scholarly journals Structure and function of the Toscana virus cap-snatching endonuclease

2019 ◽  
Vol 47 (20) ◽  
pp. 10914-10930 ◽  
Author(s):  
Rhian Jones ◽  
Sana Lessoued ◽  
Kristina Meier ◽  
Stéphanie Devignot ◽  
Sergio Barata-García ◽  
...  
Keyword(s):  
Metal Ion ◽  
Rna Virus ◽  
Rift Valley Fever Virus ◽  
Substrate Binding ◽  
Functional Characterization ◽  
Structure And Function ◽  
Human Pathogens ◽  
Toscana Virus ◽  
Valley Fever ◽  
And Function

Abstract Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important human pathogens such as Rift Valley fever virus (RVFV). Here, we carried out a structural and functional characterization of the TOSV cap-snatching endonuclease, an N terminal domain of the viral polymerase (L protein) that provides capped 3′OH primers for transcription. We report TOSV endonuclease crystal structures in the apo form, in complex with a di-ketoacid inhibitor (DPBA) and in an intermediate state of inhibitor release, showing details on substrate binding and active site dynamics. The structure reveals substantial folding rearrangements absent in previously reported cap-snatching endonucleases. These include the relocation of the N terminus and the appearance of new structural motifs important for transcription and replication. The enzyme shows high activity rates comparable to other His+ cap-snatching endonucleases. Moreover, the activity is dependent on conserved residues involved in metal ion and substrate binding. Altogether, these results bring new light on the structure and function of cap-snatching endonucleases and pave the way for the development of specific and broad-spectrum antivirals.

Chitosanase from Streptomyces sp. strain N174: a comparative review of its structure and function

1997 ◽  
Vol 75 (6) ◽  
pp. 687-696 ◽  
Author(s):  
Tamo Fukamizo ◽  
Ryszard Brzezinski
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Substrate Binding ◽  
Structure And Function ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Streptomyces Sp ◽  
Binding Cleft ◽  
And Function

Novel information on the structure and function of chitosanase, which hydrolyzes the beta -1,4-glycosidic linkage of chitosan, has accumulated in recent years. The cloning of the chitosanase gene from Streptomyces sp. strain N174 and the establishment of an efficient expression system using Streptomyces lividans TK24 have contributed to these advances. Amino acid sequence comparisons of the chitosanases that have been sequenced to date revealed a significant homology in the N-terminal module. From energy minimization based on the X-ray crystal structure of Streptomyces sp. strain N174 chitosanase, the substrate binding cleft of this enzyme was estimated to be composed of six monosaccharide binding subsites. The hydrolytic reaction takes place at the center of the binding cleft with an inverting mechanism. Site-directed mutagenesis of the carboxylic amino acid residues that are conserved revealed that Glu-22 and Asp-40 are the catalytic residues. The tryptophan residues in the chitosanase do not participate directly in the substrate binding but stabilize the protein structure by interacting with hydrophobic and carboxylic side chains of the other amino acid residues. Structural and functional similarities were found between chitosanase, barley chitinase, bacteriophage T4 lysozyme, and goose egg white lysozyme, even though these proteins share no sequence similarities. This information can be helpful for the design of new chitinolytic enzymes that can be applied to carbohydrate engineering, biological control of phytopathogens, and other fields including chitinous polysaccharide degradation. Key words: chitosanase, amino acid sequence, overexpression system, reaction mechanism, site-directed mutagenesis.

scholarly journals Unique structure and function of viral rhodopsins

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Dmitry Bratanov ◽  
Kirill Kovalev ◽  
Jan-Philipp Machtens ◽  
Roman Astashkin ◽  
Igor Chizhov ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Structure And Function ◽  
Proton Donor ◽  
Dna Viruses ◽  
Host Interactions ◽  
Hydrophobic Barrier ◽  
High Resolution Structure ◽  
Group 2 ◽  
Marine Protists ◽  
And Function

Abstract Recently, two groups of rhodopsin genes were identified in large double-stranded DNA viruses. The structure and function of viral rhodopsins are unknown. We present functional characterization and high-resolution structure of an Organic Lake Phycodnavirus rhodopsin II (OLPVRII) of group 2. It forms a pentamer, with a symmetrical, bottle-like central channel with the narrow vestibule in the cytoplasmic part covered by a ring of 5 arginines, whereas 5 phenylalanines form a hydrophobic barrier in its exit. The proton donor E42 is placed in the helix B. The structure is unique among the known rhodopsins. Structural and functional data and molecular dynamics suggest that OLPVRII might be a light-gated pentameric ion channel analogous to pentameric ligand-gated ion channels, however, future patch clamp experiments should prove this directly. The data shed light on a fundamentally distinct branch of rhodopsins and may contribute to the understanding of virus-host interactions in ecologically important marine protists.

Structure and Function of the Xenobiotic Substrate-Binding Site and Location of a Potential Non-Substrate-Binding Site in a Class π GlutathioneS-Transferase†,‡

Biochemistry ◽  
1997 ◽  
Vol 36 (32) ◽  
pp. 9690-9702 ◽  
Author(s):  
Xinhua Ji ◽  
Maria Tordova ◽  
Rosemary O'Donnell ◽  
James F. Parsons ◽  
Janet B. Hayden ◽  
...  
Keyword(s):  
Binding Site ◽  
Substrate Binding ◽  
Structure And Function ◽  
Substrate Binding Site ◽  
And Function

scholarly journals A ΩXaV motif in the Rift Valley fever virus NSs protein is essential for degrading p62, forming nuclear filaments and virulence

2015 ◽  
Vol 112 (19) ◽  
pp. 6021-6026 ◽  
Author(s):  
Normand Cyr ◽  
Cynthia de la Fuente ◽  
Lauriane Lecoq ◽  
Irene Guendel ◽  
Philippe R. Chabot ◽  
...  
Keyword(s):  
Rift Valley ◽  
Rift Valley Fever ◽  
Excision Repair ◽  
Rna Virus ◽  
Nonstructural Protein ◽  
Rift Valley Fever Virus ◽  
Hemorrhagic Fever ◽  
Fever Virus ◽  
Valley Fever ◽  
Infected Cells

Rift Valley fever virus (RVFV) is a single-stranded RNA virus capable of inducing fatal hemorrhagic fever in humans. A key component of RVFV virulence is its ability to form nuclear filaments through interactions between the viral nonstructural protein NSs and the host general transcription factor TFIIH. Here, we identify an interaction between a ΩXaV motif in NSs and the p62 subunit of TFIIH. This motif in NSs is similar to ΩXaV motifs found in nucleotide excision repair (NER) factors and transcription factors known to interact with p62. Structural and biophysical studies demonstrate that NSs binds to p62 in a similar manner as these other factors. Functional studies in RVFV-infected cells show that the ΩXaV motif is required for both nuclear filament formation and degradation of p62. Consistent with the fact that the RVFV can be distinguished from otherBunyaviridae-family viruses due to its ability to form nuclear filaments in infected cells, the motif is absent in the NSs proteins of otherBunyaviridae-family viruses. Taken together, our studies demonstrate that p62 binding to NSs through the ΩXaV motif is essential for degrading p62, forming nuclear filaments and enhancing RVFV virulence. In addition, these results show how the RVFV incorporates a simple motif into the NSs protein that enables it to functionally mimic host cell proteins that bind the p62 subunit of TFIIH.

scholarly journals Polyamines and Hypusination Are Required for Ebolavirus Gene Expression and Replication

mBio ◽  
2016 ◽  
Vol 7 (4) ◽  
Author(s):  
Michelle E. Olsen ◽  
Claire Marie Filone ◽  
Dan Rozelle ◽  
Chad E. Mire ◽  
Krystle N. Agans ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Virus ◽  
Hemorrhagic Fever ◽  
Cell Types ◽  
Host Protein ◽  
Initiation Factor ◽  
Virus Protein ◽  
Human Pathogens ◽  
Viral Polymerase ◽  
And Function

ABSTRACTEbolavirus (EBOV) is an RNA virus that is known to cause severe hemorrhagic fever in humans and other primates.EBOV successfully enters and replicates in many cell types. This replication is dependent on the virus successfully coopting a number of cellular factors. Many of these factors are currently unidentified but represent potential targets for antiviral therapeutics. Here we show that cellular polyamines are critical for EBOV replication. We found that small-molecule inhibitors of polyamine synthesis block gene expression driven by the viral RNA-dependent RNA polymerase. Short hairpin RNA (shRNA) knockdown of the polyamine pathway enzyme spermidine synthase also resulted in reduced EBOV replication. These findings led us to further investigate spermidine, a polyamine that is essential for the hypusination of eukaryotic initiation factor 5A (eIF5A). Blocking the hypusination of eIF5A (and thereby inhibiting its function) inhibited both EBOV gene expression and viral replication. The mechanism appears to be due to the importance of hypusinated eIF5A for the accumulation of VP30, an essential component of the viral polymerase. The same reduction in hypusinated eIF5A did not alter the accumulation of other viral polymerase components. This action makes eIF5A function an important gate for proper EBOV polymerase assembly and function through the control of a single virus protein.IMPORTANCEEbolavirus (EBOV) is one of the most lethal human pathogens known. EBOV requires host factors for replication due to its small RNA genome. Here we show that the host protein eIF5A in its activated form is necessary for EBOV replication. We further show that the mechanism is through the accumulation of a single EBOV protein, VP30. To date, no other host proteins have been shown to interfere with the translation or stability of an EBOV protein. Activated eIF5A is the only protein in the cell known to contain the specific modification of hypusine; therefore, this pathway is a target for drug development. Further investigation into the mechanism of eIF5A interaction with VP30 could provide insight into therapeutics to combat EBOV.

scholarly journals Solvation dynamics-powered structure and function of multi-molecular cellular systems exemplified by non-equilibrium cereblon-degrader-CK1α ternary complex formation

2021 ◽  
Author(s):  
Hongbin Wan ◽  
Vibhas Aravamuthan ◽  
Sarah Williams ◽  
Charles Wartchow ◽  
Jose Duca ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Rate Constant ◽  
Surface Composition ◽  
Substrate Binding ◽  
Structure And Function ◽  
Enzyme Activation ◽  
Cellular Systems ◽  
State Transitions ◽  
Solvation Dynamics ◽  
And Function

Cellular functions are executed via a form of analog computing that is based on the switchable covalent and non-covalent states of multi-molecular fluxes (i.e., time-dependent species/state concentrations) operating in the non-linear dynamics regime. We and others have proposed that the non-covalent states and state transitions of aqueous fluxes are powered principally by the storage and release of potential energy to/from the anisotropic H-bond network of solvating water (which we refer to as the 'solvation field'), which is a key tenet of a first principles theory on cellular structure and function (called Biodynamics) that we outlined previously. This energy is reflected in water occupancy as a function of solute surface position, which can be probed computationally using WATMD software. In our previous work, we used this approach to deduce the structural dynamics of the COVID main protease, including substrate binding-induced enzyme activation and dimerization, and product release-induced dimer dissociation. Here, we examine: 1) The general relationships between surface composition/topology and solvation field properties for both high and low molecular weight (HMW and LMW) solutes. 2) The general means by which structural dynamics are powered by solvation free energy, which we exemplify via binding between the E3 ligase CUL4A/RBX1/DDB1/CRBN, LMW degraders, and substrates. We propose that degraders organize the substrate binding surface of cereblon toward complementarity with native and neo substrates, thereby speeding the association rate constant and incrementally slowing the dissociation rate constant. 3) Structure-activity relationships (SAR) based on complementarity between the solvation fields of cognate protein-ligand partners exemplified via LMW degraders.

scholarly journals Virion-associated spermidine transmits with Rift Valley fever virus particles to maintain infectivity

2020 ◽  
Author(s):  
Vincent Mastrodomenico ◽  
Jeremy J. Esin ◽  
Shefah Qazi ◽  
Oreoluwa S. Omoba ◽  
Brittany L. Fung ◽  
...  
Keyword(s):  
Virus Replication ◽  
Rift Valley ◽  
Rift Valley Fever ◽  
Rna Virus ◽  
Rift Valley Fever Virus ◽  
Acid Synthesis ◽  
Fever Virus ◽  
Virus Infectivity ◽  
Cellular Functions ◽  
Valley Fever

AbstractViruses require host cell metabolites to productively infect, and the mechanisms by which viruses usurp these molecules is diverse. One group of cellular metabolites important in virus infection is the polyamines, small positively-charged molecules involved in cell cycle, translation, and nucleic acid synthesis, among other cellular functions. Polyamines also support replication of diverse viruses, and they are important for processes such as transcription, translation, and viral protein enzymatic activity. Rift Valley fever virus (RVFV) is a negative-sense RNA virus that requires polyamines to produce infectious particles. In polyamine depleted conditions, noninfectious particles are produced that interfere with virus replication and stimulate immune signaling. Here, we find that RVFV relies on virion-associated polyamines to maintain infectivity. We show that RVFV replication is facilitated by any of the three biogenic polyamines; however, we specifically find spermidine associated with purified virions. Using a panel of polyamine homologs, we observe that virions can also associate with (R)-3-methylspermidine and norspermidine, though not with other less homologous molecules. Using polyamine reporter cells, we demonstrate that virion-associated polyamines transmit from one infected cell to another. Finally, we find that virions devoid of polyamines are unstable and cannot be supplemented with exogenous polyamines to regain stability or infectivity. These data highlight a unique role for polyamines, and spermidine in particular, in maintaining virus infectivity, a function not previously appreciated. Further, these studies are the first to identify polyamines associated with RVFV virions. Targeting polyamines represents a promising antiviral strategy, and this work highlights a new mechanism by which we can inhibit virus replication through FDA-approved polyamine depleting pharmaceuticals.

scholarly journals Novel Ionophores Active against La Crosse Virus Identified through Rapid Antiviral Screening

2020 ◽  
Vol 64 (6) ◽  
Author(s):  
Zachary J. Sandler ◽  
Mason R. Firpo ◽  
Oreoluwa S. Omoba ◽  
Michelle N. Vu ◽  
Vineet D. Menachery ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Virus Replication ◽  
Viral Infections ◽  
Rift Valley Fever Virus ◽  
Virus Titer ◽  
Potassium Ions ◽  
Dependent Manner ◽  
La Crosse Virus ◽  
Human Pathogens ◽  
Valley Fever

ABSTRACT Bunyaviruses are significant human pathogens, causing diseases ranging from hemorrhagic fevers to encephalitis. Among these viruses, La Crosse virus (LACV), a member of the California serogroup, circulates in the eastern and midwestern United States. While LACV infection is often asymptomatic, dozens of cases of encephalitis are reported yearly. Unfortunately, no antivirals have been approved to treat LACV infection. Here, we developed a method to rapidly test potential antivirals against LACV infection. From this screen, we identified several potential antiviral molecules, including known antivirals. Additionally, we identified many novel antivirals that exhibited antiviral activity without affecting cellular viability. Valinomycin, a potassium ionophore, was among our top targets. We found that valinomycin exhibited potent anti-LACV activity in multiple cell types in a dose-dependent manner. Valinomycin did not affect particle stability or infectivity, suggesting that it may preclude virus replication by altering cellular potassium ions, a known determinant of LACV entry. We extended these results to other ionophores and found that the antiviral activity of valinomycin extended to other viral families, including bunyaviruses (Rift Valley fever virus, Keystone virus), enteroviruses (coxsackievirus, rhinovirus), flavirivuses (Zika virus), and coronaviruses (human coronavirus 229E [HCoV-229E] and Middle East respiratory syndrome CoV [MERS-CoV]). In all viral infections, we observed significant reductions in virus titer in valinomycin-treated cells. In sum, we demonstrate the importance of potassium ions to virus infection, suggesting a potential therapeutic target to disrupt virus replication.

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