Nucleoplasmin-like domain of FKBP39 from Drosophila melanogaster forms a tetramer with partly disordered tentacle-like C-terminal segments

Małgorzata Kozłowska,Marek Orłowski,Andrzej Dziembowski,Aneta Tarczewska,Andrzej Ożyhar,Maciej Kozak,Michał Jakób,Michał Taube,Mariusz Czarnocki-Cieciura,Katarzyna Tkocz,Dominika Bystranowska

doi:10.1038/srep40405

Abstract

Nucleoplasmins are a nuclear chaperone family defined by the presence of a highly conserved N-terminal core domain. X-ray crystallographic studies of isolated nucleoplasmin core domains revealed a β-propeller structure consisting of a set of five monomers that together form a stable pentamer. Recent studies on isolated N-terminal domains from Drosophila 39-kDa FK506-binding protein (FKBP39) and from other chromatin-associated proteins showed analogous, nucleoplasmin-like (NPL) pentameric structures. Here, we report that the NPL domain of the full-length FKBP39 does not form pentameric complexes. Multi-angle light scattering (MALS) and sedimentation equilibrium ultracentrifugation (SE AUC) analyses of the molecular mass of the full-length protein indicated that FKBP39 forms homotetrameric complexes. Molecular models reconstructed from small-angle X-ray scattering (SAXS) revealed that the NPL domain forms a stable, tetrameric core and that FK506-binding domains are linked to it by intrinsically disordered, flexible chains that form tentacle-like segments. Analyses of full-length FKBP39 and its isolated NPL domain suggested that the distal regions of the polypeptide chain influence and determine the quaternary conformation of the nucleoplasmin-like protein. These results provide new insights regarding the conserved structure of nucleoplasmin core domains and provide a potential explanation for the importance of the tetrameric structural organization of full-length nucleoplasmins.

Highlights

Our findings stand in opposition to those of a recent structural study on an isolated N-terminal NPL domain[18] from D. melanogaster FKBP39, and we report for the first time the quaternary structure of the tetrameric arrangement of the NPL domain in the context of the full-length protein
Based on resolved crystal structures of the N-terminal core domains of different nucleoplasmins widely described in the literature, the defining hallmark of this family is assumed to be an oligomeric β-propeller structure that consists of a set of five monomers that fit together to form a stable pentamer[40,41,42,43]
TgNF3 from Toxoplasma gondii, which associates with chromatin and binds certain gene promoters, consists of an N-terminal NPL domain followed by an acidic region and a divergent C-terminal domain of enigmatic function[44]

Summary

Introduction

Despite the lack of a stable, well-defined structure, IDPs/ IDRs are fully functional and very often multifunctional Their flexible conformations allow IDPs/IDRs to expose short linear peptide motifs, which are responsible for multiple interactions. Their pliable structures can adapt to different binding partners. Interactome analysis revealed a physical association of Fpr[4] with ribosome biogenesis factors[16,17] These findings indicate that FKBP39-related proteins perform important and complex but still vague nuclear functions that require further exploration. The importance of this unique structural organization and the subcellular localization of FKBP39 in hormonal signal transduction and chromatin remodelling are discussed

Methods

Results

Conclusion