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13 results for “enzyme promiscuity”
Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation
<p>The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikatis. The detailed description of the datafiles and scripts is provided in the accompanying README.rtf file.</p>
Fig. 8 in Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity
Fig. 8. Proposed mechanisms for the conversion of FPP into sesquiterpene products catalysed by PmSTS WT and its mutants (L454G and L454A). The scheme is derived from the proposed mechanism of monoterpenes synthases (Gatto et al., 2015; Piechulla et al., 2016). The products generated by the PmSTSΔ24WT are shown in black. New products generated by mutant L454G and L454A in this study are shown in red. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 9 in Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity
Fig. 9. The homology modelling illustration of the active site of PmSTSΔ24WT and PmSTSΔ24L454G. The residue L454 and Y418 are shown as stick and coloured in purple and orange, respectively. (A) The side chain of the L454 provides steric hindrance, preventing the rotation of the Y418 toward the interior of the active site. (B) The mutation of L454G provide sufficient space to allow the Y418 to undergo rotation toward the interior of the active site and (C) thus allowing interaction with other amino acid in the active site. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 5 in Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity
Fig. 5. Relative activity of PmSTSΔ24 WT and mutants (0.1 μM) incubated with the substrate FPP (50 μM). The relative activity of PmSTS were measured using Malachite Green Assay. The relative activity of PmSTS were calculated using the wild type as 100% with error bars representing SE (n = 3). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 7 in Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity
Fig. 7. Mass spectra and retention index of the hydroxylated sesquiterpene generated by PmSTS mutants L454G and L454A. NIST library mass spectra of (A) sesquicineole, (B) cis-sesquisabinene hydrate, (C) trans-sesquisabinene hydrate, and (D) α-bisabolol are shown at bottom of each respective sample mass spectra.
Fig. 4 in Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity
Fig. 4. Structural analysis by circular dichroism (CD) of PmSTSΔ24WT and L454 mutants. Far-UV CD spectra (190–260 nm) of PmSTSΔ24 WT, PmSTSΔ24Y390S/L454G, PmSTSΔ24L454G and PmSTSΔ24L454A are shown. Buffer used was 20 mM Tris pH 8.0, 100 mM NaCl 2 mM βME. Protein concentration was 10 μM. Further secondary structure variations in percentages for each L454 mutant and WT were determined using the JASCO SSE program are presented in Table S2.
Fig. 3 in Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity
Fig. 3. Analysis of monomeric fraction of PmSTS Wild Type and mutant proteins using (A) 12% SDS PAGE and (B) 10% Native PAGE. The SDS PAGE showed high purity of PmSTS protein were obtained for wild type and for all mutants except for PmSTSΔ24W286A and PmSTSΔ24Y390S. The native PAGE showed several species of PmSTSΔ24WT, PmSTSΔ24V466E, and PmSTSΔ24Y390S/L454G that can be resolved on a 10% native gel. However, only one species of PmSTSΔ24L454G and PmSTSΔ24L454A was resolved on a 10% native gel. Smearing bands were observed for PmSTSΔ24W286A and PmSTSΔ24Y390S on the 10% native gel, probably due to the low purity as judged by 12% SDS PAGE.
Fig. 1 in Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity
Fig. 1. Superimposition of PmSTS homology model (green) with the crystal structure of Nicotiana tabacum 5-epi-aristolochene synthase (NtEAS, PDB ID:3M01). NtEAS has a FPP ligand analog (2-trans, 6-trans)-2- fluorofarnesyl diphosphate (FPF) bound in the active site (pink) shows an RMSD of 1.4 Å over 518 aligned Cα atoms. The Mg2+ ions in the active site of NtEAS are shown in yellow spheres. PmSTS and NtEAS share ~38% sequence identify. The putative active residues of PmSTS (W286, Y390, L454 and V466) shown heavier sticks were selected for mutagenesis studies. The structure superimposition was carried out using SSM in COOT (Emsley et al., 2010). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 2 in Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity
Fig. 2. Size exclusion chromatography (SEC) profiles of affinity chromatography purified wild-type and mutant proteins. The chromatography was performed on a HiLoad Superdex column 200 PG. Detection was at 280 nm. (A) PmSTSΔ24 WT, (B) PmSTSΔ24 V466E, (C) PmSTSΔ24 W286A, (D) PmSTSΔ24 Y390S, (E) PmSTSΔ24L454A, (F) PmSTSΔ24L454G, and (G) PmSTSΔ24Y390S/L454G were run over a size exclusion column to verify the oligomeric status of generated proteins. Elution profiles of β-sesquiphellandrene synthase proteins are represented together with protein standard: bovine thyroglobulin (670 kDa), bovine gamma globulin (158 kDa), ovalbumin (44 kDa), myoglobin (17 kDa), vitamin B12 (1.35 kDa). The peaks eluted at ~48 mL correspond to protein aggregated during the purification process, and peaks eluted at ~80 mL correspond to the monomeric size of PmSTSΔ24 protein (65 kDa).
Understanding the enzyme (S)-Norcoclaurine Synthase promiscuity to aldehydes and ketones
<p>Files of the work 'Understanding the enzyme (S)-Norcoclaurine Synthase promiscuity to aldehydes and ketones' where was studied the application of methods in silico to understand the reactivity of compounds</p>
Fig. 6 in Site-directed mutagenesis of β sesquiphellandrene synthase enhances enzyme promiscuity
Fig. 6. Hydroxylated sesquiterpene product of PmSTS mutants L454G and L454A.
A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.
GEO Series GSE92601. Escherichia coli str. K-12 substr. MG1655. 10 samples. Type: Expression profiling by high throughput sequencing.
Enzyme promiscuity shapes evolutionary innovation and optimization
GEO Series GSE114358. Escherichia coli str. K-12 substr. MG1655. 22 samples. Type: Expression profiling by high throughput sequencing.
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