Crystal Structure of the Yeast Phox Homology (PX) Domain Protein Grd19p Complexed to Phosphatidylinositol-3-phosphate

Zhou, Cong‐Zhao; Sierra-Gallay, I. Li de la; Quevillon‐Chéruel, Sophie; Collinet, Bruno; Minard, Philippe; Blondeau, Karine; Henckes, Gilles; Aufrère, Robert; Leulliot, Nicolas; Graille, Marc; Sorel, Isabelle; Savarin, Philippe; Torre, Françoise de la; Poupon, Anne; Janin, Joël; Tilbeurgh, Herman van

doi:10.1074/jbc.m304392200

Cited by 65 publications

(88 citation statements)

References 36 publications

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“…For example, a recent NMR study on the PX domain of Vam7p revealed that residues in its putative membrane binding loops underwent large changes in chemical shift when dodecylphosphocholine micelles were added to the PX domain-PtdIns3P complex (35). Also, crystal structures of the Grd19p PX domain in the absence and presence of a bound PtdIns3P showed conformational differences in the putative membrane attachment loop (46). This, in conjunction with the PI3K-C2␣ PX domain structure showing high flexibility of the PP II /␣2 loop, suggests that PtdIns(4,5)P 2 binding may also induce the conformational change and thereby facilitate the membrane penetration of hydrophobic side chains.…”

Section: Discussionmentioning

confidence: 99%

“…PX domains are similar to PH domains in that they have highly variable PI specificities and affinities. High resolution structures of several PX domains that bind the 3Ј-phosphate have been determined as either free proteins or complexes with PI (43)(44)(45)(46). However, the structural information for the PX domains that specifically bind non-3Ј-phosphate-PI has not been available.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, it has been shown that hydrophobic residues surrounding the PI-binding pockets of FYVE (67,68), PX (46,58), and ENTH (66, 69) domains can penetrate the membrane following PI binding. We thus measured the effects of mutations of hydrophobic residues (Val 1490 and Leu 1491 ) surrounding the PI-binding pocket of the PI3K-C2␣ PX domain to see if they are involved in membrane penetration.…”

Section: Figure 4 Equilibrium Spr Binding Analysis Of Pi3k-c2␣ Pxmentioning

confidence: 99%

“…Similarly, a mutational and homology modeling study of the phospholipase D1 PX domain suggested that it also has two binding sites, one specifically binding PtdIns(3,4,5)P 3 and the other interacting nonspecifically with anionic phospholipids (41). The crystal structures of the free and PtdIns3P-bound PX domain of yeast Grd19p protein showed the lipid-induced local conformational changes involving putative membrane-penetrating hydrophobic residues (46).…”

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confidence: 99%

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Structural and Membrane Binding Analysis of the Phox Homology Domain of Phosphoinositide 3-Kinase-C2α

Stahelin

Karathanassis

Bruzik

et al. 2006

Journal of Biological Chemistry

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Phox homology (PX) domains, which have been identified in a variety of proteins involved in cell signaling and membrane trafficking, have been shown to interact with phosphoinositides (PIs) with different affinities and specificities. To elucidate the structural origin of diverse PI specificities of PX domains, we determined the crystal structure of the PX domain from phosphoinositide 3-kinase C2␣ (PI3K-C2␣), which binds phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P 2 ). To delineate the mechanism by which this PX domain interacts with membranes, we measured the membrane binding of the wild type domain and mutants by surface plasmon resonance and monolayer techniques. This PX domain contains a signature PI-binding site that is optimized for PtdIns(4,5)P 2 binding. The membrane binding of the PX domain is initiated by nonspecific electrostatic interactions followed by the membrane penetration of hydrophobic residues. Membrane penetration is specifically enhanced by PtdIns(4,5)P 2 . Furthermore, the PX domain displayed significantly higher PtdIns(4,5)P 2 membrane affinity and specificity when compared with the PI3K-C2␣ C2 domain, demonstrating that high affinity PtdIns(4,5)P 2 binding was facilitated by the PX domain in full-length PI3K-C2␣. Together, these studies provide new structural insight into the diverse PI specificities of PX domains and elucidate the mechanism by which the PI3K-C2␣ PX domain interacts with PtdIns(4,5)P 2 -containing membranes and thereby mediates the membrane recruitment of PI3K-C2␣.Numerous cellular processes, including cell signaling and membrane trafficking, involve complex arrays of protein-protein and lipid-protein interactions. Research in the past decade has revealed that a large number of cellular proteins reversibly translocate to specific subcellular locations to form lipid-protein interactions (1, 2). These proteins, collectively known as peripheral proteins, typically contain one or more modular domains specialized in lipid binding (3,4). Common targets of many of these lipid-binding domains are phosphoinositides (PIs), 4 which play a crucial role in cell signaling and membrane trafficking by serving as site-specific membrane signals to modulate the intracellular localization and/or biological activity of effector proteins (5-8). PIs are metabolized by kinases and phosphatases, which catalyze the phosphorylation and dephosphorylation of PI at the 3Ј-, 4Ј-, or 5Ј-position (9 -12). PI 3-kinases (PI3Ks) are enzymes that catalyze the phosphorylation of phosphatidylinositol (PtdIns), phosphatidylinositol 4-phosphate (PtdIns4P), or phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P 2 ) at the 3Ј-position of the inositol ring (13-15). PI3Ks are divided into three classes (class I, II, and III) based upon their structures and in vitro activities (16,17). Class II PI3K includes PI3K-C2␣, PI3K-C2␤, and PI3K-C2␥. These enzymes phosphorylate PtdIns and PtdIns4P at the 3Ј-position in vitro (18 -21) and act downstream of receptors for growth factors (22), chemokines (23), and integr...

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Figure 4 Equilibrium Spr Binding Analysis Of Pi3k-c2␣ Pxmentioning

confidence: 99%

mentioning

confidence: 99%

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Structural and Membrane Binding Analysis of the Phox Homology Domain of Phosphoinositide 3-Kinase-C2α

Stahelin

Karathanassis

Bruzik

et al. 2006

Journal of Biological Chemistry

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“…(11) The sequence of 1OCU and SNX10 PX were realigned with other sequences that belong to the PX-only subfamily using ClustalW. Models of PX wild-type and mutants were predicted using the program Modeller (ver 9.10).…”

Section: In Silico Studiesmentioning

confidence: 99%

SNX10 mutations define a subgroup of human autosomal recessive osteopetrosis with variable clinical severity

Pangrazio

Fasth

Sbardellati

et al. 2012

Journal of Bone and Mineral Research

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Human Autosomal Recessive Osteopetrosis (ARO) is a genetically heterogeneous disorder caused by reduced bone resorption by osteoclasts. In 2000, we found that mutations in the TCIRG1 gene encoding for a subunit of the proton pump (V-ATPase) are responsible for more than one-half of ARO cases. Since then, five additional genes have been demonstrated to be involved in the pathogenesis of the disease, leaving approximately 25% of cases that could not be associated with a genotype. Very recently, a mutation in the sorting nexin 10 (SNX10) gene, whose product is suggested to interact with the proton pump, has been found in 3 consanguineous families of Palestinian origin, thus adding a new candidate gene in patients not previously classified. Here we report the identification of 9 novel mutations in this gene in 14 ARO patients from 12 unrelated families of different geographic origin. Interestingly, we define the molecular defect in three cases of ''Västerbottenian osteopetrosis,'' named for the Swedish Province where a higher incidence of the disease has been reported. In our cohort of more than 310 patients from all over the world, SNX10-dependent ARO constitutes 4% of the cases, with a frequency comparable to the receptor activator of NF-kB ligand (RANKL), receptor activator of NF-kB (RANK) and osteopetrosisassociated transmembrane protein 1 (OSTM1)-dependent subsets. Although the clinical presentation is relatively variable in severity, bone seems to be the only affected tissue and the defect can be almost completely rescued by hematopoietic stem cell transplantation (HSCT). These results confirm the involvement of the SNX10 gene in human ARO and identify a new subset with a relatively favorable prognosis as compared to TCIRG1-dependent cases. Further analyses will help to better understand the role of SNX10 in osteoclast physiology and verify whether this protein might be considered a new target for selective antiresorptive therapies. ß

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Structure of the PX domain of SNX25 reveals a novel phospholipid recognition model by dimerization in the PX domain

Zhu

et al. 2017

FEBS Letters

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SNX25, a regulator of GPCR signaling-phox-homology (PX) domain containing sorting nexin (SNX) member, has been proposed to be involved in the lysosomal degradation of the transforming growth factor β receptor and the development of temporal lobe epilepsy. Targeting to the endosomal membranes by the specific binding of phosphorylated phosphatidylinositols (PIPs) through the PX domain is critical for the function of SNXs. However, the mechanism for SNX25-PX targeting to the endosomes remains unclear. Here, we demonstrate that the PX domain of zebrafish SNX25 (zSNX25-PX) is capable of binding to PI3P only in its dimeric form. We also present the crystal structure of zSNX25-PX. Combined with biochemical experiments, we further identify a potential PI3P-binding region and propose a novel PI-binding model based on dimerization in the PX domain of SNXs.

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Crystal Structure of the Yeast Phox Homology (PX) Domain Protein Grd19p Complexed to Phosphatidylinositol-3-phosphate

Cited by 65 publications

References 36 publications

Structural and Membrane Binding Analysis of the Phox Homology Domain of Phosphoinositide 3-Kinase-C2α

Structural and Membrane Binding Analysis of the Phox Homology Domain of Phosphoinositide 3-Kinase-C2α

SNX10 mutations define a subgroup of human autosomal recessive osteopetrosis with variable clinical severity

Structure of the PX domain of SNX25 reveals a novel phospholipid recognition model by dimerization in the PX domain

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