scholarly journals Structural Insight on Functional Regulation of Human MINERVA Protein

2020 ◽  
Vol 21 (21) ◽  
pp. 8186
Author(s):  
Hyunggu Hahn ◽  
Dong-Eun Lee ◽  
Dong Man Jang ◽  
Jiyoun Kim ◽  
Yeon Lee ◽  
...  
Keyword(s):  
Lipid Binding ◽  
Ph Domain ◽  
Binding Assays ◽  
Rich Domain ◽  
Exact Function ◽  
Proliferation And Apoptosis ◽  
Specific Affinity ◽  
Flexible Region ◽  
Functional Regulation ◽  
Α Helix

MINERVA (melanoma invasion by ERK), also known as FAM129B, is a member of the FAM129 protein family, which is only present in vertebrates. MINERVA is involved in key signaling pathways regulating cell survival, proliferation and apoptosis and found upregulated in many types of cancer promoting invasion. However, the exact function of the protein remains elusive. X-ray crystallographic methods were implemented to determine the crystal structure of MINERVAΔC, lacking C-terminal flexible region. Trypsin digestion was required before crystallization to obtain diffraction-quality crystals. While the N-terminal pleckstrin homology (PH) domain exhibits the typical fold of PH domains, lipid binding assay indicates specific affinity towards phosphatidic acid and inositol 3-phosphate. A helix-rich domain that constitutes the rest of the molecule demonstrates a novel L-shaped fold that encompasses the PH domain. The overall structure of MINERVAΔC with binding assays and cell-based experiments suggest plasma membrane association of MINERVA and its function seem to be tightly regulated by various motifs within the C-terminal flexible region. Elucidation of MINERVAΔC structure presents a novel fold for an α-helix bundle domain that would provide a binding platform for interacting partners.

scholarly journals Oligomerization and Ca2+/calmodulin control binding of the ER Ca2+-sensors STIM1 and STIM2 to plasma membrane lipids

2013 ◽  
Vol 33 (5) ◽  
Author(s):  
Rajesh Bhardwaj ◽  
Hans-Michael Müller ◽  
Walter Nickel ◽  
Matthias Seedorf
Keyword(s):  
Plasma Membrane ◽  
Membrane Lipids ◽  
Lipid Binding ◽  
Dependent Manner ◽  
Activation Threshold ◽  
Concentration Dependent Manner ◽  
Rich Domain ◽  
Α Helix ◽  
Distinct Features ◽  
Ca2 Channels

Ca2+ (calcium) homoeostasis and signalling rely on physical contacts between Ca2+ sensors in the ER (endoplasmic reticulum) and Ca2+ channels in the PM (plasma membrane). STIM1 (stromal interaction molecule 1) and STIM2 Ca2+ sensors oligomerize upon Ca2+ depletion in the ER lumen, contact phosphoinositides at the PM via their cytosolic lysine (K)-rich domains, and activate Ca2+ channels. Differential sensitivities of STIM1 and STIM2 towards ER luminal Ca2+ have been studied but responses towards elevated cytosolic Ca2+ concentration and the mechanism of lipid binding remain unclear. We found that tetramerization of the STIM1 K-rich domain is necessary for efficient binding to PI(4,5)P2-containing PM-like liposomes consistent with an oligomerization-driven STIM1 activation. In contrast, dimerization of STIM2 K-rich domain was sufficient for lipid binding. Furthermore, the K-rich domain of STIM2, but not of STIM1, forms an amphipathic α-helix. These distinct features of the STIM2 K-rich domain cause an increased affinity for PI(4,5)P2, consistent with the lower activation threshold of STIM2 and a function as regulator of basal Ca2+ levels. Concomitant with higher affinity for PM lipids, binding of CaM (calmodulin) inhibited the interaction of the STIM2 K-rich domain with liposomes in a Ca2+ and PI(4,5)P2 concentration-dependent manner. Therefore we suggest that elevated cytosolic Ca2+ concentration down-regulates STIM2-mediated ER–PM contacts via CaM binding.

scholarly journals Tumor Suppressor SMAR1 Activates and Stabilizes p53 through Its Arginine-Serine-rich Motif

2005 ◽  
Vol 280 (16) ◽  
pp. 16019-16029 ◽  
Author(s):  
Archana Jalota ◽  
Kamini Singh ◽  
Lakshminarasimhan Pavithra ◽  
Ruchika Kaul-Ghanekar ◽  
Shahid Jameel ◽  
...  
Keyword(s):  
Cell Fate ◽  
The Novel ◽  
Nuclear Retention ◽  
Post Translational Modifications ◽  
Rich Domain ◽  
Dna Damaging Agents ◽  
Proliferation And Apoptosis ◽  
Interfering Rna ◽  
The Guardian

Various stresses and DNA-damaging agents trigger transcriptional activity of p53 by post-translational modifications, making it a global regulatory switch that controls cell proliferation and apoptosis. Earlier we have shown that the novel MAR-associated protein SMAR1 interacts with p53. Here we delineate the minimal domain of SMAR1 (the arginine-serine-rich domain) that is phosphorylated by protein kinase C family proteins and is responsible for p53 interaction, activation, and stabilization within the nucleus. SMAR1-mediated stabilization of p53 is brought about by inhibiting Mdm2-mediated degradation of p53. We also demonstrate that this arginine-serine (RS)-rich domain triggers the various cell cycle modulating proteins that decide cell fate. Furthermore, phenotypic knock-down experiments using small interfering RNA showed that SMAR1 is required for activation and nuclear retention of p53. The level of phosphorylated p53 was significantly increased in the thymus of SMAR1 transgenic mice, showingin vivosignificance of SMAR1 expression. This is the first report that demonstrates the mechanism of action of the MAR-binding protein SMAR1 in modulating the activity of p53, often referred to as the “guardian of the genome.”

scholarly journals The lipid transfer protein Saposin B does not directly bind CD1d for lipid antigen loading

2019 ◽  
Vol 4 ◽  
pp. 117
Author(s):  
Maria Shamin ◽  
Tomasz H. Benedyk ◽  
Stephen C. Graham ◽  
Janet E. Deane
Keyword(s):  
Lipid Transfer Protein ◽  
Direct Interaction ◽  
Lipid Binding ◽  
Lipid Transfer ◽  
Binding Assays ◽  
Lipid Transfer Proteins ◽  
Lipid Antigens ◽  
Saposin B ◽  
Protein Components ◽  
Lipid Loading

Background: Lipid antigens are presented on the surface of cells by the CD1 family of glycoproteins, which have structural and functional similarity to MHC class I molecules. The hydrophobic lipid antigens are embedded in membranes and inaccessible to the lumenal lipid-binding domain of CD1 molecules. Therefore, CD1 molecules require lipid transfer proteins for lipid loading and editing. CD1d is loaded with lipids in late endocytic compartments, and lipid transfer proteins of the saposin family have been shown to play a crucial role in this process. However, the mechanism by which saposins facilitate lipid binding to CD1 molecules is not known and is thought to involve transient interactions between protein components to ensure CD1-lipid complexes can be efficiently trafficked to the plasma membrane for antigen presentation. Of the four saposin proteins, the importance of Saposin B (SapB) for loading of CD1d is the most well-characterised. However, a direct interaction between CD1d and SapB has yet to be described. Methods: In order to determine how SapB might load lipids onto CD1d, we used purified, recombinant CD1d and SapB and carried out a series of highly sensitive binding assays to monitor direct interactions. We performed equilibrium binding analysis, chemical cross-linking and co-crystallisation experiments, under a range of different conditions. Results: We could not demonstrate a direct interaction between SapB and CD1d using any of these binding assays. Conclusions: This work establishes comprehensively that the role of SapB in lipid loading does not involve direct binding to CD1d. We discuss the implication of this for our understanding of lipid loading of CD1d and propose several factors that may influence this process.

scholarly journals Functional assessment of perforin C2 domain mutations illustrates the critical role for calcium-dependent lipid binding in perforin cytotoxic function

Blood ◽  
2009 ◽  
Vol 113 (2) ◽  
pp. 338-346 ◽  
Author(s):  
Ramon Urrea Moreno ◽  
Juana Gil ◽  
Carmen Rodriguez-Sainz ◽  
Elena Cela ◽  
Victor LaFay ◽  
...  
Keyword(s):  
Calcium Binding ◽  
Critical Role ◽  
Lipid Binding ◽  
Inflammatory Disorder ◽  
C2 Domain ◽  
Biophysical Modeling ◽  
Binding Assays ◽  
Calcium Dependent ◽  
Pathogen Elimination ◽  
Cytotoxic Function

Abstract Perforin-mediated lymphocyte cytotoxicity is critical for pathogen elimination and immune homeostasis. Perforin disruption of target cell membranes is hypothesized to require binding of a calcium-dependent, lipid-inserting, C2 domain. In a family affected by hemophagocytic lymphohistiocytosis, a severe inflammatory disorder caused by perforin deficiency, we identified 2 amino acid substitutions in the perforin C2 domain: T435M, a previously identified mutant with disputed pathogenicity, and Y438C, a novel substitution. Using biophysical modeling, we predicted that the T435M substitution, but not Y438C, would interfere with calcium binding and thus cytotoxic function. The capacity for cytotoxic function was tested after expression of the variant perforins in rat basophilic leukemia cells and murine cytotoxic T lymphocytes. As predicted, cells transduced with perforin-T435M lacked cytotoxicity, but those expressing perforin-Y438C displayed intact cytotoxic function. Using novel antibody-capture and liposome-binding assays, we found that both mutant perforins were secreted; however, only nonmutated and Y438C-substituted perforins were capable of calcium-dependent lipid binding. In addition, we found that perforin-Y438C was capable of mediating cytotoxicity without apparent proteolytic maturation. This study clearly demonstrates the pathogenicity of the T435M mutation and illustrates, for the first time, the critical role of the human perforin C2 domain for calcium-dependent, cytotoxic function.

scholarly journals Unsaturated fatty acyl recognition by Frizzled receptors mediates dimerization upon Wnt ligand binding

2017 ◽  
Vol 114 (16) ◽  
pp. 4147-4152 ◽  
Author(s):  
Aaron H. Nile ◽  
Susmith Mukund ◽  
Karen Stanger ◽  
Weiru Wang ◽  
Rami N. Hannoush
Keyword(s):  
Crystal Structure ◽  
Fatty Acid ◽  
Wnt Signaling ◽  
Bone Growth ◽  
Cell Activity ◽  
Fatty Acyl ◽  
Lipid Binding ◽  
Receptor Expression ◽  
Rich Domain ◽  
Binding Groove

Frizzled (FZD) receptors mediate Wnt signaling in diverse processes ranging from bone growth to stem cell activity. Moreover, high FZD receptor expression at the cell surface contributes to overactive Wnt signaling in subsets of pancreatic, ovarian, gastric, and colorectal tumors. Despite the progress in biochemical understanding of Wnt–FZD receptor interactions, the molecular basis for recognition of Wnt cis-unsaturated fatty acyl groups by the cysteine-rich domain (CRD) of FZD receptors remains elusive. Here, we determined a crystal structure of human FZD7 CRD unexpectedly bound to a 24-carbon fatty acid. We also report a crystal structure of human FZD5 CRD bound to C16:1 cis-Δ9 unsaturated fatty acid. Both structures reveal a dimeric arrangement of the CRD. The lipid-binding groove exhibits flexibility and spans both monomers, adopting a U-shaped geometry that accommodates the fatty acid. Re-evaluation of the published mouse FZD8 CRD structure reveals that it also shares the same architecture as FZD5 and FZD7 CRDs. Our results define a common molecular mechanism for recognition of the cis-unsaturated fatty acyl group, a necessary posttranslational modification of Wnts, by multiple FZD receptors. The fatty acid bridges two CRD monomers, implying that Wnt binding mediates FZD receptor dimerization. Our data uncover possibilities for the arrangement of Wnt–FZD CRD complexes and shed structural insights that could aide in the identification of pharmacological strategies to modulate FZD receptor function.

scholarly journals Nbr1 Is a Novel Inhibitor of Ligand-Mediated Receptor Tyrosine Kinase Degradation

2010 ◽  
Vol 30 (24) ◽  
pp. 5672-5685 ◽  
Author(s):  
Faraz K. Mardakheh ◽  
Giulio Auciello ◽  
Tim R. Dafforn ◽  
Joshua Z. Rappoport ◽  
John K. Heath
Keyword(s):  
Tyrosine Kinases ◽  
Protein Localization ◽  
Negative Regulator ◽  
Receptor Internalization ◽  
C Terminus ◽  
Late Endosomes ◽  
Exact Function ◽  
Α Helix ◽  
And Function

ABSTRACT Neighbor of BRCA1 (Nbr1) is a highly conserved multidomain scaffold protein with proposed roles in endocytic trafficking and selective autophagy. However, the exact function of Nbr1 in these contexts has not been studied in detail. Here we investigated the role of Nbr1 in the trafficking of receptor tyrosine kinases (RTKs). We report that ectopic Nbr1 expression inhibits the ligand-mediated lysosomal degradation of RTKs, and this is probably done via the inhibition of receptor internalization. Conversely, the depletion of endogenous NBR1 enhances RTK degradation. Analyses of truncation mutations demonstrated that the C terminus of Nbr1 is essential but not sufficient for this activity. Moreover, the C terminus of Nbr1 is essential but not sufficient for the localization of the protein to late endosomes. We demonstrate that the C terminus of Nbr1 contains a novel membrane-interacting amphipathic α-helix, which is essential for the late endocytic localization of the protein but not for its effect on RTK degradation. Finally, autophagic and late endocytic localizations of Nbr1 are independent of one another, suggesting that the roles of Nbr1 in each context might be distinct. Our results define Nbr1 as a negative regulator of ligand-mediated RTK degradation and reveal the interplay between its various regions for protein localization and function.

scholarly journals Identification and characterization of the lipid-binding property of GrlR, a locus of enterocyte effacement regulator

2009 ◽  
Vol 420 (2) ◽  
pp. 191-201 ◽  
Author(s):  
Chacko Jobichen ◽  
Aaron Z. Fernandis ◽  
Adrian Velazquez-Campoy ◽  
Ka Yin Leung ◽  
Yu-Keung Mok ◽  
...  
Keyword(s):  
Lipid Binding ◽  
Titration Calorimetry ◽  
Binding Property ◽  
C Terminus ◽  
Lipid Species ◽  
Unknown Lipid ◽  
Enterocyte Effacement ◽  
Highly Hydrophobic ◽  
Α Helix ◽  
Lipid Binding Proteins

Lipocalins are a broad family of proteins identified initially in eukaryotes and more recently in Gram-negative bacteria. The functions of lipocalin or lipid-binding proteins are often elusive and very diverse. Recently, we have determined the structure of GrlR (global regulator of LEE repressor), which plays a key role in the regulation of LEE (locus of enterocyte effacement) proteins. GrlR adopts a lipocalin-like fold that is composed of an eight-stranded β-barrel followed by an α-helix at the C-terminus. GrlR has a highly hydrophobic cavity region and could be a potential transporter of lipophilic molecules. To verify this hypothesis, we carried out structure-based analysis of GrlR, determined the structure of the lipid–GrlR complex and measured the binding of lipid to recombinant GrlR by ITC (isothermal titration calorimetry). In addition, we identified phosphatidylglycerol and phosphatidylethanolamine as the endogenously bound lipid species of GrlR using electrospray-ionization MS. Furthermore, we have shown that the lipid-binding property of GrlR is similar to that of its closest lipocalin structural homologue, β-lactoglobulin. Our studies demonstrate the hitherto unknown lipid-binding property of GrlR.

scholarly journals ROR and RYK extracellular region structures suggest that receptor tyrosine kinases have distinct WNT-recognition modes

2021 ◽  
Author(s):  
Fumin Shi ◽  
Jeannine M Mendrola ◽  
Joshua B Sheetz ◽  
Neo Wu ◽  
Anselm Sommer ◽  
...  
Keyword(s):  
Tyrosine Kinases ◽  
Receptor Tyrosine Kinases ◽  
Acyl Chain ◽  
Lipid Binding ◽  
Receptor Interaction ◽  
Transmembrane Receptors ◽  
Binding Characteristics ◽  
Interaction Sites ◽  
Rich Domain ◽  
Extracellular Region

WNTs play key roles in development and disease, by binding both Frizzled (FZD) seven-pass transmembrane receptors and numerous co-receptors that include the ROR and RYK receptor tyrosine kinases (RTKs). We describe crystal structures and WNT-binding characteristics of extracellular regions from the Drosophila ROR and RYK orthologs Nrk (neurospecific receptor tyrosine kinase) and Derailed-2 (Drl-2). RORs bind WNTs though a FZD-related cysteine-rich domain (CRD), and RYKs through a WNT-inhibitory factor (WIF) domain. Our structures suggest that neither the Nrk CRD nor the Drl-2 WIF domain can accommodate the acyl chain typically attached to WNTs. The Nrk CRD contains a deeply buried bound fatty acid, unlikely to be exchangeable with a WNT acyl chain. The Drl-2 WIF domain lacks the lipid-binding site seen in WIF-1. We also show that DWnt-5, which regulates Drosophila ROR and RYK orthologs, lacks an acyl chain. Together with analysis of WNT/receptor interaction sites, these structures provide new insight into how WNTs recruit their RTK co-receptors into signaling complexes.

scholarly journals Crystal structures of Arabidopsis and Physcomitrella CR4 reveal the molecular architecture of CRINKLY4 receptor kinases

2020 ◽  
Author(s):  
Satohiro Okuda ◽  
Ludwig A. Hothorn ◽  
Michael Hothorn
Keyword(s):  
Crystal Structures ◽  
Disulfide Bonds ◽  
Physcomitrella Patens ◽  
Tumor Necrosis Factor Receptor ◽  
Peptide Hormone ◽  
Molecular Architecture ◽  
Binding Assays ◽  
Rich Domain ◽  
Receptor Kinases ◽  
Wd40 Domain

AbstractPlant-unique receptor kinases harbor conserved cytoplasmic kinase domains and sequence-diverse ectodomains. Here we report crystal structures of CRINKLY4-type ectodomains from Arabidopsis ACR4 and Physcomitrella patens PpCR4 at 1.95 Å and 2.70 Å resolution, respectively. Monomeric CRINKLY4 ectodomains harbor a N-terminal WD40 domain and a cysteine-rich domain (CRD) connected by a short linker. The WD40 domain forms a seven-bladed β-propeller with the N-terminal strand buried in its center. Each propeller blade is stabilized by a disulfide bond and contributes to the formation of a putative ligand binding groove. The CRD forms a β-sandwich structure stabilized by six disulfide bonds and shares low structural homology with tumor necrosis factor receptor domains. Quantitative binding assays reveal that ACR4 is not a direct receptor for the peptide hormone CLE40. An ACR4 variant lacking the entire CRD can rescue the known acr4-2 mutant phenotype, as can expression of PpCR4. Together, an evolutionary conserved signaling function for CRINKLY4 receptor kinases is encoded in its WD40 domain.

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