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Model‐Building of Fnr and FixK DNA‐binding domains suggests a basis for specific DNA recognition
Author(s) -
Cherfils Jacqueline,
Gibrat JeanFrançois,
Levin Jonathan,
Batut Jacques,
Kahn Daniel
Publication year - 1989
Publication title -
journal of molecular recognition
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.401
H-Index - 79
eISSN - 1099-1352
pISSN - 0952-3499
DOI - 10.1002/jmr.300020303
Subject(s) - thymine , dna , escherichia coli , biochemistry , biology , valine , dna binding protein , gene , stereochemistry , chemistry , amino acid , transcription factor
Abstract The DNA‐binding C‐terminal domains of the regulatory proteins Fnr from Escherichia coli and FixK from Rhizobium meliloti have been modelled on the basis of their homologies to the CAP protein from E. coli . Residues Glu181, Thr182 and Arg185 of CAP, which are exposed residues of the DNA‐recognition helix α F , are conserved in Fnr and FixK. However, Arg180 and Gly184 are substituted by Val and Ser respectively in Fnr. We propose that this valine makes a Van der Waals' contact with the first thymine in the Fnr consensus TTGA‐N 6 ‐TCAA, and that the serine contributes to the binding by displacing a thymine‐bound water molecule. The corresponding residues in FixK, Ile and Ser allow the same interactions with a thymine. Therefore we predict that FixK may recognize the same sites as Fnr. This is supported experimentally by showing that Fnr can substitute for FixK in activating the fixN gene in E. coli .

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