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  • Analysis
  • Published:

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.

Abstract

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.

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Figure 1: Sequence alignment of characterized ribbon–helix–helix (RHH) proteins.
Figure 2: The overall structure and DNA binding of ribbon–helix–helix (RHH) proteins.
Figure 3: Domain organization of ribbon–helix–helix (RHH) transcription factors.
Figure 4: Selected ribbon–helix–helix–DNA complex structures and mechanisms of DNA binding.
Figure 5: Superimposition of DNA-bound ribbon–helix–helix dimer (RHH2) domains.
Figure 6: Specific polar contacts between NikR, CopG β-strands and DNA operator sub-sites.

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Acknowledgements

The authors acknowledge support from the National Institutes of Health grants RR016439 and GM69857.

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Correspondence to Eric R. Schreiter.

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DATABASES

Entrez Genome Project

Escherichia coli

UniProt

Arc

AlgZ

CcdA

CopG

FitA

HP0222

MetJ

Mnt

NikR

omega

ParD

ParG

PutA

TraY

TrwA

7kMk

FURTHER INFORMATION

HMMER

InterPro

Predict Protein

PyMOL

Swiss-Prot

TrEMBL

Glossary

Promoter

A region of DNA that is upstream of a gene or operon and that is required for its transcription. In bacteria, RNA polymerase and an associated σ factor protein bind the promoter and initiate transcription. Promoters can also contain regulatory regions of DNA, such as operators, that are recognized by transcription factors.

Motif

A pattern of residues with biological significance. A sequence motif refers to a linear sequence of nucleotides or amino acids, whereas a structural motif can refer to residues that are not consecutive but are in close proximity in the natively folded molecule.

Operator

The DNA sequence that is specifically recognized by a transcription factor. Often, operator DNA sequences contain either direct or inverted repeats of smaller DNA sub-sites, which multiple molecules of the transcription factor bind to cooperatively.

Root mean square deviation

(RMSD). A metric unit that represents the similarity between two structures and that is calculated by comparing the positions of atoms in one structure with the positions of the equivalent atoms in another. Here, RMSD is measured in units of Ångströms (Å) or 10−10 m. For two perfectly identical structures, the RMSD value would be 0 Å; for two randomly chosen dissimilar proteins, the RMSD is likely to be 10 Å or higher.

Hydrophobic core

The interior portion of a folded globular protein that is composed of primarily hydrophobic amino-acid side chains. The burial of hydrophobic side chains is a primary driving force for protein folding.

Toxin–antitoxin

A post-segregational cell-killing system that is usually composed of a pair of plasmid-encoded proteins that form a complex. If a plasmid-free cell arises, the antitoxin cannot be replenished and the liberated toxin causes cell death or severe growth impairment.

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Schreiter, E., Drennan, C. Ribbon–helix–helix transcription factors: variations on a theme. Nat Rev Microbiol 5, 710–720 (2007). https://doi.org/10.1038/nrmicro1717

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