Structural analysis of phosphatidylinositol 4-kinase IIIβ (PI4KB) – 14-3-3 protein complex reveals internal flexibility and explains 14-3-3 mediated protection from degradation in vitro

Chalupská, Dominika; Eisenreichová, Andrea; Różycki, Bartosz; Rezabkova, Lenka; Humpolíčková, Jana; Klíma, Martin; Bouřa, Evžen

doi:10.1016/j.jsb.2017.08.006

Cited by 32 publications

(37 citation statements)

References 72 publications

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“…PI4KB was originally identified in yeast (yeast protein PIK1) as an essential gene [48], with its activity playing a key role in secretion from the Golgi [49]. Phosphorylation of PI4KB by PKD at Ser294 mediates binding to 14-3-3 proteins, with this leading to an increase in PI4KB activity [22,23], that has been suggested to correspond with an increase in PI4KB stability [24]. The first identified Golgi activator of PI4KB was the GTPase Arf1 [21].…”

Section: Discussionmentioning

confidence: 99%

“…The helical domain of PI4KB forms a non-canonical interaction with the small GTPase Rab11a that mediates localization of a pool of Rab11 to the Golgi and TGN [14,20]. Phosphorylation of Ser294 drives binding of 14-3-3, which stabilizes PI4KB, prevents degradation, and increases Golgi PI4P levels [22][23][24]. PI4KB is activated downstream of ADP-ribosylation factor 1 (Arf1) [21]; however, no evidence for a direct Arf1-PI4KB interface has been found, suggesting that this may be an indirect effect.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of the c10orf76‐PI4KB complex and its necessity for Golgi PI4P levels and enterovirus replication

et al. 2019

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The lipid kinase PI4KB, which generates phosphatidylinositol 4phosphate (PI4P), is a key enzyme in regulating membrane transport and is also hijacked by multiple picornaviruses to mediate viral replication. PI4KB can interact with multiple protein binding partners, which are differentially manipulated by picornaviruses to facilitate replication. The protein c10orf76 is a PI4KB-associated protein that increases PI4P levels at the Golgi and is essential for the viral replication of specific enteroviruses. We used hydrogendeuterium exchange mass spectrometry to characterize the c10orf76-PI4KB complex and reveal that binding is mediated by the kinase linker of PI4KB, with formation of the heterodimeric complex modulated by PKA-dependent phosphorylation. Complexdisrupting mutations demonstrate that PI4KB is required for membrane recruitment of c10orf76 to the Golgi, and that an intact c10orf76-PI4KB complex is required for the replication of c10orf76dependent enteroviruses. Intriguingly, c10orf76 also contributed to proper Arf1 activation at the Golgi, providing a putative mechanism for the c10orf76-dependent increase in PI4P levels at the Golgi.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Characterization of the c10orf76‐PI4KB complex and its necessity for Golgi PI4P levels and enterovirus replication

et al. 2019

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“…Information obtained from different biophysical experiments can be combined to obtain structural insights represented by molecular models. Combination of X-ray crystallography with SAXS data and other techniques including NMR chemical shift perturbation or FRET has proven very useful for obtaining detailed models of dynamic protein complexes such as the ESCRT membrane-protein trafficking system [5,6] or protein kinases and their regulatory partners [7].…”

Section: Introductionmentioning

confidence: 99%

Conformational Flexibility of Proteins Involved in Ribosome Biogenesis: Investigations via Small Angle X-ray Scattering (SAXS)

et al. 2018

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Abstract:The dynamism of proteins is central to their function, and several proteins have been described as flexible, as consisting of multiple domains joined by flexible linkers, and even as intrinsically disordered. Several techniques exist to study protein structures, but small angle X-ray scattering (SAXS) has proven to be particularly powerful for the quantitative analysis of such flexible systems. In the present report, we have used SAXS in combination with X-ray crystallography to highlight their usefulness at characterizing flexible proteins, using as examples two proteins involved in different steps of ribosome biogenesis. The yeast BRCA2 and CDKN1A-interactig protein, Bcp1, is a chaperone for Rpl23 of unknown structure. We showed that it consists of a rigid, slightly elongated protein, with a secondary structure comprising a mixture of alpha helices and beta sheets. As an example of a flexible molecule, we studied the SBDS (Shwachman-Bodian-Diamond Syndrome) protein that is involved in the cytoplasmic maturation of the 60S subunit and constitutes the mutated target in the Shwachman-Diamond Syndrome. In solution, this protein coexists in an ensemble of three main conformations, with the N-and C-terminal ends adopting different orientations with respect to the central domain. The structure observed in the protein crystal corresponds to an average of those predicted by the SAXS flexibility analysis.

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“…Study of multi-domain cellulosomes [58,59]; coupled with SAXS to study highly flexible protein complexes [60,61]; phase behavior of intrinsically disordered proteins [62].…”

Section: Prime Four Beads Per Residuementioning

confidence: 99%

Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications

Singh

2019

IJMS

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Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.

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Structural analysis of phosphatidylinositol 4-kinase IIIβ (PI4KB) – 14-3-3 protein complex reveals internal flexibility and explains 14-3-3 mediated protection from degradation in vitro

Cited by 32 publications

References 72 publications

Characterization of the c10orf76‐PI4KB complex and its necessity for Golgi PI4P levels and enterovirus replication

Characterization of the c10orf76‐PI4KB complex and its necessity for Golgi PI4P levels and enterovirus replication

Conformational Flexibility of Proteins Involved in Ribosome Biogenesis: Investigations via Small Angle X-ray Scattering (SAXS)

Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications

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