jmbi.1997.1123