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.

scholarly journals Plant photoreceptors and their signaling components compete for binding to the ubiquitin ligase COP1 using their VP-peptide motifs

2019 ◽  
Author(s):  
Kelvin Lau ◽  
Roman Podolec ◽  
Richard Chappuis ◽  
Roman Ulm ◽  
Michael Hothorn
Keyword(s):  
Transcription Factors ◽  
Crystal Structures ◽  
Ubiquitin Ligase ◽  
Light Signaling ◽  
Binding Assays ◽  
Light Spectrum ◽  
Signaling Specificity ◽  
Peptide Motifs ◽  
Wd40 Domain ◽  
Signaling Components

SUMMARYPlants sense different parts of the sun’s light spectrum using specialized photoreceptors, many of which signal through the E3 ubiquitin ligase COP1. Photoreceptor binding modulates COP1’s ubiquitin ligase activity towards transcription factors. Here we analyze why many COP1-interacting transcription factors and photoreceptors harbor sequence-divergent Val-Pro (VP) peptide motifs. We demonstrate that VP motifs enable different light signaling components to bind to the WD40 domain of COP1 with various binding affinities. Crystal structures of the VP motifs of the UV-B photoreceptor UVR8 and the transcription factor HY5 in complex with COP1, quantitative binding assays and reverse genetic experiments together suggest that UVR8 and HY5 compete for the COP1 WD40 domain. Photoactivation of UVR8 leads to high-affinity cooperative binding of its VP domain and its photosensing core to COP1, interfering with the binding of COP1 to its substrate HY5. Functional UVR8 – VP motif chimeras suggest that UV-B signaling specificity resides in the UVR8 photoreceptor core, not its VP motif. Crystal structures of different COP1 – VP peptide complexes highlight sequence fingerprints required for COP1 targeting. The functionally distinct blue light receptors CRY1 and CRY2 also compete with downstream transcription factors for COP1 binding using similar VP-peptide motifs. Together, our work reveals that photoreceptors and their components compete for COP1 using a conserved displacement mechanism to control different light signaling cascades in plants.

scholarly journals Crystal Structures of the Armadillo Repeat Domain of Adenomatous Polyposis Coli and Its Complex with the Tyrosine-Rich Domain of Sam68

Structure ◽  
2011 ◽  
Vol 19 (12) ◽  
pp. 1896
Author(s):  
Ella Czarina Morishita ◽  
Kazutaka Murayama ◽  
Miyuki Kato-Murayama ◽  
Yoshiko Ishizuka-Katsura ◽  
Yuri Tomabechi ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Adenomatous Polyposis Coli ◽  
Adenomatous Polyposis ◽  
Polyposis Coli ◽  
Rich Domain ◽  
Repeat Domain ◽  
Armadillo Repeat

Nogo Receptor crystal structures with a native disulfide pattern suggest a novel mode of self-interaction

2017 ◽  
Vol 73 (11) ◽  
pp. 860-876 ◽  
Author(s):  
Matti F. Pronker ◽  
Roderick P. Tas ◽  
Hedwich C. Vlieg ◽  
Bert J. C. Janssen
Keyword(s):  
Crystal Structures ◽  
Disulfide Bonds ◽  
Crystal Packing ◽  
Surface Protein ◽  
Terminal Segment ◽  
Structural Basis ◽  
Crystal Forms ◽  
Nogo Receptor ◽  
Terminal Loop ◽  
Lrr Domain

The Nogo Receptor (NgR) is a glycophosphatidylinositol-anchored cell-surface protein and is a receptor for three myelin-associated inhibitors of regeneration: myelin-associated glycoprotein, Nogo66 and oligodendrocyte myelin glycoprotein. In combination with different co-receptors, NgR mediates signalling that reduces neuronal plasticity. The available structures of the NgR ligand-binding leucine-rich repeat (LRR) domain have an artificial disulfide pattern owing to truncated C-terminal construct boundaries. NgR has previously been shown to self-associateviaits LRR domain, but the structural basis of this interaction remains elusive. Here, crystal structures of the NgR LRR with a longer C-terminal segment and a native disulfide pattern are presented. An additional C-terminal loop proximal to the C-terminal LRR cap is stabilized by two newly formed disulfide bonds, but is otherwise mostly unstructured in the absence of any stabilizing interactions. NgR crystallized in six unique crystal forms, three of which share a crystal-packing interface. NgR crystal-packing interfaces from all eight unique crystal forms are compared in order to explore how NgR could self-interact on the neuronal plasma membrane.

Structure and allosteric regulation of eukaryotic 6-phosphofructokinases

2013 ◽  
Vol 394 (8) ◽  
pp. 977-993 ◽  
Author(s):  
Torsten Schöneberg ◽  
Marco Kloos ◽  
Antje Brüser ◽  
Jürgen Kirchberger ◽  
Norbert Sträter
Keyword(s):  
Crystal Structures ◽  
Structural Information ◽  
Current Knowledge ◽  
Allosteric Regulation ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Directed Mutagenesis ◽  
Special Focus ◽  
Molecular Architecture ◽  
Key Enzyme

Abstract Although the crystal structures of prokaryotic 6-phosphofructokinase, a key enzyme of glycolysis, have been available for almost 25 years now, structural information about the more complex and highly regulated eukaryotic enzymes is still lacking until now. This review provides an overview of the current knowledge of eukaryotic 6-phosphofructokinase based on recent crystal structures, kinetic analyses and site-directed mutagenesis data with special focus on the molecular architecture and the structural basis of allosteric regulation.

scholarly journals Crystal Structures of Bat and Human Coronavirus ORF8 Protein Ig-Like Domain Provide Insights Into the Diversity of Immune Responses

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaoxue Chen ◽  
Zhechong Zhou ◽  
Chunliu Huang ◽  
Ziliang Zhou ◽  
Sisi Kang ◽  
...  
Keyword(s):  
Immune Responses ◽  
Crystal Structures ◽  
Immune Cell ◽  
Crystal Packing ◽  
Human Peripheral Blood ◽  
Structural Characteristics ◽  
Binding Assays ◽  
Cell Binding ◽  
Bat Coronavirus

ORF8 is a viral immunoglobulin-like (Ig-like) domain protein encoded by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA genome. It tends to evolve rapidly and interfere with immune responses. However, the structural characteristics of various coronavirus ORF8 proteins and their subsequent effects on biological functions remain unclear. Herein, we determined the crystal structures of SARS-CoV-2 ORF8 (S84) (one of the epidemic isoforms) and the bat coronavirus RaTG13 ORF8 variant at 1.62 Å and 1.76 Å resolution, respectively. Comparison of these ORF8 proteins demonstrates that the 62-77 residues in Ig-like domain of coronavirus ORF8 adopt different conformations. Combined with mutagenesis assays, the residue Cys20 of ORF8 is responsible for forming the covalent disulfide-linked dimer in crystal packing and in vitro biochemical conditions. Furthermore, immune cell-binding assays indicate that various ORF8 (SARS-CoV-2 ORF8 (L84), ORF8 (S84), and RaTG13 ORF8) proteins have different interaction capabilities with human CD14+ monocytes in human peripheral blood. These results provide new insights into the specific characteristics of various coronavirus ORF8 and suggest that ORF8 variants may influence disease-related immune responses.

scholarly journals Mechanistic basis for the activation of plant membrane receptor kinases by SERK-family coreceptors

2018 ◽  
Vol 115 (13) ◽  
pp. 3488-3493 ◽  
Author(s):  
Ulrich Hohmann ◽  
Julia Santiago ◽  
Joël Nicolet ◽  
Vilde Olsson ◽  
Fabio M. Spiga ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Specific Binding ◽  
Peptide Hormone ◽  
Receptor Activation ◽  
Kinase Domain ◽  
Membrane Receptor ◽  
Activation Mechanism ◽  
In Planta ◽  
Affinity Ligand ◽  
Receptor Kinases

Plant-unique membrane receptor kinases with leucine-rich repeat ectodomains (LRR-RKs) can sense small molecule, peptide, and protein ligands. Many LRR-RKs require SERK-family coreceptor kinases for high-affinity ligand binding and receptor activation. How one coreceptor can contribute to the specific binding of distinct ligands and activation of different LRR-RKs is poorly understood. Here we quantitatively analyze the contribution of SERK3 to ligand binding and activation of the brassinosteroid receptor BRI1 and the peptide hormone receptor HAESA. We show that while the isolated receptors sense their respective ligands with drastically different binding affinities, the SERK3 ectodomain binds the ligand-associated receptors with very similar binding kinetics. We identify residues in the SERK3 N-terminal capping domain, which allow for selective steroid and peptide hormone recognition. In contrast, residues in the SERK3 LRR core form a second, constitutive receptor–coreceptor interface. Genetic analyses of protein chimera between BRI1 and SERK3 define that signaling-competent complexes are formed by receptor–coreceptor heteromerization in planta. A functional BRI1–HAESA chimera suggests that the receptor activation mechanism is conserved among different LRR-RKs, and that their signaling specificity is encoded in the kinase domain of the receptor. Our work pinpoints the relative contributions of receptor, ligand, and coreceptor to the formation and activation of SERK-dependent LRR-RK signaling complexes regulating plant growth and development.

scholarly journals Structure-Based Functional Analysis of a Hormone Belonging to an Ecdysozoan Peptide Superfamily: Revelation of a Common Molecular Architecture and Residues Possibly for Receptor Interaction

2021 ◽  
Vol 22 (20) ◽  
pp. 11142
Author(s):  
Yun-Ru Chen ◽  
Nai-Wan Hsiao ◽  
Yi-Zong Lee ◽  
Shiau-Shan Huang ◽  
Chih-Chun Chang ◽  
...  
Keyword(s):  
Atpase Activity ◽  
Receptor Binding ◽  
Binding Sites ◽  
Disulfide Bonds ◽  
Solution Structure ◽  
Receptor Interaction ◽  
Resonance Spectroscopy ◽  
Molecular Architecture ◽  
Major Factors

A neuropeptide (Sco-CHH-L), belonging to the crustacean hyperglycemic hormone (CHH) superfamily and preferentially expressed in the pericardial organs (POs) of the mud crab Scylla olivacea, was functionally and structurally studied. Its expression levels were significantly higher than the alternative splice form (Sco-CHH) in the POs, and increased significantly after the animals were subjected to a hypo-osmotic stress. Sco-CHH-L, but not Sco-CHH, significantly stimulated in vitro the Na+, K+-ATPase activity in the posterior (6th) gills. Furthermore, the solution structure of Sco-CHH-L was resolved using nuclear magnetic resonance spectroscopy, revealing that it has an N-terminal tail, three α-helices (α2, Gly9−Asn28; α3, His34−Gly38; and α5, Glu62−Arg72), and a π-helix (π4, Cys43−Tyr54), and is structurally constrained by a pattern of disulfide bonds (Cys7–Cys43, Cys23–Cys39, and Cys26–Cys52), which is characteristic of the CHH superfamily-peptides. Sco-CHH-L is topologically most similar to the molt-inhibiting hormone from the Kuruma prawn Marsupenaeus japonicus with a backbone root-mean-square-deviation of 3.12 Å. Ten residues of Sco-CHH-L were chosen for alanine-substitution, and the resulting mutants were functionally tested using the gill Na+, K+-ATPase activity assay, showing that the functionally important residues (I2, F3, E45, D69, I71, and G73) are located at either end of the sequence, which are sterically close to each other and presumably constitute the receptor binding sites. Sco-CHH-L was compared with other members of the superfamily, revealing a folding pattern, which is suggested to be common for the crustacean members of the superfamily, with the properties of the residues constituting the presumed receptor binding sites being the major factors dictating the ligand–receptor binding specificity.

scholarly journals The Interaction of TRAF6 With Neuroplastin Promotes Spinogenesis During Early Neuronal Development

2020 ◽  
Vol 8 ◽  
Author(s):  
Sampath Kumar Vemula ◽  
Ayse Malci ◽  
Lennart Junge ◽  
Anne-Christin Lehmann ◽  
Ramya Rama ◽  
...  
Keyword(s):  
Neuronal Development ◽  
Synapse Formation ◽  
Tumor Necrosis Factor Receptor ◽  
Physical Interaction ◽  
Binding Assays ◽  
C Terminus ◽  
Synapse Density ◽  
Pharmacological Blockade ◽  
Necrosis Factor

Correct brain wiring depends on reliable synapse formation. Nevertheless, signaling codes promoting synaptogenesis are not fully understood. Here, we report a spinogenic mechanism that operates during neuronal development and is based on the interaction of tumor necrosis factor receptor-associated factor 6 (TRAF6) with the synaptic cell adhesion molecule neuroplastin. The interaction between these proteins was predicted in silico and verified by co-immunoprecipitation in extracts from rat brain and co-transfected HEK cells. Binding assays show physical interaction between neuroplastin’s C-terminus and the TRAF-C domain of TRAF6 with a Kd value of 88 μM. As the two proteins co-localize in primordial dendritic protrusions, we used young cultures of rat and mouse as well as neuroplastin-deficient mouse neurons and showed with mutagenesis, knock-down, and pharmacological blockade that TRAF6 is required by neuroplastin to promote early spinogenesis during in vitro days 6-9, but not later. Time-framed TRAF6 blockade during days 6–9 reduced mEPSC amplitude, number of postsynaptic sites, synapse density and neuronal activity as neurons mature. Our data unravel a new molecular liaison that may emerge during a specific window of the neuronal development to determine excitatory synapse density in the rodent brain.

scholarly journals Structural insights into the assembly and polyA signal recognition mechanism of the human CPSF complex

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Marcello Clerici ◽  
Marco Faini ◽  
Ruedi Aebersold ◽  
Martin Jinek
Keyword(s):  
Mammalian Cells ◽  
Rna Binding ◽  
Molecular Architecture ◽  
Binding Assays ◽  
Critical Determinant ◽  
Recognition Mechanism ◽  
Cleavage And Polyadenylation ◽  
Specificity Factor ◽  
Motif Recognition ◽  
Mrna Polyadenylation

3’ polyadenylation is a key step in eukaryotic mRNA biogenesis. In mammalian cells, this process is dependent on the recognition of the hexanucleotide AAUAAA motif in the pre-mRNA polyadenylation signal by the cleavage and polyadenylation specificity factor (CPSF) complex. A core CPSF complex comprising CPSF160, WDR33, CPSF30 and Fip1 is sufficient for AAUAAA motif recognition, yet the molecular interactions underpinning its assembly and mechanism of PAS recognition are not understood. Based on cross-linking-coupled mass spectrometry, crystal structure of the CPSF160-WDR33 subcomplex and biochemical assays, we define the molecular architecture of the core human CPSF complex, identifying specific domains involved in inter-subunit interactions. In addition to zinc finger domains in CPSF30, we identify using quantitative RNA-binding assays an N-terminal lysine/arginine-rich motif in WDR33 as a critical determinant of specific AAUAAA motif recognition. Together, these results shed light on the function of CPSF in mediating PAS-dependent RNA cleavage and polyadenylation.

scholarly journals Molecular architecture of a dynamin adaptor: implications for assembly of mitochondrial fission complexes

2010 ◽  
Vol 191 (6) ◽  
pp. 1127-1139 ◽  
Author(s):  
Sajjan Koirala ◽  
Huyen T. Bui ◽  
Heidi L. Schubert ◽  
Debra M. Eckert ◽  
Christopher P. Hill ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Crystal Structures ◽  
Binding Sites ◽  
Mitochondrial Fission ◽  
Coiled Coil ◽  
Adaptor Proteins ◽  
Molecular Architecture ◽  
Cellular Membranes ◽  
Membrane Scission ◽  
Antiparallel Coiled Coil

Recruitment and assembly of some dynamin-related guanosine triphosphatases depends on adaptor proteins restricted to distinct cellular membranes. The yeast Mdv1 adaptor localizes to mitochondria by binding to the membrane protein Fis1. Subsequent Mdv1 binding to the mitochondrial dynamin Dnm1 stimulates Dnm1 assembly into spirals, which encircle and divide the mitochondrial compartment. In this study, we report that dimeric Mdv1 is joined at its center by a 92-Å antiparallel coiled coil (CC). Modeling of the Fis1–Mdv1 complex using available crystal structures suggests that the Mdv1 CC lies parallel to the bilayer with N termini at opposite ends bound to Fis1 and C-terminal β-propeller domains (Dnm1-binding sites) extending into the cytoplasm. A CC length of appropriate length and sequence is necessary for optimal Mdv1 interaction with Fis1 and Dnm1 and is important for proper Dnm1 assembly before membrane scission. Our results provide a framework for understanding how adaptors act as scaffolds to orient and stabilize the assembly of dynamins on membranes.

Sign in / Sign up

Export Citation Format

Share Document