The Inverting Mechanism of the Metal Ion-Independent LanGT2: The First Step to Understand the Glycosylation of Natural Product Antibiotic Precursors Through QM/MM Simulations

2021 ◽  
Author(s):  
Fernanda Mendoza ◽  
Gonzalo Jaña
Keyword(s):  
Natural Product ◽  
Metal Ion ◽  
Peptide Antibiotics ◽  
Inverting Mechanism

Glycosyltransferases (GTs) from GT1 family are responsible for the glycosylation of various important organic structures such as terpenes, steroids or peptide antibiotics, making this one of the most intensely studied...

scholarly journals Characterization of a Solvent-Tolerant Amidohydrolase Involved in Natural Product Heterocycle Formation

Catalysts ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 892
Author(s):  
Lea Winand ◽  
Dustin Joshua Vollmann ◽  
Jacqueline Hentschel ◽  
Markus Nett
Keyword(s):  
Natural Product ◽  
Metal Ion ◽  
Building Blocks ◽  
Maximal Activity ◽  
Kinetic Properties ◽  
Pharmaceutical Drugs ◽  
Highly Active ◽  
Km Value ◽  
Amidohydrolase Superfamily ◽  
Solvent Tolerant

Heterocycles are important building blocks in pharmaceutical drugs and their enzymatic synthesis is attracting increasing interest. In recent years, various enzymes of the amidohydrolase superfamily were reported to catalyze heterocycle-forming condensation reactions. One of these enzymes, MxcM, is biochemically and kinetically characterized in this study. MxcM generates an imidazoline moiety in the biosynthesis of the natural product pseudochelin A, which features potent anti-inflammatory properties. The enzyme shows maximal activity at 50 °C and pH 10 as well as a kcat/Km value of 22,932 s−1 M−1 at its temperature optimum. Experimental data suggest that the activity of MxcM does not depend on a catalytic metal ion, which is uncommon among amidohydrolases. MxcM is highly active in diverse organic solvents and concentrated salt solutions. Furthermore, we show that MxcM is also capable to introduce imidazoline rings into derivatives of its natural substrate myxochelin B. Overall, MxcM is a solvent-stable, halotolerant enzyme with promising biochemical and kinetic properties and, in future, might become a valuable biocatalyst for the manufacturing of pharmaceutical drugs.

Aspects of high-resolution imaging with a scanning ion microprobe

1986 ◽  
Vol 44 ◽  
pp. 750-751
Author(s):  
R. Levi-Setti ◽  
J. M. Chabala ◽  
Y. L. Wang
Keyword(s):  
Metal Ion ◽  
Secondary Ion Mass Spectrometry ◽  
Chromatic Aberration ◽  
Ion Source ◽  
Ion Microprobe ◽  
Emission Pattern ◽  
Intrinsic Resolution ◽  
Resolution Imaging ◽  
20 Nm ◽  
Secondary Ion

We have shown the feasibility of 20 nm lateral resolution in both topographic and elemental imaging using probes of this size from a liquid metal ion source (LMIS) scanning ion microprobe (SIM). This performance, which approaches the intrinsic resolution limits of secondary ion mass spectrometry (SIMS), was attained by limiting the size of the beam defining aperture (5μm) to subtend a semiangle at the source of 0.16 mr. The ensuing probe current, in our chromatic-aberration limited optical system, was 1.6 pA with Ga+ or In+ sources. Although unique applications of such low current probes have been demonstrated,) the stringent alignment requirements which they imposed made their routine use impractical. For instance, the occasional tendency of the LMIS to shift its emission pattern caused severe misalignment problems.

Scanning ion microscopy images

1987 ◽  
Vol 45 ◽  
pp. 180-181
Author(s):  
R. Levi-Setti ◽  
J.M. Chabala ◽  
Y.L. Wang
Keyword(s):  
Metal Ion ◽  
Secondary Emission ◽  
Scanning Method ◽  
Ion Channeling ◽  
Secondary Ions ◽  
High Resolution Images ◽  
Ion Microscopy ◽  
Z Contrast ◽  
Focused Beams ◽  
Microscopy Images

Finely focused beams extracted from liquid metal ion sources (LMIS) provide a wealth of secondary signals which can be exploited to create high resolution images by the scanning method. The images of scanning ion microscopy (SIM) encompass a variety of contrast mechanisms which we classify into two broad categories: a) Emission contrast and b) Analytical contrast.Emission contrast refers to those mechanisms inherent to the emission of secondaries by solids under ion bombardment. The contrast-carrying signals consist of ion-induced secondary electrons (ISE) and secondary ions (ISI). Both signals exhibit i) topographic emission contrast due to the existence of differential geometric emission and collection effects, ii) crystallographic emission contrast, due to primary ion channeling phenomena and differential oxidation of crystalline surfaces, iii) chemical emission or Z-contrast, related to the dependence of the secondary emission yields on the Z and surface chemical state of the target.

Freeze-etch TEM of aqueous polymer gel network morphology

1986 ◽  
Vol 44 ◽  
pp. 796-797
Author(s):  
J. A. N. Zasadzinski ◽  
R. K. Prud'homme
Keyword(s):  
Metal Ion ◽  
Polymer Network ◽  
Polymer Gels ◽  
Polymer Gel ◽  
Deformation History ◽  
Crosslinked Polymer ◽  
Aqueous Polymer ◽  
History Of ◽  
Gel Network ◽  
Network Morphology

The rheological and mechanical properties of crosslinked polymer gels arise from the structure of the gel network. In turn, the structure of the gel network results from: thermodynamically determined interactions between the polymer chain segments, the interactions of the crosslinking metal ion with the polymer, and the deformation history of the network. Interpretations of mechanical and rheological measurements on polymer gels invariably begin with a conceptual model of,the microstructure of the gel network derived from polymer kinetic theory. In the present work, we use freeze-etch replication TEM to image the polymer network morphology of titanium crosslinked hydroxypropyl guars in an attempt to directly relate macroscopic phenomena with network structure.

Synthetic studies toward inducamide C

2021 ◽  
Author(s):  
Ardalan A. Nabi ◽  
Lydia M. Scott ◽  
Daniel P. Furkert ◽  
Jonathan Sperry
Keyword(s):  
Natural Product ◽  
Structural Revision ◽  
Synthetic Studies

The rare benzoxazepine ring in the alkaloid inducamide C is unstable and prone to rearrangement, indicating that structural revision of the natural product may be necessary.

Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen
Keyword(s):  
Active Site ◽  
Metal Binding ◽  
Metal Ion ◽  
Triosephosphate Isomerase ◽  
Catalytic Mechanism ◽  
Degradation Mechanism ◽  
Structural Basis ◽  
Conserved Residues ◽  
Phosphodiester Bond ◽  
Cyclic Dinucleotides

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.

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