Review
Winged helix proteins

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Abstract

The winged helix proteins constitute a subfamily within the large ensemble of helix-turn-helix proteins. Since the discovery of the winged helix/fork head motif in 1993, a large number of topologically related proteins with diverse biological functions have been characterized by X-ray crystallography and solution NMR spectroscopy. Recently, a winged helix transcription factor (RFX1) was shown to bind DNA using unprecedented interactions between one of its eponymous wings and the major groove. This surprising observation suggests that the winged helix proteins can be subdivided into at least two classes with radically different modes of DNA recognition.

Introduction

Functional studies of the winged helix proteins began with the discovery of the hepatocyte nuclear factor-3 (HNF-3) family of liver-specific transcription factors [1]. Proteins from the HNF-3 family share a highly conserved DNA-binding region with the Drosophila homeotic fork head proteins, which are involved in proper formation of terminal structures in fly embryos. Hence, winged helix proteins are also referred to as belonging to the HNF-3/fork head (HFH) family [2]. The co-crystal structure of the DNA-binding domain (DBD) of an HNF-3γ–DNA complex was the first to show the mechanism of DNA recognition by a winged helix protein [3]. Subsequently, X-ray and solution NMR structures of a number of winged helix proteins have been determined. This review focuses on more recent structural characterizations of winged helix proteins, their versatility in DNA recognition and diversity of biological function.

Section snippets

Structure of the winged helix motif

Topologically, the winged helix motif is a compact α/β structure consisting of two wings (W1 and W2), three α helices (H1, H2 and H3) and three β strands (S1, S2 and S3), arranged in order H1-S1-H2-H3-S2-W1-S3-W2 (Figure 1). The N-terminal half of the motif is largely helical, whereas the C-terminal half is composed of two of the three strands forming the twisted antiparallel β sheet and the two large loops or wings, W1 and W2 [3]. Wing W1 connects strands S2 and S3, and wing W2 extends from

DNA recognition by canonical winged helix proteins

HNF-3γ is a liver-specific transcription factor that plays an important role in cell differentiation and tissue-specific gene expression [10]. Its co-crystal structure showed that helix H3, the recognition helix of the HTH motif, is presented to the major groove of a duplex oligonucleotide derived from the transthyretin gene promoter (Figure 3) [3]. In total, 14 protein–DNA contacts are distributed throughout the length of the polypeptide chain (Figure 2). Five of the observed interactions,

Atypical DNA recognition by a winged helix protein

The winged helix protein RFX1 uses an unprecedented wing-based strategy to recognize the bipartite DNA sequence known as an X-box (5′-CGTTACCATGGTAACG-3′) (Figure 3) (KS Gajiwala et al., unpublished data). RFX1 is a cellular transcription factor that regulates the expression of a number of biologically important gene products 28, 29. The co-crystal structure of the RFX1–DNA complex revealed that wing W1 of RFX1 makes most of the contacts with DNA via its major groove. The so-called recognition

Biological importance of winged helix proteins

While structural biologists were busy characterizing winged helix proteins, considerable progress has been made in studies of the important biological roles of these molecules.

In the mouse, HNF-3α and HNF-3β were shown to be critical developmental regulators. Homozygous HNF-3α null mice exhibit a complex phenotype and die within the first two weeks of life 35, 36. During gut development, HNF-3α acts as a transcriptional activator of a genetic program leading to the orderly differentiation of

Conclusions

X-ray crystallographic and solution NMR studies of winged helix proteins and their complexes with DNA have shown that the motif is extremely versatile. These proteins exhibit two different modes of DNA binding and appear to be able to recognize both specific sequences in B-form DNA and distinct double helical conformations (i.e. B-form versus Z-form). Both monomeric, homodimeric and heterodimeric protein–DNA complexes have been characterized. It is also clear that this motif can participate in

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

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