scholarly journals Structural Basis for Receptor Recognition by Lujo Virus

2018 ◽  
Author(s):  
Hadas Cohen-Dvashi ◽  
Itay Kilimnik ◽  
Ron Diskin
Keyword(s):  
Metal Ion ◽  
New World ◽  
Cell Attachment ◽  
Evolutionary Relationship ◽  
Structural Data ◽  
Structural Basis ◽  
Human Populations ◽  
X Ray Crystallography ◽  
Transferrin Receptor 1 ◽  
Receptor Recognition

AbstractLujo virus (LUJV) has emerged as a novel and highly fatal human pathogen. Despite its membership among the Arenaviridae, LUJV does not classify with the known Old and New World groups of that viral family. Likewise, LUJV was recently found to use neuropilin-2 (NRP2) as a cellular receptor instead of the canonical α-dystroglycan (α-DG) or transferrin receptor 1 (TfR1) utilized by Old World (OW) and New World (NW) arenaviruses, respectively. The emergence of a deadly new pathogen into human populations using an unprecedented entry route raises many questions regarding the mechanism of cell recognition and the risk that Arenaviruses are further diversifying their infection strategies. To provide the basis for combating LUJV in particular, and to increase our general understanding of the molecular changes that accompany an evolutionary switch to a new receptor for Arenaviruses, we used X-ray crystallography to reveal how the GP1 receptor-binding domain of LUJV (LUJVGP1) recognizes NRP2. Our structural data imply that LUJV is evolutionary closer to OW than to NW arenaviruses. Structural analysis supported by experimental validation further suggests that NRP2 recognition is metal ion dependent and that the complete NRP2 binding is formed in the context of the trimeric spike. Taken together, our data provide the mechanism for the cell attachment step of LUJV, the evolutionary relationship between the GP1 domain of this novel pathogen and other arenaviruses, and indispensable information for combating LUJV.

scholarly journals Mutation of outer-shell residues modulates metal ion co-ordination strength in a metalloenzyme

2010 ◽  
Vol 429 (2) ◽  
pp. 313-321 ◽  
Author(s):  
Jee-Loon Foo ◽  
Colin J. Jackson ◽  
Paul D. Carr ◽  
Hye-Kyung Kim ◽  
Gerhard Schenk ◽  
...  
Keyword(s):  
Metal Ion ◽  
Structural Data ◽  
Biochemical Properties ◽  
Outer Shell ◽  
Model Systems ◽  
Spectroscopic Techniques ◽  
Structural Determinants ◽  
Ion Specificity ◽  
X Ray Crystallography ◽  
Metal Ion Interactions

The metal ion co-ordination sites of many metalloproteins have been characterized by a variety of spectroscopic techniques and small-molecule model systems, revealing many important insights into the structural determinants of metal ion co-ordination. However, our understanding of this fundamentally and practically important phenomenon remains frustratingly simplistic; in many proteins it is essentially impossible to predict metal ion specificity and the effects of remote ‘outer-shell’ residues on metal ion co-ordination strength are also poorly defined. This is exemplified by our inability to explain why metalloenzymes with identical metal ion co-ordination spheres, such as the closely related orthologues of bacterial PTE (phosphotriesterase) from Agrobacterium radiobacter and Pseudomonas diminuta, display different metal ion specificity and co-ordination strength. In the present study, we present a series of PTE variants that all possess identical metal ion co-ordination spheres, yet display large differences in their metal ion co-ordination strength. Using measurement of the rates of metal ion dissociation from the active site alongside analysis of structural data obtained through X-ray crystallography, we show that ‘outer-shell’ residues provide essential support for the metal ion ligands, in effect buttressing them in their optimal orientation. Remote mutations appear to modulate metal ion interactions by increasing or decreasing the stabilizing effects of these networks. The present study therefore provides a description of how the greater protein fold can be modified to ‘tune’ the strength of metal ion co-ordination and metal ion specificity, as well as reinforcing the concept of proteins as ensembles of conformational states with unique structures and biochemical properties.

scholarly journals Structural basis for distinctive recognition of fibrinogen γC peptide by the platelet integrin αIIbβ3

2008 ◽  
Vol 182 (4) ◽  
pp. 791-800 ◽  
Author(s):  
Timothy A. Springer ◽  
Jianghai Zhu ◽  
Tsan Xiao
Keyword(s):  
Metal Ion ◽  
Structural Data ◽  
Structural Basis ◽  
Side Chain ◽  
Α Subunit ◽  
Integrin Αiibβ3 ◽  
Rgd Motif ◽  
Γ Subunit ◽  
Fibrinogen Binding ◽  
C Terminus

Hemostasis and thrombosis (blood clotting) involve fibrinogen binding to integrin αIIbβ3 on platelets, resulting in platelet aggregation. αvβ3 binds fibrinogen via an Arg-Asp-Gly (RGD) motif in fibrinogen's α subunit. αIIbβ3 also binds to fibrinogen; however, it does so via an unstructured RGD-lacking C-terminal region of the γ subunit (γC peptide). These distinct modes of fibrinogen binding enable αIIbβ3 and αvβ3 to function cooperatively in hemostasis. In this study, crystal structures reveal the integrin αIIbβ3–γC peptide interface, and, for comparison, integrin αIIbβ3 bound to a lamprey γC primordial RGD motif. Compared with RGD, the GAKQAGDV motif in γC adopts a different backbone configuration and binds over a more extended region. The integrin metal ion–dependent adhesion site (MIDAS) Mg2+ ion binds the γC Asp side chain. The adjacent to MIDAS (ADMIDAS) Ca2+ ion binds the γC C terminus, revealing a contribution for ADMIDAS in ligand binding. Structural data from this natively disordered γC peptide enhances our understanding of the involvement of γC peptide and integrin αIIbβ3 in hemostasis and thrombosis.

scholarly journals Recognition and deubiquitination of free 40S for translational reset by Otu2

2021 ◽  
Author(s):  
Ken Ikeuchi ◽  
Nives Ivic ◽  
Jingdong Cheng ◽  
Robert Buschauer ◽  
Yoshitaka Matsuo ◽  
...  
Keyword(s):  
Ribosomal Subunit ◽  
Structural Data ◽  
Structural Basis ◽  
Crucial Importance ◽  
Initiation Complex ◽  
Exact Role ◽  
80S Ribosome ◽  
X Ray ◽  
X Ray Crystallography ◽  
Ubiquitin Moiety

In actively translating 80S ribosomes the ribosomal protein eS7 of the 40S subunit is monoubiquitinated by the E3 ligase Not4 and deubiquitinated by the deubiquitination enzyme Otu2 upon ribosomal subunit recycling. Despite its importance for general efficiency of translation the exact role and structural basis for this specific translational reset are only poorly understood. Here we present biochemical and structural data showing that Otu2 can engage the recycled 40S subunit together with the recycling factors ABCE1 and Tma64 immediately after 60S dissociation for mRNA recycling, and that it dissociates before 48S initiation complex formation. A combined structural analysis of Otu2 and Otu2-40S complexes by X-ray crystallography, AlphaFold2 prediction and cryo-EM revealed how Otu2 can specifically be recruited to the 40S, but not to the 80S ribosome, for removal of the eS7-bound ubiquitin moiety. Here, interactions of the largely helical N-terminal domain of Otu2 to sites that are masked and therefore inaccessible in the 80S ribosome are of crucial importance. Collectively, we provide the structural basis for the Otu2 driven deubiquitination step providing a first mechanistic understanding of this translational reset step during ribosome recycling/(re)initiation.

scholarly journals Structural basis for receptor recognition by New World hemorrhagic fever arenaviruses

2010 ◽  
Vol 17 (4) ◽  
pp. 438-444 ◽  
Author(s):  
Jonathan Abraham ◽  
Kevin D Corbett ◽  
Michael Farzan ◽  
Hyeryun Choe ◽  
Stephen C Harrison
Keyword(s):  
New World ◽  
Hemorrhagic Fever ◽  
Structural Basis ◽  
Receptor Recognition

scholarly journals Convergent immunological solutions to Argentine hemorrhagic fever virus neutralization

2017 ◽  
Vol 114 (27) ◽  
pp. 7031-7036 ◽  
Author(s):  
Antra Zeltina ◽  
Stefanie A. Krumm ◽  
Mehmet Sahin ◽  
Weston B. Struwe ◽  
Karl Harlos ◽  
...  
Keyword(s):  
New World ◽  
Specific Interaction ◽  
Neutralizing Antibody ◽  
Hemorrhagic Fever ◽  
Virus Neutralization ◽  
Structural Basis ◽  
Human Populations ◽  
Binding Modes ◽  
Hemorrhagic Fever Virus ◽  
Human Transferrin Receptor

Transmission of hemorrhagic fever New World arenaviruses from their rodent reservoirs to human populations poses substantial public health and economic dangers. These zoonotic events are enabled by the specific interaction between the New World arenaviral attachment glycoprotein, GP1, and cell surface human transferrin receptor (hTfR1). Here, we present the structural basis for how a mouse-derived neutralizing antibody (nAb), OD01, disrupts this interaction by targeting the receptor-binding surface of the GP1 glycoprotein from Junín virus (JUNV), a hemorrhagic fever arenavirus endemic in central Argentina. Comparison of our structure with that of a previously reported nAb complex (JUNV GP1–GD01) reveals largely overlapping epitopes but highly distinct antibody-binding modes. Despite differences in GP1 recognition, we find that both antibodies present a key tyrosine residue, albeit on different chains, that inserts into a central pocket on JUNV GP1 and effectively mimics the contacts made by the host TfR1. These data provide a molecular-level description of how antibodies derived from different germline origins arrive at equivalent immunological solutions to virus neutralization.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

scholarly journals Identification of V6.51L as a selectivity hotspot in stereoselective A2B adenosine receptor antagonist recognition

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Xuesong Wang ◽  
Willem Jespers ◽  
Rubén Prieto-Díaz ◽  
Maria Majellaro ◽  
Adriaan P. IJzerman ◽  
...  
Keyword(s):  
Radioligand Binding ◽  
Structural Data ◽  
Binding Mode ◽  
Selective Recognition ◽  
Chiral Hplc ◽  
Binding Assays ◽  
Structural Determinants ◽  
X Ray Crystallography ◽  
Adenosine Receptor Antagonist ◽  
Energy Perturbation

AbstractThe four adenosine receptors (ARs) A1AR, A2AAR, A2BAR, and A3AR are G protein-coupled receptors (GPCRs) for which an exceptional amount of experimental and structural data is available. Still, limited success has been achieved in getting new chemical modulators on the market. As such, there is a clear interest in the design of novel selective chemical entities for this family of receptors. In this work, we investigate the selective recognition of ISAM-140, a recently reported A2BAR reference antagonist. A combination of semipreparative chiral HPLC, circular dichroism and X-ray crystallography was used to separate and unequivocally assign the configuration of each enantiomer. Subsequently affinity evaluation for both A2A and A2B receptors demonstrate the stereospecific and selective recognition of (S)-ISAM140 to the A2BAR. The molecular modeling suggested that the structural determinants of this selectivity profile would be residue V2506.51 in A2BAR, which is a leucine in all other ARs including the closely related A2AAR. This was herein confirmed by radioligand binding assays and rigorous free energy perturbation (FEP) calculations performed on the L249V6.51 mutant A2AAR receptor. Taken together, this study provides further insights in the binding mode of these A2BAR antagonists, paving the way for future ligand optimization.

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