The active site of penicillinase from Staphylococcus aureus PC1. Isolation of a specific covalent complex with the substrate quinacillin.
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ABSTRACT:
SUBMITTER: Virden R
PROVIDER: S-EPMC1165633 | biostudies-other | 1975 Aug
REPOSITORIES: biostudies-other
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Project description:The caseinolytic protease is a highly conserved serine protease, seminal in prokaryotic and eukaryotic protein homeostasis and regulatory proteolysis, and a promising antibacterial and anticancer drug target. Here, we describe the cystargolides as potent and the first natural β-lactone inhibitors of the proteolytic core ClpP. Based on the discovery of two clpP genes next to the cystargolide biosynthetic genes in Kitasatospora cystarginea, we explored ClpP as a potential cystargolide target. We show covalent inhibition of Staphylococcus aureus ClpP by cystargolide A and B by different biochemical methods in vitro. Synthesis of semi-synthetic derivatives with improved cell permeability allowed us to confirm ClpP as a specific target within intact S. aureus cells and to demonstrate anti-virulence activity. In Streptomycetes griseus growth inhibition occurs. Crystal structures show cystargolide A covalently bound to all 14 active sites of S. aureus ClpP. Although synthetic β-lactones are known as the pioneering group of ClpP inhibitors, their co-crystallisation has not been successful, so far. The cystargolides now reveal the molecular mechanism of ClpP inhibition by β-lactone inhibitors.
2023-11-30 | PXD045453 | Pride
Project description:The amino acid sequence of the penicillinase (penicillin amido-beta-lactamhydrolase, EC 3.5.2.6) from Staphylococcus aureus strain PC1 was determined. The protein consists of a single polypeptide chain of 257 residues, and the sequence was determined by characterization of tryptic, chymotryptic, peptic and CNBr peptides, with some additional evidence from thermolysin and S. aureus proteinase peptides. A mistake in the preliminary report of the sequence is corrected; residues 113-116 are now thought to be -Lys-Lys-Val-Lys- rather than -Lys-Val-Lys-Lys-. Detailed evidence for the amino acid sequence has been deposited as Supplementary Publication SUP 50056 (91 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1975) 145, 5.
| S-EPMC1172349 | biostudies-other
Project description:1. Growth of Staphylococcus aureus (8325; alphai(-)p(+)), constitutive for the production of penicillinase, in CY medium results in about 40% of the enzyme being free in the medium. By modifying the medium, 98% of the enzyme remains cell-bound. 2. Part of this is bound ionically to the surface of the cell wall and may be liberated instantaneously by certain inorganic anions. Maximum liberation was achieved with either phosphate or arsenate, both of which showed marked pH-dependence. 3. Polyanions that do not penetrate the cell wall, such as heparin, RNA and dextran sulphate, are also effective in liberating penicillinase. 4. Polyanions added to the growth medium prevent the appearance of ionically bound penicillinase owing to their strong affinity for the sites on the cell wall required for binding of the enzyme.
| S-EPMC1270322 | biostudies-other
Project description:Genetically encoded non-canonical amino acids are powerful tools of protein research and engineering; in particular they allow substitution of individual chemical groups or atoms in a protein of interest. One such amino acid is the tryptophan (Trp) analog 3-benzothienyl-l-alanine (Bta) with an imino-to-sulfur substitution in the five-membered ring. Unlike Trp, Bta is not capable of forming a hydrogen bond, but preserves other properties of a Trp residue. Here we present a pyrrolysyl-tRNA synthetase-derived, engineered enzyme BtaRS that enables efficient and site-specific Bta incorporation into proteins of interest in vivo. Furthermore, we report a 2.1 Å-resolution crystal structure of a BtaRS•Bta complex to show how BtaRS discriminates Bta from canonical amino acids, including Trp. To show utility in protein mutagenesis, we used BtaRS to introduce Bta to replace the Trp28 residue in the active site of Staphylococcus aureus thioredoxin. This experiment showed that not the hydrogen bond between residues Trp28 and Asp58, but the bulky aromatic side chain of Trp28 is important for active site maintenance. Collectively, our study provides a new and robust tool for checking the function of Trp in proteins.
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Project description:1. A further fraction of ;cell-bound exopenicillinase', in addition to that bound ionically to the surface of the cell wall, has been identified in Staphylococcus aureus. 2. Treatment of cells with low concentrations (0.01m) of organic anions liberates part of this exopenicillinase, such liberation being dependent on both time and temperature, but independent of an external supply of energy. 3. Tricarboxylic acids tend to be more effective than dicarboxylic or monocarboxylic, although there are large differences between ionic species even when tested at the same normalities.
| S-EPMC1270323 | biostudies-other
Project description:Sortase cysteine transpeptidases covalently attach proteins to the bacterial cell wall or assemble fiber-like pili that promote bacterial adhesion. Members of this enzyme superfamily are widely distributed in Gram-positive bacteria that frequently utilize multiple sortases to elaborate their peptidoglycan. Sortases catalyze transpeptidation using a conserved active site His-Cys-Arg triad that joins a sorting signal located at the C terminus of their protein substrate to an amino nucleophile located on the cell surface. However, despite extensive study, the catalytic mechanism and molecular basis of substrate recognition remains poorly understood. Here we report the crystal structure of the Staphylococcus aureus sortase B enzyme in a covalent complex with an analog of its NPQTN sorting signal substrate, revealing the structural basis through which it displays the IsdC protein involved in heme-iron scavenging from human hemoglobin. The results of computational modeling, molecular dynamics simulations, and targeted amino acid mutagenesis indicate that the backbone amide of Glu(224) and the side chain of Arg(233) form an oxyanion hole in sortase B that stabilizes high energy tetrahedral catalytic intermediates. Surprisingly, a highly conserved threonine residue within the bound sorting signal substrate facilitates construction of the oxyanion hole by stabilizing the position of the active site arginine residue via hydrogen bonding. Molecular dynamics simulations and primary sequence conservation suggest that the sorting signal-stabilized oxyanion hole is a universal feature of enzymes within the sortase superfamily.
| S-EPMC3979406 | biostudies-literature
Project description:BackgroundStaphylococcus aureus is a Gram-positive, pathogenic bacterium that causes a wide range of symptoms in humans and can form biofilm, which is a multicellular community of microorganisms that attaches to nonbiological and biological surfaces.MethodsHere, we aimed to isolate and characterize an S. aureus phage and examine the bactericidal activity alone and in conjunction with streptomycin treatment.ResultsWe isolated a virulent phage, WV, from a slaughterhouse in Jiangsu, China. This strain belonged to the family Myoviridae and presented a genome size of 141,342 bp. The optimal pH of the preservation buffer was 6-7, optimal growth temperature was 37°C, and optimal multiplicity of infection was 0.01. Phage WV can sterilize most clinical strains of S. aureus that had been isolated from clinical patients in the First People's Hospital of the Yunnan Province. Against low-concentration S. aureus culture, streptomycin demonstrated a greater antibiofilm effect than that of phage WV. By contrast, in high-concentration S. aureus culture, phage WV demonstrated greater antibiofilm effect than that of streptomycin. The use of phage WV and streptomycin together had a substantially greater overall antibiofilm effect than that achieved using either component alone.ConclusionThis study provides strong evidence for the effectiveness of phage application for the reduction of S. aureus biofilm growth and suggests that phages can be considered as a viable alternative to antibiotics in clinical settings.
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Project description:Increasing evidence shows that active sites of proteins have non-trivial conformational dynamics. These dynamics include active site residues sampling different local conformations that allow for multiple, and possibly novel, inhibitor binding poses. Yet, active site dynamics garner only marginal attention in most inhibitor design efforts and exert little influence on synthesis strategies. This is partly because synthesis requires a level of atomic structural detail that is frequently missing in current characterizations of conformational dynamics. In particular, while the identity of the mobile protein residues may be clear, the specific conformations they sample remain obscure. Here, we show how an appropriate choice of ligand can significantly sharpen our abilities to describe the interconverting binding poses (conformations) of protein active sites. Specifically, we show how 2-(2'-carboxyphenyl)-benzoyl-6-aminopenicillanic acid (CBAP) exposes otherwise hidden dynamics of a protein active site that binds β-lactam antibiotics. When CBAP acylates (binds) the active site serine of the β-lactam sensor domain of BlaR1 (BlaRS), it shifts the time scale of the active site dynamics to the slow exchange regime. Slow exchange enables direct characterization of inter-converting protein and bound ligand conformations using NMR methods. These methods include chemical shift analysis, 2-d exchange spectroscopy, off-resonance ROESY of the bound ligand, and reduced spectral density mapping. The active site architecture of BlaRS is shared by many β-lactamases of therapeutic interest, suggesting CBAP could expose functional motions in other β-lactam binding proteins. More broadly, CBAP highlights the utility of identifying chemical probes common to structurally homologous proteins to better expose functional motions of active sites.
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Project description:The pH- and temperature-dependence of steady-state kinetic parameters for 6-beta-(2-furyl)-acryloylamido-penicillanic acid showed it to be a good substrate of staphylococcal PC1 beta-lactamase, and the viscosity-dependence of K(m)/k(cat) indicated that steps up to the formation of the acyl-enzyme were partially diffusion-limited. In the pH range 4-9, a pre-steady-state transient blue shift in the UV absorption spectrum of the bound furyl-acryloylamido chromophore was of constant amplitude and decayed to the spectrum of the product with a first-order rate constant equal to k(cat). The spectrum of the isolated denatured acyl-enzyme was similar to that of the methyl ester of furyl-acryloylpenicilloic acid, pointing to non-covalent interactions with the folded protein, possibly associated with the charge on Glu-166, as the source of the blue-shifted spectrum. Taken together, these results point to a rapid acylation and slower deacylation at Ser-70 and imply that ionization of groups affecting enzyme activity at alkaline pH, for which likely candidates are Lys-73 and Lys-234, affect the rate of deacylation.
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Project description:Dengue virus (DENV) protease is an attractive target for drug development; however, no compounds have reached clinical development to date. In this study, we utilized a potent West Nile virus protease inhibitor of the pyrazole ester derivative class as a chemical starting point for DENV protease drug development. Compound potency and selectivity for DENV protease were improved through structure-guided small molecule optimization, and protease-inhibitor binding interactions were validated biophysically using nuclear magnetic resonance. Our work strongly suggests that this class of compounds inhibits flavivirus protease through targeted covalent modification of active site serine, contrary to an allosteric binding mechanism as previously described.
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