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The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity

DOI: 10.1074/jbc.RA119.010365 DOI Help

Authors: Joseph A. Newman (Structural Genomics Consortium, University of Oxford) , Hazel Aitkenhead (University of Oxford) , Angeline E. Gavard (Structural Genomics Consortium, University of Oxford) , Ioanna A Rota (University of Oxford) , Adam E. Handel (University of Oxford) , Georg A. Hollander (University of Oxford) , Opher Gileadi (Structural Genomics Consortium, University of Oxford)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of Biological Chemistry

State: Published (Approved)
Published: December 2019
Diamond Proposal Number(s): 15433

Abstract: Forkhead box N1 (FOXN1) is a member of the forkhead box family of transcription factors, and plays an important role in thymic epithelial cell differentiation and development. FOXN1 mutations in humans and mice give rise to the “nude” phenotype, which is marked by athymia. FOXN1 belongs to a subset of the FOX family that recognizes an alternative forkhead-like (FHL) consensus sequence (GACGC), that is different from the more widely-recognized forkhead (FKH) sequence RYAAAYA (R = purine, Y = pyrimidine). Here, we present the FOXN1 structure in complex with DNA containing an FHL motif at 1.6 Å resolution, in which the DNA sequence is recognized by a mixture of direct and water-mediated contacts provided by residues in an α-helix inserted in the DNA major groove (the recognition helix). Comparisons with the structure of other FOX family members revealed that the FKH and FHL DNA sequences are bound in two distinct modes, with partially different registers for the protein DNA contacts. We identified a single alternative rotamer within the recognition helix itself as an important determinant of DNA specificity and found protein sequence features in the recognition helix that could be used to predict the specificity of other FOX family members. Finally, we demonstrate that the C-terminal region of FOXN1 is required for high-affinity DNA binding and that FOXN1 has a significantly reduced affinity for DNA that contains 5’-methylcytosine, which may have implications for the role of FOXN1 in thymic involution.

Journal Keywords: forkhead box N1; Thymus; gene regulation; immunodeficiency; DNA-protein interaction; transcription factor; crystal structure

Subject Areas: Biology and Bio-materials, Chemistry

Instruments: I03-Macromolecular Crystallography , I04-Macromolecular Crystallography