Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-α

Fontes, Marcos R.M.; Teh, Trazel; Tóth, Gábor; John, Anna; Pávó, Imre; Jans, David A.; Kobe, Boštjan

doi:10.1042/bj20030510

Cited by 102 publications

(112 citation statements)

References 51 publications

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“…Co-crystal structures of both S. cerevisiae and M. musculus importin-a have been solved in complex with various NLS peptides (52)(53)(54)(55)(56)(57)(58)(59). The three-dimensional structures reveal that NLS peptides bind specifically in two binding grooves created by flexible armadillo (ARM) motifs in the central domain of importin-a (54, 55).…”

Section: Classical Nls Sequencesmentioning

confidence: 99%

“…These grooves interact specifically with the basic, positively charged residues of the cNLS through hydrophobic and electrostatic interactions (3). Between these two binding pockets is a linker-binding region that interacts with the NLS peptide backbone (52,55,57). Changes to specific residues within each of these three regions of importin-a disrupt the nuclear localization and binding of cNLScargoes to importin-a (60,61).…”

Section: Classical Nls Sequencesmentioning

confidence: 99%

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Nuclear localization signals and human disease

McLane

Corbett

2009

IUBMB Life

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SummaryIn eukaryotic cells, the physical separation of the genetic material in the nucleus from the translation and signaling machinery in the cytoplasm by the nuclear envelope creates a requirement for a mechanism through which macromolecules can enter or exit the nucleus as necessary. Nucleocytoplasmic transport involves the specific recognition of cargo molecules by transport receptors in one compartment followed by the physical relocation of that cargo into the other compartment through regulated pores that perforate the nuclear envelope. The recognition of protein cargoes by their transport receptors occurs via amino acid sequences in cargo proteins called nuclear targeting signals. Both nuclear import and export of proteins are highly regulated processes that control, not only what cargo can enter and/or exit the nucleus, but also when in the cell cycle and in what cell type, the cargo can be transported. Deregulation of the nuclear transport of specific cargoes has been linked to numerous cancers and developmental disorders highlighting the importance of understanding the mechanisms underlying nucleocytoplasmic transport and particularly the modulation of the specific interactions between transporter receptors and nuclear targeting signals within target cargo proteins.2009 IUBMB IUBMB Life, 61(7): [697][698][699][700][701][702][703][704][705][706] 2009

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Section: Classical Nls Sequencesmentioning

confidence: 99%

Section: Classical Nls Sequencesmentioning

confidence: 99%

Nuclear localization signals and human disease

McLane

Corbett

2009

IUBMB Life

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“…Phosphorylation within or around an NLS is the usual strategy for the regulated nuclear transport of a protein (4,(10)(11)(12)(13). It has been shown that acidic amino acids adjacent to the basic core of an importin-␣-dependent NLS inhibit the NLS activity (5,14).…”

mentioning

confidence: 99%

Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs

Kosugi

Hasebe

Tomita

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

1,109

1,028

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The cell cycle-dependent nucleocytoplasmic transport of proteins is predominantly regulated by CDK kinase activities; however, it is currently difficult to predict the proteins thus regulated, largely because of the low prediction efficiency of the motifs involved. Here, we report the successful prediction of CDK1-regulated nucleocytoplasmic shuttling proteins using a prediction system for nuclear localization signals (NLSs). By systematic amino acid replacement analyses in budding yeast, we created activity-based profiles for different classes of importin-␣-dependent NLSs that represent the functional contributions of different amino acids at each position within an NLS class. We then developed a computer program for prediction of the classical importin-␣/␤ pathway-specific NLSs (cNLS Mapper, available at http//nls-mapper.iab.keio.ac.jp/) that calculates NLS activities by using these profiles and an additivity-based motif scoring algorithm. This calculation method achieved significantly higher prediction accuracy in terms of both sensitivity and specificity than did current methods. The search for NLSs that overlap the consensus CDK1 phosphorylation site by using cNLS Mapper identified all previously reported and 5 previously uncharacterized yeast proteins (Yen1, Psy4, Pds1, Msa1, and Dna2) displaying CDK1-and cell cycle-regulated nuclear transport. CDK1 activated or repressed their nuclear import activity, depending on the position of CDK1-phosphorylation sites within NLSs. The application of this strategy to other functional linear motifs should be useful in systematic studies of protein-protein networks.CDK ͉ computational method ͉ nuclear localization signal ͉ nuclear import ͉ phosphorylation R egulated nuclear import controls the nuclear function of many proteins that shuttle between the nucleus and cytoplasm or other cellular compartments in response to certain physiological conditions or extracellular stimuli (1). Nucleocytoplasmic shuttling comprises both nuclear import and nuclear export activities. Nuclear import is mediated by the interaction of nuclear localization signals (NLSs) with transport receptor importins, among which the importin-␣ family recognizes most major classes of NLSs with 1 or 2 basic stretches, called the classical NLSs (2-4). Six different classes of monopartite and bipartite NLSs bind to distinct binding grooves of importin-␣ (5-7). Nuclear export is mediated by nuclear export signals (NESs), which are recognized by Crm1/exportin or Msn5 in yeast (1, 8). The regulation of these 2 antagonistic activities directs a protein to either the nucleus or the cytoplasm. In general, these activities are regulated by the modification of the NLSs/NESs, by intermolecular or intramolecular interactions that lead to the structural masking of NLSs/NESs, or by the supply of an NLS/NES by another protein (9).Phosphorylation within or around an NLS is the usual strategy for the regulated nuclear transport of a protein (4, 10-13). It has been shown that acidic amino acids adjacent to the basic core ...

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“…Flexible and contiguous NLS regions within target proteins ranging in length from 5 to 25 amino acids (40) are typical. Crystal structures of NLS peptides bound to importin-␣ reveal extended backbone conformations (43)(44)(45)(46), similar to the putative NLS region of the EcCdtB crystal structure. In the EcCdtB crystal structure, the formation of helix E results in the NLS Arg 191 -Arg 192 side chains being extended into the solvent (43) (Figs.…”

Section: Distinct Eccdtb Solution and Crystal States Provide Insightsmentioning

confidence: 88%

Differences in Crystal and Solution Structures of the Cytolethal Distending Toxin B Subunit

Hontz¹,

Villar-Lecumberri²,

Potter

et al. 2006

Journal of Biological Chemistry

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Cytolethal distending toxin (CDT) induces cell cycle arrest and apoptosis in eukaryotic cells, which are mediated by the DNA-damaging CdtB subunit. Here we report the first x-ray structure of an isolated CdtB subunit (Escherichia coli-II CdtB, EcCdtB). In conjunction with previous structural and biochemical observations, active site structural comparisons between free and holotoxin-assembled CdtBs suggested that CDT intoxication is contingent upon holotoxin disassembly. Solution NMR structural and 15 N relaxation studies of free EcCdtB revealed disorder in the interface with the CdtA and CdtC subunits (residues Gly 233 -Asp 242 ). Residues Leu 186 -Thr 209 of EcCdtB, which encompasses tandem arginine residues essential for nuclear translocation and intoxication, were also disordered in solution. In stark contrast, nearly identical well defined ␣-helix and ␤-strand secondary structures were observed in this region of the free and holotoxin CdtB crystallographic models, suggesting that distinct changes in structural ordering characterize subunit disassembly and nuclear localization factor binding functions. Cytolethal distending toxin (CDT)4 is a DNA-damaging bacterial toxin produced by a number of important bacterial pathogens (1, 2). The cytopathic effects associated with CDT intoxication are a direct result of chromosomal DNA damage inflicted by the CdtB subunit, a homolog of eukaryotic type I DNase (3, 4). CdtB-mediated chromosome strand breakage signals the induction of an ATM (ataxia telangiectasia-mutated)-or ATR (ataxia telangiectasia-mutated and Rad3-related)-dependent mitotic checkpoint resulting in the sequestration of Cdc25, a block in the cell cycle at the G 2 /M boundary, cellular distension, and ultimately cell death by endoreduplication or apoptosis (2, 5).The CDT holotoxin is a heterotrimer composed of CdtA, CdtB, and CdtC subunits. Although the catalyst for CDT-mediated apoptosis is ultimately attributed to the DNase activity of CdtB, all three subunits are required for cellular entry of CDT (6, 7). The CdtA and CdtC subunits are lectin-like domains that bind carbohydrate residues on the target cell surface, whereby CDT is subsequently internalized by receptor-mediated endocytosis (8, 9). The Haemophilus ducreyi holotoxin structure (HdCDT) has demonstrated that CDT is an AB type toxin, with the catalytically active A subunit of the AB toxin corresponding to the CdtB subunit (10). Inspection of this structure and of the structurally similar CDT holotoxin from Actinobacillus actinomycetemcomitans (AaCDT) (11) revealed that one face of the CdtA-CdtC dimer binds the CdtB subunit. Mutagenesis studies of HdCDT suggest that another face of the dimer with a grooved ricin B-chain fold mediates cell surface binding (10).Trafficking of CDT to the nucleus is thought to involve retrograde transport through the Golgi and the ultimate translocation of CdtB from the endoplasmic reticulum to the nuclear envelope by an apparent ERAD (endoplasmic reticulum-associated degradation)-independent step (9). CdtB traverse...

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Role of flanking sequences and phosphorylation in the recognition of the simian-virus-40 large T-antigen nuclear localization sequences by importin-α

Cited by 102 publications

References 51 publications

Nuclear localization signals and human disease

Nuclear localization signals and human disease

Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs

Differences in Crystal and Solution Structures of the Cytolethal Distending Toxin B Subunit

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