Fine Tuning of the Copper Active Site in Polysaccharide Monooxygenases

2020 ◽  
Vol 124 (10) ◽  
pp. 1859-1865
Author(s):  
Son Tung Ngo ◽  
Han N. Phan ◽  
Chinh N. Le ◽  
Nhung C. T. Ngo ◽  
Khanh Bao Vu ◽  
...  
Keyword(s):  
Active Site ◽  
Fine Tuning ◽  
Polysaccharide Monooxygenases

Recent insights into lytic polysaccharide monooxygenases (LPMOs)

2018 ◽  
Vol 46 (6) ◽  
pp. 1431-1447 ◽  
Author(s):  
Tobias Tandrup ◽  
Kristian E. H. Frandsen ◽  
Katja S. Johansen ◽  
Jean-Guy Berrin ◽  
Leila Lo Leggio
Keyword(s):  
Active Site ◽  
Room Temperature ◽  
Experimental Studies ◽  
Binding Mode ◽  
Structural Features ◽  
Oxygen Species ◽  
Animal Kingdom ◽  
X Ray ◽  
Lytic Polysaccharide Monooxygenases ◽  
Polysaccharide Monooxygenases

Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes discovered within the last 10 years. By degrading recalcitrant substrates oxidatively, these enzymes are major contributors to the recycling of carbon in nature and are being used in the biorefinery industry. Recently, two new families of LPMOs have been defined and structurally characterized, AA14 and AA15, sharing many of previously found structural features. However, unlike most LPMOs to date, AA14 degrades xylan in the context of complex substrates, while AA15 is particularly interesting because they expand the presence of LPMOs from the predominantly microbial to the animal kingdom. The first two neutron crystallography structures have been determined, which, together with high-resolution room temperature X-ray structures, have putatively identified oxygen species at or near the active site of LPMOs. Many recent computational and experimental studies have also investigated the mechanism of action and substrate-binding mode of LPMOs. Perhaps, the most significant recent advance is the increasing structural and biochemical evidence, suggesting that LPMOs follow different mechanistic pathways with different substrates, co-substrates and reductants, by behaving as monooxygenases or peroxygenases with molecular oxygen or hydrogen peroxide as a co-substrate, respectively.

scholarly journals Formation of a Copper(II)–Tyrosyl Complex at the Active Site of Lytic Polysaccharide Monooxygenases Following Oxidation by H2O2

2019 ◽  
Vol 141 (46) ◽  
pp. 18585-18599 ◽  
Author(s):  
Alessandro Paradisi ◽  
Esther M. Johnston ◽  
Morten Tovborg ◽  
Callum R. Nicoll ◽  
Luisa Ciano ◽  
...  
Keyword(s):  
Active Site ◽  
Lytic Polysaccharide Monooxygenases ◽  
Polysaccharide Monooxygenases

scholarly journals (−)-Homosalinosporamide A and Its Mode of Proteasome Inhibition: An X-ray Crystallographic Study

Marine Drugs ◽  
2018 ◽  
Vol 16 (7) ◽  
pp. 240 ◽  
Author(s):  
Michael Groll ◽  
Henry Nguyen ◽  
Sreekumar Vellalath ◽  
Daniel Romo
Keyword(s):  
Natural Product ◽  
Active Site ◽  
Late Stage ◽  
Enzyme Assay ◽  
Proteasome Inhibition ◽  
Fine Tuning ◽  
Synthetic Approach ◽  
X Ray ◽  
Salinosporamide A ◽  
Crystallographic Study

Upon acylation of the proteasome by the β-lactone inhibitor salinosporamide A (SalA), tetrahydrofuran formation occurs by intramolecular alkylation of the incipient alkoxide onto the choroethyl sidechain and irreversibly blocks the active site. Our previously described synthetic approach to SalA, utilizing a bioinspired, late-stage, aldol-β-lactonization strategy to construct the bicyclic β-lactone core, enabled synthesis of (–)-homosalinosporamide A (homoSalA). This homolog was targeted to determine whether an intramolecular tetrahydropyran is formed in a similar manner to SalA. Herein, we report the X-ray structure of the yeast 20S proteasome:homoSalA-complex which reveals that tetrahydropyran ring formation does not occur despite comparable potency at the chymotrypsin-like active site in a luminogenic enzyme assay. Thus, the natural product derivative homoSalA blocks the proteasome by a covalent reversible mode of action, opening the door for further fine-tuning of proteasome inhibition.

scholarly journals Fine tuning of the active site modulates specificity in the interaction of O-acetylserine sulfhydrylase isozymes with serine acetyltransferase

2013 ◽  
Vol 1834 (1) ◽  
pp. 169-181 ◽  
Author(s):  
Francesca Spyrakis ◽  
Paolo Felici ◽  
Alexander S. Bayden ◽  
Enea Salsi ◽  
Riccardo Miggiano ◽  
...  
Keyword(s):  
Active Site ◽  
Fine Tuning ◽  
Serine Acetyltransferase

scholarly journals The Role of the Active Site Tyrosine in the Mechanism of Lytic Polysaccharide Monooxygenase

2020 ◽  
Author(s):  
Aina McEvoy ◽  
Joel Creutzberg ◽  
Raushan Kumar Singh ◽  
Morten J. Bjerrum ◽  
Erik Hedegård
Keyword(s):  
Active Site ◽  
Density Functional ◽  
Renewable Resource ◽  
Lytic Polysaccharide Monooxygenase ◽  
Functional Theory ◽  
Polysaccharide Monooxygenases ◽  
Active Site Tyrosine ◽  
The Difference ◽  
First Time

Natural polysaccharides (such as cellulose) comprise a large bio-renewable resource. However, exploitation of this resource requires energy-efficient polysaccharide degradation, which is currently limited by the inherent recalcitrance of many naturally occurring polysaccharides. Catalytic breakdown of polysaccharides can be achieved more efficiently by means of the enzymes lytic polysaccharide monooxygenases (LPMOs). However, the LPMO mechanism has remained controversial, preventing full exploitation of their potential. One of the controversies has centered around an active site tyrosine, present in most LPMOs. Different roles for this tyrosine have been proposed without direct evidence, but two recent investigations have for the first time obtained direct (spectroscopic) evidence for that chemical modification of this tyrosine is possible. Surprisingly, the spectroscopic features obtained in the two investigations are remarkably different. In this paper we use density functional theory (DFT) in a QM/MM formulation to reconcile these (apparently) conflicting results. By modeling the spectroscopy as well as the underlying reaction mechanism we can show how formation of two isomers (both involving deprotonation of tyrosine) explain the difference in the experimental observed spectroscopic features. The link between our structures and the observed spectroscopy provides a firm ground to investigate the role of tyrosine.

scholarly journals Atomic design and fine-tuning of sub-nanometric Pt catalysts to tame hydrogen generation

2020 ◽  
Author(s):  
Jie Yang ◽  
Wenzhao Fu ◽  
Chaoqiu Chen ◽  
Wenyao Chen ◽  
Wugen Huang ◽  
...  
Keyword(s):  
Active Site ◽  
Catalytic Mechanism ◽  
Hydrogen Generation ◽  
Atomic Layer ◽  
Fine Tuning ◽  
Superior Performance ◽  
Single Atom ◽  
Intrinsic Activity ◽  
Atomic Structures ◽  
Metal Metal

Abstract Rational synthesis of sub-nanocatalysts with controllable electronic and atomic structures remains a challenge to break the limits of traditional catalysts for superior performance. Here we report the atomic-level precise synthesis of Pt/graphene sub-nanocatalysts (from single atom, dimer, and to cluster) by atomic layer deposition, achieved by a novel high temperature pulsed ozone strategy to controllably pre-create abundant in-plane epoxy groups on graphene as anchoring sites. The specific in-plane epoxy structure endows the deposited Pt species with outstanding uniformity, controllability and stability. Their size-depended electronic and geometric effects have been observed for ammonia borane hydrolysis, revealing a volcano-type dependence of intrinsic activity on their sizes. Their active site structures have been identified based on extensive characterizations, dynamic compensation effect, kinetic isotope experiments and density function theory simulation. The Pt dimers show the highest catalytic activity and good durability than Pt single atoms and nanoparticles, ascribed to the unique C-Pt-Pt-O (C5Pt2O, metal-metal bond dimer) active site structure. Our work provides new insights into the precise tailoring and catalytic mechanism in sub-nanometer level.

scholarly journals Configuration of active site segments in lytic polysaccharide monooxygenases steers oxidative xyloglucan degradation

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Peicheng Sun ◽  
Christophe V. F. P. Laurent ◽  
Stefan Scheiblbrandner ◽  
Matthias Frommhagen ◽  
Dimitrios Kouzounis ◽  
...  
Keyword(s):  
Active Site ◽  
Lytic Polysaccharide Monooxygenases ◽  
Polysaccharide Monooxygenases

scholarly journals Combination of SAXS and Protein Painting Discloses the Three-Dimensional Organization of the Bacterial Cysteine Synthase Complex, a Potential Target for Enhancers of Antibiotic Action

2019 ◽  
Vol 20 (20) ◽  
pp. 5219
Author(s):  
Brenda Rosa ◽  
Marialaura Marchetti ◽  
Gianluca Paredi ◽  
Heinz Amenitsch ◽  
Nina Franko ◽  
...  
Keyword(s):  
Complex Formation ◽  
Active Site ◽  
Solution Structure ◽  
Three Dimensional ◽  
Direct Interaction ◽  
Site Directed Mutagenesis ◽  
Fine Tuning ◽  
Bacterial Cells ◽  
Saxs Data ◽  
Cysteine Synthase

The formation of multienzymatic complexes allows for the fine tuning of many aspects of enzymatic functions, such as efficiency, localization, stability, and moonlighting. Here, we investigated, in solution, the structure of bacterial cysteine synthase (CS) complex. CS is formed by serine acetyltransferase (CysE) and O-acetylserine sulfhydrylase isozyme A (CysK), the enzymes that catalyze the last two steps of cysteine biosynthesis in bacteria. CysK and CysE have been proposed as potential targets for antibiotics, since cysteine and related metabolites are intimately linked to protection of bacterial cells against redox damage and to antibiotic resistance. We applied a combined approach of small-angle X-ray scattering (SAXS) spectroscopy and protein painting to obtain a model for the solution structure of CS. Protein painting allowed the identification of protein–protein interaction hotspots that were then used as constrains to model the CS quaternary assembly inside the SAXS envelope. We demonstrate that the active site entrance of CysK is involved in complex formation, as suggested by site-directed mutagenesis and functional studies. Furthermore, complex formation involves a conformational change in one CysK subunit that is likely transmitted through the dimer interface to the other subunit, with a regulatory effect. Finally, SAXS data indicate that only one active site of CysK is involved in direct interaction with CysE and unambiguously unveil the quaternary arrangement of CS.

scholarly journals Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass

2018 ◽  
Vol 82 (4) ◽  
Author(s):  
Bastien Bissaro ◽  
Anikó Várnai ◽  
Åsmund K. Røhr ◽  
Vincent G. H. Eijsink
Keyword(s):  
Reactive Oxygen Species ◽  
Plant Cell Wall ◽  
Biomass Conversion ◽  
Hydrolytic Enzymes ◽  
Reactive Oxygen ◽  
Industrial Applications ◽  
Fine Tuning ◽  
Oxygen Species ◽  
Redox Systems ◽  
Polysaccharide Monooxygenases

SUMMARYBiomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as lytic polysaccharide monooxygenases (LPMOs), which, by catalyzing the oxidative cleavage of recalcitrant polysaccharides, allow canonical hydrolytic enzymes to depolymerize the biomass more efficiently. Very recently, it has been shown that LPMOs are not classical monooxygenases in that they can also use hydrogen peroxide (H2O2) as an oxidant. This discovery calls for a revision of our understanding of how lignocellulolytic enzymes are connected since H2O2is produced and used by several of them. The first part of this review is dedicated to the LPMO paradigm, describing knowns, unknowns, and uncertainties. We then present different lignocellulolytic redox systems, enzymatic or not, that depend on fluxes of reactive oxygen species (ROS). Based on an assessment of these putatively interconnected systems, we suggest that fine-tuning of H2O2levels and proximity between sites of H2O2production and consumption are important for fungal biomass conversion. In the last part of this review, we discuss how our evolving understanding of redox processes involved in biomass depolymerization may translate into industrial applications.

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