Biochemical propensity mapping for structural and functional anatomy of importin α IBB domain

Abstract

Importin α has been described as a nuclear protein transport receptor that enables proteins synthesized in the cytoplasm to translocate into the nucleus. Besides its function in nuclear transport, an increasing number of studies have examined its non‐nuclear transport functions. In both nuclear transport and non‐nuclear transport, a functional domain called the IBB domain (importin β binding domain) plays a key role in regulating importin α behavior, and is a common interacting domain for multiple binding partners. However, it is not yet fully understood how the IBB domain interacts with multiple binding partners, which leads to the switching of importin α function. In this study, we have distinguished the location and propensities of amino acids important for each function of the importin α IBB domain by mapping the biochemical/physicochemical propensities of evolutionarily conserved amino acids of the IBB domain onto the structure associated with each function. We found important residues that are universally conserved for IBB functions across species and family members, in addition to those previously known, as well as residues that are presumed to be responsible for the differences in complex‐forming ability among family members and for functional switching.

Toxoplasma Gondii Importin α Shows Weak Auto-Inhibition

“…The strength of auto-inhibition could also depend on other features in the protein as observed by in silico prediction analysis, the structure of the IBB domain of T. gondii importin α hints that this domain could be helical. The available forms of the IBB domain in complex with different importin proteins show helical structures in some cases and an unstructured domain in others, indicating structural polymorphism of the IBB domain (Cingolani et al, 1999, Matsuura & Stewart, 2004, Jibiki et al, 2021. Nevertheless, our structure prediction analyses indicate that in direct comparison to MmImpα2, there appears to be a higher α-helical content in the IBB domain of TgImpα.…”

“…The importin α structure consists of NLS-binding sites within a tandem series of Armadillo (ARM) repeats and an N-terminal importin β-binding (IBB) domain (Görlich et al, 1996;Conti et al, 1998). The structurally polymorphic IBB domain mimics positively charged NLS sequences (Fanara et al, 2000;Jibiki et al, 2021;Lott & Cingolani, 2011) and binds to the ARM repeats of importin α, thereby blocking the NLS-binding sites, a phenomenon called auto-inhibition. Auto-inhibition has been mapped to the third of the three basic amino acid clusters in the IBB domain (Harreman et al, 2003;Kobe, 1999).…”

Nuclear localization of HD-Zip IV transcription factor GLABRA2 is driven by Importin α

“…The IMPβ Binding (IBB) domain, an autoinhibitory domain spanning the first ~90 N-terminal residues, was removed prior to structural prediction. The IBB domain contains a segment of basic residues resembling an NLS, resulting in autoinhibition of the NLS interacting domain of IMPα in the absence of IMPβ (Cingolani et al, 1999;Chang et al, 2012;Jibiki et al, 2022). Following 3D structural prediction, loop refinement was performed to enhance the structural integrity and robustness of the interaction models.…”

Toxoplasma gondii importin α shows weak auto-inhibition

“…The importin α structure consists of NLS-binding sites within a tandem series of Armadillo (ARM) repeats and an N-terminal importin β-binding (IBB) domain (Görlich et al, 1996; Conti et al, 1998). The structurally polymorphic IBB domain mimics positively charged NLS sequences (Fanara et al, 2000; Jibiki et al, 2021; Lott & Cingolani, 2011) and binds to the ARM repeats of importin α, thereby blocking the NLS-binding sites, a phenomenon called auto-inhibition. Auto-inhibition has been mapped to the third of the three basic amino acid clusters in the IBB domain (Harreman et al, 2003; Kobe, 1999).…”