Ribbon–helix–helix transcription factors: variations on a theme

Key Points This Analysis covers the ribbon–helix–helix (RHH) transcription-factor superfamily of proteins and focuses on the wealth of new structural information that has become available in the past year. Instead of binding to DNA through the insertion of an α-helix into the DNA major groove — a motif which is used by the ubiquitous helix–turn–helix family of transcription factors — RHH proteins use an anti-parallel β-sheet to recognize specific nucleotide sequences and α-helices to anchor the β-sheet in the DNA major groove. RHH proteins have a range of regulatory functions in prokaryotes and bacteriophages, several of which are of prime importance for human pathogen–host interactions. A sequence and structural comparison of the characterized RHH-transcription factors is given for important motifs, which provides a better framework for bioinformatic studies of this protein family. RHH proteins share a low sequence identity but have similar structures, despite multiple insertions and deletions between the α-helices of this small domain. DNA binding does not alter the structure of RHH-transcription factors, and they are regulated in their affinity for DNA in various ways. Prediction of a DNA-binding sequence is non-trivial based on knowledge of the RHH protein sequence. Different RHH proteins use the same amino-acid side chains to contact DNA bases, yet recognize unique DNA sequences. Despite sharing common features with the helix–turn–helix family of transcription factors, ribbon–helix–helix proteins recognize different operator sequences, bind to both symmetric and asymmetric DNA sites, bend DNA by varying amounts and make unique protein–protein interactions to stabilize their complexes with DNA. The ribbon–helix–helix (RHH) superfamily of transcription factors uses a conserved three-dimensional structural motif to bind to DNA in a sequence-specific manner. This functionally diverse protein superfamily regulates the transcription of genes that are involved in the uptake of metals, amino-acid biosynthesis, cell division, the control of plasmid copy number, the lytic cycle of bacteriophages and, perhaps, many other cellular processes. In this Analysis, the structures of different RHH transcription factors are compared in order to evaluate the sequence motifs that are required for RHH-domain folding and DNA binding, as well as to identify conserved protein–DNA interactions in this superfamily.