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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

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 o...

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Autores principales: Newman, Joseph A., Aitkenhead, Hazel, Gavard, Angeline E., Rota, Ioanna A., Handel, Adam E., Hollander, Georg A., Gileadi, Opher
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Biochemistry and Molecular Biology 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7062188/
https://www.ncbi.nlm.nih.gov/pubmed/31914405
http://dx.doi.org/10.1074/jbc.RA119.010365
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author Newman, Joseph A.
Aitkenhead, Hazel
Gavard, Angeline E.
Rota, Ioanna A.
Handel, Adam E.
Hollander, Georg A.
Gileadi, Opher
author_facet Newman, Joseph A.
Aitkenhead, Hazel
Gavard, Angeline E.
Rota, Ioanna A.
Handel, Adam E.
Hollander, Georg A.
Gileadi, Opher
author_sort Newman, Joseph A.
collection PubMed
description 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 (where R is purine, and Y is 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.
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spelling pubmed-70621882020-03-16 The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity Newman, Joseph A. Aitkenhead, Hazel Gavard, Angeline E. Rota, Ioanna A. Handel, Adam E. Hollander, Georg A. Gileadi, Opher J Biol Chem Gene Regulation 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 (where R is purine, and Y is 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. American Society for Biochemistry and Molecular Biology 2020-03-06 2019-12-30 /pmc/articles/PMC7062188/ /pubmed/31914405 http://dx.doi.org/10.1074/jbc.RA119.010365 Text en © 2020 Newman et al. Author's Choice—Final version open access under the terms of the Creative Commons CC-BY license (http://creativecommons.org/licenses/by/4.0) .
spellingShingle Gene Regulation
Newman, Joseph A.
Aitkenhead, Hazel
Gavard, Angeline E.
Rota, Ioanna A.
Handel, Adam E.
Hollander, Georg A.
Gileadi, Opher
The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity
title The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity
title_full The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity
title_fullStr The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity
title_full_unstemmed The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity
title_short The crystal structure of human forkhead box N1 in complex with DNA reveals the structural basis for forkhead box family specificity
title_sort crystal structure of human forkhead box n1 in complex with dna reveals the structural basis for forkhead box family specificity
topic Gene Regulation
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7062188/
https://www.ncbi.nlm.nih.gov/pubmed/31914405
http://dx.doi.org/10.1074/jbc.RA119.010365
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