Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structural origins of gentamicin antibiotic action.

ABSTRACT: Aminoglycoside antibiotics that bind to the ribosomal A site cause misreading of the genetic code and inhibit translocation. The clinically important aminoglycoside, gentamicin C, is a mixture of three components. Binding of each gentamicin component to the ribosome and to a model RNA oligonucleotide was studied biochemically and the structure of the RNA complexed to gentamicin C1a was solved using magnetic resonance nuclear spectroscopy. Gentamicin C1a binds in the major groove of the RNA. Rings I and II of gentamicin direct specific RNA-drug interactions. Ring III of gentamicin, which distinguishes this subclass of aminoglycosides, also directs specific RNA interactions with conserved base pairs. The structure leads to a general model for specific ribosome recognition by aminoglycoside antibiotics and a possible mechanism for translational inhibition and miscoding. This study provides a structural rationale for chemical synthesis of novel aminoglycosides.

SUBMITTER: Yoshizawa S

PROVIDER: S-EPMC1170992 | biostudies-other | 1998 Nov

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Publications

Structural origins of gentamicin antibiotic action.

Yoshizawa S S Fourmy D D Puglisi J D JD

The EMBO journal 19981101 22

Aminoglycoside antibiotics that bind to the ribosomal A site cause misreading of the genetic code and inhibit translocation. The clinically important aminoglycoside, gentamicin C, is a mixture of three components. Binding of each gentamicin component to the ribosome and to a model RNA oligonucleotide was studied biochemically and the structure of the RNA complexed to gentamicin C1a was solved using magnetic resonance nuclear spectroscopy. Gentamicin C1a binds in the major groove of the RNA. Ring ...[more]

PMID: 9822590

Similar Datasets

Structural basis for plazomicin antibiotic action and resistance.

Project description:The approval of plazomicin broadened the clinical library of aminoglycosides available for use against emerging bacterial pathogens. Contrarily to other aminoglycosides, resistance to plazomicin is limited; still, instances of resistance have been reported in clinical settings. Here, we present structural insights into the mechanism of plazomicin action and the mechanisms of clinical resistance. The structural data reveal that plazomicin exclusively binds to the 16S ribosomal A site, where it likely interferes with the fidelity of mRNA translation. The unique extensions to the core aminoglycoside scaffold incorporated into the structure of plazomicin do not interfere with ribosome binding, which is analogously seen in the binding of this antibiotic to the AAC(2')-Ia resistance enzyme. The data provides a structural rationale for resistance conferred by drug acetylation and ribosome methylation, i.e., the two mechanisms of resistance observed clinically. Finally, the crystal structures of plazomicin in complex with both its target and the clinically relevant resistance factor provide a roadmap for next-generation drug development that aims to ameliorate the impact of antibiotic resistance.

| S-EPMC8195987 | biostudies-literature

Silica-Gentamicin Nanohybrids: Synthesis and Antimicrobial Action.

Project description:Orthopedic applications commonly require the administration of systemic antibiotics. Gentamicin is one of the most commonly used aminoglycosides in the treatment and prophylaxis of infections associated with orthopedic applications, but gentamicin has a short half-life. However, silica nanoparticles (SiO₂ NPs) can be used as elegant carriers for antibiotics to prolong their release. Our goal is the preparation and characterization of SiO₂-gentamicin nanohybrids for their potential antimicrobial administration in orthopedic applications. In vitro gentamicin release profile from the nanohybrids (gentamicin-conjugated SiO₂ NPs) prepared by the base-catalyzed precipitation exhibited fast release (21.4%) during the first 24 h and further extension with 43.9% release during the five-day experiment. Antimicrobial studies of the SiO₂-gentamicin nanohybrids versus native SiO₂ NPs and free gentamicin were performed against Bacillus subtilis (B. subtilis), Pseudomonas fluorescens (P. fluorescens) and Escherichia coli (E. coli). SiO₂-gentamicin nanohybrids were most effective against B. subtilis. SiO₂ NPs play no antimicrobial role. Parallel antimicrobial studies for the filter-sterilized gentamicin were performed to assess the effect of ultraviolet (UV)-irradiation on gentamicin. In summary, the initial fast gentamicin release fits the need for high concentration of antibiotics after orthopedic surgical interventions. Moreover, the extended release justifies the promising antimicrobial administration of the nanohybrids in bone applications.

| S-EPMC5456682 | biostudies-literature

Delineating the biosynthesis of gentamicin x2, the common precursor of the gentamicin C antibiotic complex.

Project description:Gentamicin C complex is a mixture of aminoglycoside antibiotics used worldwide to treat severe Gram-negative bacterial infections. Despite its clinical importance, the enzymology of its biosynthetic pathway has remained obscure. We report here insights into the four enzyme-catalyzed steps that lead from the first-formed pseudotrisaccharide gentamicin A2 to gentamicin X2, the last common intermediate for all components of the C complex. We have used both targeted mutations of individual genes and reconstitution of portions of the pathway in vitro to show that the secondary alcohol function at C-3″ of A2 is first converted to an amine, catalyzed by the tandem operation of oxidoreductase GenD2 and transaminase GenS2. The amine is then specifically methylated by the S-adenosyl-l-methionine (SAM)-dependent N-methyltransferase GenN to form gentamicin A. Finally, C-methylation at C-4″ to form gentamicin X2 is catalyzed by the radical SAM-dependent and cobalamin-dependent enzyme GenD1.

| S-EPMC4340712 | biostudies-literature

Structural insight into the antibiotic action of telithromycin against resistant mutants.

Project description:The crystal structure of the ketolide telithromycin bound to the Deinococcus radiodurans large ribosomal subunit shows that telithromycin blocks the ribosomal exit tunnel and interacts with domains II and V of the 23S RNA. Comparisons to other clinically relevant macrolides provided structural insights into its enhanced activity against macrolide-resistant strains.

| S-EPMC164882 | biostudies-literature

Zika Virus: Origins, Pathological Action, and Treatment Strategies.

Project description:The Zika virus (ZIKV) global epidemic prompted the World Health Organization to declare it a 2016 Public Health Emergency of International Concern. The overwhelming experience over the past several years teaches us that ZIKV and the associated neurological complications represent a long-term world-wide challenge to public health. Although the number of ZIKV cases in the Western Hemisphere has dropped since 2016, the need for basic research and anti-ZIKV drug development remains strong. Re-emerging viruses like ZIKV are an ever-present threat in the 21st century where fast transcontinental travel lends itself to viral epidemics. Here, we first present the origin story for ZIKV and review the rapid progress researchers have made toward understanding of the ZIKV pathology and in the design, re-purposing, and testing-particularly in vivo-drug candidates for ZIKV prophylaxis and therapy ZIKV. Quite remarkably, a short, but intensive, drug-repurposing effort has already resulted in several readily available FDA-approved drugs that are capable of effectively combating the virus in infected adult mouse models and, most importantly, in both preventing maternal-fetal transmission and severe microcephaly in newborns in pregnant mouse models.

| S-EPMC6330993 | biostudies-literature

Structural Origins of Silk Piezoelectricity.

Project description:Uniaxially oriented, piezoelectric silk films were prepared by a two-step method that involved: (1) air drying aqueous, regenerated silk fibroin solutions into films, and (2) drawing the silk films to a desired draw ratio. The utility of two different drawing techniques, zone drawing and water immersion drawing were investigated for processing the silk for piezoelectric studies. Silk films zone drawn to a ratio of ?= 2.7 displayed relatively high dynamic shear piezoelectric coefficients of d(14) = -1.5 pC/N, corresponding to over two orders of magnitude increase in d(14) due to film drawing. A strong correlation was observed between the increase in the silk II, ?-sheet content with increasing draw ratio measured by FTIR spectroscopy (C(?)? e(2.5) (?)), the concomitant increasing degree of orientation of ?-sheet crystals detected via WAXD (FWHM = 0.22° for ?= 2.7), and the improvement in silk piezoelectricity (d(14)? e(2.4) (?)). Water immersion drawing led to a predominantly silk I structure with a low degree of orientation (FWHM = 75°) and a much weaker piezoelectric response compared to zone drawing. Similarly, increasing the ?-sheet crystallinity without inducing crystal alignment, e.g. by methanol treatment, did not result in a significant enhancement of silk piezoelectricity. Overall, a combination of a high degree of silk II, ?-sheet crystallinity and crystalline orientation are prerequisites for a strong piezoelectric effect in silk. Further understanding of the structural origins of silk piezoelectricity will provide important options for future biotechnological and biomedical applications of this protein.

| S-EPMC3546528 | biostudies-literature

Synergistic action of gentamicin and bacteriophage in a continuous culture population of Staphylococcus aureus.

Project description:With the increasing frequency of antibiotic resistance and the decreasing frequency of new antibiotics entering the market, interest has returned to developing bacteriophage as a therapeutic agent. Acceptance of phage therapy, however, is limited by the unknown pharmacodynamics of a replicating agent, as well as the potential for the evolution of resistant bacteria. One way to overcome some of these limitations is to incorporate phage and antibiotics into a dual therapy regimen; however, this increases the complexity of the pharmacodynamics. The aim of this study is to develop an experimental system to evaluate the pharmacodynamics of dual phage-drug therapy. A continuous culture system for Staphylococcus aureus is used to simulate the pharmacokinetics of periodic antibiotic dosing alone and in combination with lytic phage. A computer model representation of the system allows further evaluation of the conditions governing the observed pharmacodynamics. The results of this experimental/modeling approach suggest that dual therapy can be more efficacious than single therapies, particularly if there is an overlap in the physiological pathways targeted by the individual agents. In this case, treatment with gentamicin induces a population of cells with a strong aggregation phenotype. These aggregators also have an increased ability to form biofilm, which is a well-known, non-genetic mechanism of drug resistance. However, the aggregators are also more susceptible than the parental strain to the action of the phage. Thus, dual treatment with gentamicin and phage resulted in lower final cell densities than either treatment alone. Unlike in the phage-only treatment, phage-resistant isolates were not detected in the dual treatment.

| S-EPMC3511404 | biostudies-literature

Synthesis of Gentamicin Minor Components: Gentamicin B1 and Gentamicin X2.

Project description:The clinical aminoglycoside antibiotic gentamicin is a mixture of several difficult-to-separate major and minor components. The relative inaccessibility of the minor components in particular complicates efforts to separate antibacterial activity from nephro- and/or ototoxicity and to clarify the origin of the potentially therapeutically important read-through activity. With a view to facilitating such studies, the synthesis of a fully and selectively protected garamine-based acceptor has been developed from readily available sisomicin. Glycosylation of this acceptor with a 6-azido-6,7-dideoxy-d-glycero-d-glucoheptopyranosyl donor affords gentamicin B1 after deprotection, whereas employment of a 2-azido-2-deoxy-d-glucopyranosyl donor under N,N-dimethylformamide-directed glycosylation conditions affords gentamicin X2 after deprotection.

| S-EPMC7237068 | biostudies-literature

Structural origins of adenine-tract bending.

Project description:DNA sequences containing short adenine tracts are intrinsically curved and play a role in transcriptional regulation. Despite many high-resolution NMR and x-ray studies, the origins of curvature remain disputed. Long-range restraints provided by 85 residual dipolar couplings were measured for a DNA decamer containing an adenine (A)(4)-tract and used to refine the structure. The overall bend in the molecule is a result of in-phase negative roll in the A-tract and positive roll at its 5' junction, as well as positive and negative tilt inside the A-tract and near its junctions. The bend magnitude and direction obtained from NMR structures is 9.0 degrees into the minor groove in a coordinate frame located at the third AT base pair. We evaluated long-range and wedge models for DNA curvature and concluded that our data for A-tract curvature are best explained by a "delocalized bend" model. The global bend magnitude and direction of the NMR structure are in excellent agreement with the junction model parameters used to rationalize gel electrophoretic data and with preliminary results of a cyclization kinetics assay from our laboratory.

| S-EPMC151347 | biostudies-literature

Structural origins of cartilage shear mechanics.

Project description:Articular cartilage is a remarkable material able to sustain millions of loading cycles over decades of use outperforming any synthetic substitute. Crucially, how extracellular matrix constituents alter mechanical performance, particularly in shear, remains poorly understood. Here, we present experiments and theory in support of a rigidity percolation framework that quantitatively describes the structural origins of cartilage's shear properties and how they arise from the mechanical interdependence of the collagen and aggrecan networks making up its extracellular matrix. This framework explains that near the cartilage surface, where the collagen network is sparse and close to the rigidity threshold, slight changes in either collagen or aggrecan concentrations, common in early stages of cartilage disease, create a marked weakening in modulus that can lead to tissue collapse. More broadly, this framework provides a map for understanding how changes in composition throughout the tissue alter its shear properties and ultimate in vivo function.

| S-EPMC8836800 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data