Met repressor-operator complex
Escherichia coli (bacteria)
Expression of the structural genes in the methionine biosynthetic pathway of E.coli is controlled by the met repressor and activated by ligand binding. The met repressor protein forms a complex with the corepressor S-adenosylmethionine (SAM), which is the metabolic product from the methionine, to suppress transcription of the genes in the methionine biosynthetic pathway including its own gene (metJ) and genes for the biosynthesis of methionine and SAM. That is different from other repressors such as tryptophan repressor using amino acid itself as a corepressor. The repressor cooperatively binds to the operator, which is composed of multiple (two to five) tandem repeats of 8-base-pair unit homologous to the sequence (AGACGTCT) and refereed to as the 'met box'.
In this crystal structure of the repressor-operator complex, the repressor forms a symmetric homodimer, each dimer binding to one of two met boxes. The two repressor dimers contact each other through antiparallel alpha-helices (A-helices) via hydrophobic interaction. According to this interaction, cooperative binding to multiple met box is achieved. Each monomer in the dimeric repressor binds with its double-stranded antiparallel beta-strand inserted into the major groove of the DNA. DNA-recognition sites of prokaryotic repressors generally have helix-turn-helix (HTH) motifs or are homologous to that of the met repressor. This was the first report of the beta-strand-based recognition site, since only HTH motif and zinc-finger motif which show alpha-helices lodged in the major groove were recognized as DNA-recognition site until the structure of this met repressor have been solved. The major contribution to the sequence specificity is hydrogen bonds between side chains on the beta-strand and the edges of base pairs on the major groove. Furthermore there is evidence of the indirect readout of CTAG sequences across the boundary between two met boxes, namely the binding of repressor side chains to phosphates which are displaced by two overwound T-A nucleotides. This T-A step is easier to bend than other site in the sequence, and this bending is necessary for binding with repressor. Thus, mutation of the central T-A sequence to A-T or G-C decreases affinity, despite the lack of direct contacts between the side chains of repressor and these base pairs. The DNA in the complex is B-form and bends about 25 degrees at the center of each met box towards the major groove. As a result the major groove is compressed to 9.4 angstroms and the minor groove is opened to 8.3 angstroms from the ideal B-form DNA 11.7 and 5.7 angstroms values, respectively. The SAM molecules bind to the faces of the repressors, remote from the DNA with positively charged sulphur atoms located at the carboxyl termini of B helices. SAS-binding does not cause significant structural changes in the repressor, though it greatly increases the affinity for the operator.
Protein Data Bank (PDB)
Somers, W.S. Phillips, S.E.; ";Crystal structure of the met repressor-operator complex at 2.8 Angstroms resolution: DNA recognition by beta-strands;"; Nature; (1992) 359:387-393 PubMed:1406951.
author: Tomoki Matsuda