Photoinactivation of the Staphylococcus aureus Lactose-Specific EIICB Phosphotransferase Component with p-azidophenyl-β-D-Galactoside and Phosphorylation of the Covalently Bound Substrate

2018 ◽  
Vol 28 (3) ◽  
pp. 147-158
Author(s):  
Gina Sossna-Wunder ◽  
Wolfgang Hengstenberg ◽  
Pierre Briozzo ◽  
Josef Deutscher
Keyword(s):  
Staphylococcus Aureus ◽  
Sequence Data ◽  
Uv Light ◽  
Acid Resistance ◽  
Binding Pocket ◽  
Phosphoryl Group ◽  
Phosphotransferase System ◽  
Substrate Binding Pocket ◽  
Hydrolysis Of ◽  
Covalently Bound

<b><i>Background:</i></b> The phosphoenolpyruvate (PEP):lactose phosphotransferase system of<i> Staphylococcus aureus</i> transports and phosphorylates lactose and various phenylgalactosides. Their phosphorylation is catalyzed by the Cys476-phosphorylated EIIB domain of the lactose-specific permease enzyme IICB (EIICB<sup>Lac</sup>). Phosphorylation causes the release of galactosides bound to the EIIC domain into the cytoplasm by a mechanism not yet understood. <b><i>Results:</i></b> Irradiation of a reaction mixture containing the photoactivatable <i>p</i>-azidophenyl-β-D-galactopyranoside and EIICB<sup>Lac</sup> with UV light caused a loss of EIICB<sup>Lac</sup> activity. Nevertheless, photoinactivated EIICB<sup>Lac</sup> could still be phosphorylated with [<sup>32</sup>P]PEP. Proteolysis of photoinactivated [<sup>32</sup>P]P-EIICB<sup>Lac</sup> with subtilisin provided an 11-kDa radioactive peptide. Only the sequence of its first three amino acids (-H-G-P-, position 245–247) could be determined. They are part of the substrate binding pocket in EIICs of the lactose/cellobiose PTS family. Surprisingly, while acid treatment caused hydrolysis of the phosphoryl group in active [<sup>32</sup>P]P∼EIICB<sup>Lac</sup>, photoinactivated [<sup>32</sup>P]P-EIICB<sup>Lac</sup> remained strongly phosphorylated. <b><i>Conclusion:</i></b> Phosphorylation of the –OH group at C6 of <i>p</i>-nitrenephenyl-β-D-galactopyranoside covalently bound to EIIC<sup>Lac</sup> by the histidyl-phosphorylated [<sup>32</sup>P]P∼EIIB<sup>Lac</sup> domain is a likely explanation for the observed acid resistance. Placing <i>p</i>-nitrenephenyl-β-D-galactopyranoside into the active site of modelled EIIC<sup>Lac</sup> suggested that the nitrene binds to the -NH- group of Ser248, which would explain why no sequence data beyond Pro247could be obtained.

scholarly journals Substantially improving the enantioconvergence of PvEH1, a Phaseolus vulgaris epoxide hydrolase, towards m-chlorostyrene oxide by laboratory evolution

2019 ◽  
Vol 18 (1) ◽  
Author(s):  
Xun-Cheng Zong ◽  
Chuang Li ◽  
Yao-Hui Xu ◽  
Die Hu ◽  
Bo-Chun Hu ◽  
...  
Keyword(s):  
Phaseolus Vulgaris ◽  
Epoxide Hydrolase ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Saturation Mutagenesis ◽  
Substrate Binding Pocket ◽  
Laboratory Evolution ◽  
E Coli ◽  
Enantioconvergent Hydrolysis ◽  
Hydrolysis Of

Abstract Background Epoxide hydrolase can regioselectively catalyze the oxirane ring-opening hydrolysis of rac-epoxides producing the corresponding chiral diols. In our laboratory, a gene named pveh1 encoding an EH from Phaseolus vulgaris was cloned. Although the directed modification of PvEH1 was carried out, the mutant PvEH1Y3 showed a limited degree of enantioconvergence towards racemic (rac-) m-chlorostyrene oxide (mCSO). Results PvEH1 and PvEH1Y3 were combinatively subjected to laboratory evolution to further enhance the enantioconvergence of PvEH1Y3 towards rac-mCSO. Firstly, the substrate-binding pocket of PvEH1 was identified using a CAVER 3.0 software, and divided into three zones. After all residues in zones 1 and 3 were subjected to leucine scanning, two E. coli transformants, E. coli/pveh1Y149L and /pveh1P184L, were selected, by which rac-mCSO was transformed into (R)-m-chlorophenyl-1,2-ethanediol (mCPED) having 55.1% and 27.2% eep. Secondly, two saturation mutagenesis libraries, E. coli/pveh1Y149X and /pveh1P184X (X: any one of 20 residues) were created at sites Y149 and P184 of PvEH1. Among all transformants, both E. coli/pveh1Y149L (65.8% αS and 55.1% eep) and /pveh1P184W (66.6% αS and 59.8% eep) possessed the highest enantioconvergences. Finally, the combinatorial mutagenesis was conducted by replacements of both Y149L and P184W in PvEH1Y3, constructing E. coli/pveh1Y3Z2, whose αS reached 97.5%, higher than that (75.3%) of E. coli/pveh1Y3. In addition, the enantioconvergent hydrolysis of 20 mM rac-mCSO was performed by E. coli/pveh1Y3Z2, giving (R)-mCPED with 95.2% eep and 97.2% yield. Conclusions In summary, the enantioconvergence of PvEH1Y3Z2 was successfully improved by laboratory evolution, which was based on the study of substrate-binding pocket by leucine scanning. Our present work introduced an effective strategy for the directed modification of enantioconvergence of PvEH1.

scholarly journals Structural basis for active-site probes targeting Staphylococcus aureus serine hydrolase virulence factors

2020 ◽  
Author(s):  
Matthias Fellner ◽  
Christian S. Lentz ◽  
Sam A. Jamieson ◽  
Jodi L. Brewster ◽  
Linhai Chen ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Active Site ◽  
Binding Pocket ◽  
Structural Basis ◽  
Serine Hydrolase ◽  
Serine Hydrolases ◽  
Substrate Binding Pocket ◽  
Hydrophobic Substrate ◽  
Substrate Analog ◽  
Insight Into

SummaryStaphylococcus aureus is a major cause of infection in the community and in hospitals. Serine hydrolases play key roles in bacterial homeostasis, in particular biofilms. Activity-based profiling has previously identified a family of serine hydrolases, designated fluorophosphonate-binding hydrolases (Fphs), which contribute to virulence of S. aureus in the biofilm niche. Here we report structures of the putative tributyrin esterase FphF, alone and covalently bound by a substrate analog, and small molecule inhibitors that occupy the hydrophobic substrate-binding pocket. We show that FphF has promiscuous esterase activity. Building from this, we extended our analysis to the wider Fph protein family using homology modeling and docking tools. We predict that other Fph enzymes, including FphB which was linked directly to virulence, may be more specific than FphF. This study provides insight into Fph function and a template for designing new imaging agents, diagnostic probes, and inhibitors to treat S. aureus infections.

Genomic Epidemiology of Invasive Methicillin-Resistant Staphylococcus aureus Infections Among Hospitalized Individuals in Ontario, Canada

2020 ◽  
Vol 222 (12) ◽  
pp. 2071-2081 ◽  
Author(s):  
Jennifer L Guthrie ◽  
Sarah Teatero ◽  
Sotaro Hirai ◽  
Alex Fortuna ◽  
Daniel Rosen ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Demographic Data ◽  
Public Health Practice ◽  
Acid Resistance ◽  
Fold Increase ◽  
High Genetic Diversity ◽  
Methicillin Resistant ◽  
Genomic Epidemiology ◽  
Healthcare Settings

Abstract Background Prevention and control of methicillin-resistant Staphylococcus aureus (MRSA) infections remain challenging. In-depth surveillance integrating patient and isolate data can provide evidence to better inform infection control and public health practice. Methods We analyzed MRSA cases diagnosed in 2010 (n = 212) and 2016 (n = 214) by hospitals in Ontario, Canada. Case-level clinical and demographic data were integrated with isolate characteristics, including antimicrobial resistance (AMR), classic genotyping, and whole-genome sequencing results. Results Community-associated MRSA (epidemiologically defined) increased significantly from 23.6% in 2010 to 43.0% in 2016 (P &lt; .001). The MRSA population structure changed over time, with a 1.5× increase in clonal complex (CC)8 strains and a concomitant decrease in CC5. The clonal shift was reflected in AMR patterns, with a decrease in erythromycin (86.7% to 78.4%, P = .036) and clindamycin resistance (84.3% to 47.9%, P &lt; .001) and a &gt;2-fold increase in fusidic acid resistance (9.0% to 22.5%, P &lt; .001). Isolates within both CC5 and CC8 were relatively genetically diverse. We identified 6 small genomic clusters—3 potentially related to transmission in healthcare settings. Conclusions Community-associated MRSA is increasing among hospitalized individuals in Ontario. Clonal shifting from CC5 to CC8 has impacted AMR. We identified a relatively high genetic diversity and limited genomic clustering within these dominant CCs.

scholarly journals Electron microscopy analysis of biofilms produced by Staphylococcus aureus exposed to UV-light on the surface of SnO2 thin films

2021 ◽  
Vol 27 (S1) ◽  
pp. 3168-3170
Author(s):  
Hazel Jaynelle Morales-Rodriguez ◽  
Javier Camarillo-Cisneros ◽  
María Alejandra Favila-Pérez ◽  
Alva Rocío Castillo-González ◽  
Celia María Quiñonez-Flores ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Thin Films ◽  
Staphylococcus Aureus ◽  
Uv Light ◽  
Electron Microscopy Analysis ◽  
Microscopy Analysis ◽  
Sno2 Thin Films

scholarly journals Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yufei Han ◽  
Qian Zhuang ◽  
Bo Sun ◽  
Wenping Lv ◽  
Sheng Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Biochemical Characterization ◽  
Substrate Binding ◽  
Binding Pocket ◽  
Substrate Binding Pocket ◽  
Transmembrane Segments ◽  
Therapeutic Molecules ◽  
Binding Cavity ◽  
Immune System Regulation ◽  
Mediated Reduction

AbstractSteroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-Δ4 structure, such as testosterone or progesterone, are catalyzed by steroid 5α-reductases (SRD5As) to generate their corresponding 3-oxo-5α steroids, which are essential for multiple physiological and pathological processes. SRD5A2 is already a target of clinically relevant drugs. However, the detailed mechanism of SRD5A-mediated reduction remains elusive. Here we report the crystal structure of PbSRD5A from Proteobacteria bacterium, a homolog of both SRD5A1 and SRD5A2, in complex with the cofactor NADPH at 2.0 Å resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic substrate binding cavity, whereas TM5-7 coordinate cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with biochemical characterization, define the substrate binding pocket of SRD5As, explain the properties of disease-related mutants and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-Δ4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible.

scholarly journals Interactions of tervalent lanthanide ions with bacterial collagenase (clostridiopeptidase A)

1981 ◽  
Vol 195 (3) ◽  
pp. 677-684 ◽  
Author(s):  
Christopher H. Evans
Keyword(s):  
Ionic Radius ◽  
Substrate Inhibition ◽  
Volume Ratio ◽  
Binding Pocket ◽  
Lanthanide Ions ◽  
Ionic Radii ◽  
Apparent Dissociation Constant ◽  
Substrate Complex ◽  
Bacterial Collagenase ◽  
Hydrolysis Of

Tervalent cations of the lanthanide (rare-earth) elements reversibly inhibit bacterial collagenase (clostridiopeptidase A; EC 3.4.24.3). Sm3+, whose ionic radius is closest to that of Ca2+, is the most effective inhibitor, completely suppressing clostridiopeptidase activity at a concentration of 100μm in the presence of 5mm-Ca2+. Er3+ and Lu3+, which both have ionic radii smaller than either Ca2+ or Sm3+, inhibit less efficiently, and La3+, which is slightly larger than Ca2+ or Sm3+, inhibits only weakly. These findings indicate a closely fitting, stereospecific, Ca2+-binding pocket in clostridiopeptidase, which excludes ions that are only slightly larger than Ca2+ [ionic radius 0.099nm (0.99 Ȧ)]. By contrast, trypsin, an enzyme whose activity does not depend on Ca2+, requires lanthanide concentrations 50–100-fold greater for inhibition. Furthermore, the relative efficiency of inhibition of trypsin by lanthanides increases as the lanthanide ions become smaller and the charge/volume ratio increases. At a concentration of 50μm, Sm3+ lowers the apparent Km for the hydrolysis of Pz-peptide by clostridiopeptidase from 5.4mm to 0.37mm and the apparent Vmax. from 0.29 Wünsch–Heidrich unit to 0.018 unit. Thus Sm3+ enhances the affinity of this enzyme for its substrate; inhibition of hydrolysis of Pz-peptide may result from the excessive stability of the enzyme–Sm3+–substrate complex. Inhibition by Sm3+ is competitive with regard to Ca2+. The apparent dissociation constant, Kd, of Ca2+ is 0.27mm, where the Ki for Sm3+ is 12μm. Clostridiopeptidase is more thermolabile in the absence of Ca2+. With Sm3+, thermoinactivation of the enzyme at 53°C or 60°C is initially accelerated, but then becomes retarded as heating continues. Lanthanide ions bind to gelatin and collagen. In so doing, they appear to protect these substrates from lysis by clostridiopeptidase through mechanisms additional to supplanting Ca2+ at its binding site on the enzyme. Collagen and gelatin sequester sufficient lanthanide ions to gain partial protection from clostridiopeptidase in the absence of an extraneous source of these inhibitors.

scholarly journals Characterization of the Acetate Binding Pocket in the Methanosarcina thermophila Acetate Kinase

2005 ◽  
Vol 187 (7) ◽  
pp. 2386-2394 ◽  
Author(s):  
Cheryl Ingram-Smith ◽  
Andrea Gorrell ◽  
Sarah H. Lawrence ◽  
Prabha Iyer ◽  
Kerry Smith ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Binding Site ◽  
Binding Pocket ◽  
Acetate Kinase ◽  
Phosphoryl Group ◽  
Acetyl Phosphate ◽  
Hydrophobic Pocket ◽  
Methanosarcina Thermophila ◽  
Methyl Group ◽  
Substrate Binding Sites

ABSTRACT Acetate kinase catalyzes the reversible magnesium-dependent synthesis of acetyl phosphate by transfer of the ATP γ-phosphoryl group to acetate. Inspection of the crystal structure of the Methanosarcina thermophila enzyme containing only ADP revealed a solvent-accessible hydrophobic pocket formed by residues Val93, Leu122, Phe179, and Pro232 in the active site cleft, which identified a potential acetate binding site. The hypothesis that this was a binding site was further supported by alignment of all acetate kinase sequences available from databases, which showed strict conservation of all four residues, and the recent crystal structure of the M. thermophila enzyme with acetate bound in this pocket. Replacement of each residue in the pocket produced variants with Km values for acetate that were 7- to 26-fold greater than that of the wild type, and perturbations of this binding pocket also altered the specificity for longer-chain carboxylic acids and acetyl phosphate. The kinetic analyses of variants combined with structural modeling indicated that the pocket has roles in binding the methyl group of acetate, influencing substrate specificity, and orienting the carboxyl group. The kinetic analyses also indicated that binding of acetyl phosphate is more dependent on interactions of the phosphate group with an unidentified residue than on interactions between the methyl group and the hydrophobic pocket. The analyses also indicated that Phe179 is essential for catalysis, possibly for domain closure. Alignments of acetate kinase, propionate kinase, and butyrate kinase sequences obtained from databases suggested that these enzymes have similar catalytic mechanisms and carboxylic acid substrate binding sites.

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