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 Protein–ligand complex structure from serial femtosecond crystallography using soaked thermolysin microcrystals and comparison with structures from synchrotron radiation

2017 ◽  
Vol 73 (8) ◽  
pp. 702-709 ◽  
Author(s):  
Hisashi Naitow ◽  
Yoshinori Matsuura ◽  
Kensuke Tono ◽  
Yasumasa Joti ◽  
Takashi Kameshima ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Room Temperature ◽  
Complex Structure ◽  
Binding Mode ◽  
Ligand Complex ◽  
X Ray ◽  
Cell Parameters ◽  
Serial Femtosecond Crystallography ◽  
Small Molecule Ligand

Serial femtosecond crystallography (SFX) with an X-ray free-electron laser is used for the structural determination of proteins from a large number of microcrystals at room temperature. To examine the feasibility of pharmaceutical applications of SFX, a ligand-soaking experiment using thermolysin microcrystals has been performed using SFX. The results were compared with those from a conventional experiment with synchrotron radiation (SR) at 100 K. A protein–ligand complex structure was successfully obtained from an SFX experiment using microcrystals soaked with a small-molecule ligand; both oil-based and water-based crystal carriers gave essentially the same results. In a comparison of the SFX and SR structures, clear differences were observed in the unit-cell parameters, in the alternate conformation of side chains, in the degree of water coordination and in the ligand-binding mode.

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 New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Louise Lassalle ◽  
Sylvain Engilberge ◽  
Dominique Madern ◽  
Pierre Vauclare ◽  
Bruno Franzetti ◽  
...  
Keyword(s):  
Renal Failure ◽  
Active Site ◽  
Ternary Complex ◽  
Substrate Recognition ◽  
Binding Mode ◽  
X Ray ◽  
Hyperoxaluria Type

Abstract Glyoxylate accumulation within cells is highly toxic. In humans, it is associated with hyperoxaluria type 2 (PH2) leading to renal failure. The glyoxylate content within cells is regulated by the NADPH/NADH dependent glyoxylate/hydroxypyruvate reductases (GRHPR). These are highly conserved enzymes with a dual activity as they are able to reduce glyoxylate to glycolate and to convert hydroxypyruvate into D-glycerate. Despite the determination of high-resolution X-ray structures, the substrate recognition mode of this class of enzymes remains unclear. We determined the structure at 2.0 Å resolution of a thermostable GRHPR from Archaea as a ternary complex in the presence of D-glycerate and NADPH. This shows a binding mode conserved between human and archeal enzymes. We also determined the first structure of GRHPR in presence of glyoxylate at 1.40 Å resolution. This revealed the pivotal role of Leu53 and Trp138 in substrate trafficking. These residues act as gatekeepers at the entrance of a tunnel connecting the active site to protein surface. Taken together, these results allowed us to propose a general model for GRHPR mode of action.

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 Polar and non-polar structures of NH4TiOF3

2019 ◽  
Vol 52 (1) ◽  
pp. 23-26
Author(s):  
O. Boytsova ◽  
I. Dovgaliuk ◽  
D. Chernyshov ◽  
A. Eliseev ◽  
P. O'Brien ◽  
...  
Keyword(s):  
Room Temperature ◽  
Phase 1 ◽  
Structural Features ◽  
X Ray Diffraction ◽  
X Ray ◽  
Β Phase ◽  
Α Phase ◽  
Starting Compound ◽  
Different Temperatures ◽  
Fourfold Axis

Ammonium oxofluorotitanate, NH4TiOF3, is probably the best known precursor for the synthesis of anatase mesocrystals. Transformation of NH4TiOF3 into TiO2 through thermal decomposition, accompanied by hydrolysis, preserves some structural features of the precursor. Currently, any discussion of the mechanism of this transformation is difficult, as the exact crystal structure of the starting compound is not available and no intermediate structures are known. This article describes the outcome of single-crystal and powder X-ray diffraction studies, revealing the existence of two polymorphs of the parent NH4TiOF3 at different temperatures. A second-order phase transition from the polar Pca21 α phase (1), stable at room temperature, to the Pma2 β phase (2) above ∼433 K has been demonstrated. The direction of the pseudo-fourfold axis in NH4TiOF3 coincides with the orientation of the fourfold axis of anatase mesocrystals, consistent with a topotactical transformation.

Transition metal azolates from metallocenes. Part 1: Dimetallic and trimetallic cyclopentadienyl nickel pyrazolates, synthesis and structural studies

1997 ◽  
Vol 75 (7) ◽  
pp. 949-958 ◽  
Author(s):  
Steven J. Rettig ◽  
Alan Storr ◽  
David A. Summers ◽  
Robert C. Thompson ◽  
James Trotter
Keyword(s):  
Room Temperature ◽  
Benzene Solution ◽  
Structural Features ◽  
Structural Studies ◽  
Structural Investigations ◽  
Crystalline Materials ◽  
Space Group ◽  
X Ray ◽  
Temperature Conditions ◽  
Representative Samples

The reactions of nickelocene with pyrazoles in benzene solution have resulted in the isolation of either dimeric compounds, [CpNi(μ-pz′)]2, (room temperature conditions) or trimetallic complexes, [CpNi(μ-pz″)2]2Ni, (elevated temperature conditions). Both dimeric and trimetallic species were obtained as red crystalline materials and X-ray structural investigations are reported for representative samples of each type. Structural features are interpreted and compared with similar, previously reported, nickel pyrazolate structures. Crystals of [CpNi(3,5-diMepz)]2 (C20H24N4Ni2), 1, are orthorhombic, a = 15.204(1), b = 17.967(2), c = 6.9786(9) Å, Z = 4, space group Ama2; those of [CpNi(4-NO2-3,5-diMepz)]2 (C20H22N6Ni2O2), 5, are orthorhombic, a = 17.145(3), b = 17.738(1), c = 7.006(1) Å, Z = 4, space group P212121; those of [CpNi(3,5-F6diMepz)]2 (C20H12F12N4Ni2), 6, are orthorhombic, a = 18.7134(8), b = 15.619(2), c = 7.7263(9) Å, Z = 4, space group Pnma; those of [CpNi(3,5-diMepz)2]2Ni (C30H38N8Ni3), 7, are triclinic, a = 10.078(2), b = 16.134(2), c = 9.992(1) Å, α = 91.586(10)°, β = 111.050(9)°, γ = 86.95(1)°, Z = 2, space group [Formula: see text]; and those of [CpNi(4-Cl-3,5-diMepz)2]2Ni (C30H34Cl4N8Ni3), 10, are monoclinic, a = 10.2201(7), b = 16.174(1), c = 10.7207(9) Å, β = 108.193(5)°, Z = 2, space group P21/a. The structures were solved by direct (dimetallic species) or Patterson (trimetallic complexes) methods and were refined by full-matrix least-squares procedures to R = 0.035, 0.032, 0.058, 0.032, and 0.033 (Rw = 0.021, 0.026, 0.053, 0.028, and 0.032) for 1157, 1894, 1642, 4499, and 2113 reflections with I ≥ 3σ(F2), respectively. Keywords: crystal structures, nickel, nickelocene, pyrazolates, cyclopentadienyl.

Electrical Resistivity Improvement by Precipitation and Strain in Al-Cu Thin Films

2010 ◽  
Vol 305-306 ◽  
pp. 33-37 ◽  
Author(s):  
S. Lallouche ◽  
M.Y. Debili
Keyword(s):  
Thin Films ◽  
Copper Content ◽  
Room Temperature ◽  
Structural Features ◽  
X Ray Diffraction ◽  
X Ray ◽  
Glass Substrates ◽  
Transmission Electron ◽  
Hall Method

This work deals with Al-Cu thin films, deposited onto glass substrates by RF (13.56MHz) magnetron sputtering, and annealed at 773K. The film thickness was approximately the same 3-4µm. They are characterized with respect to microstructure, grain size, microstrain, dislocation density and resistivity versus copper content. Al (Cu) deposits containing 1.8, 7.21, 86.17 and 92.5at%Cu have been investigated. The use of X-ray diffraction analysis and transmission electron microscopy lead to the characterization of different structural features of films deposited at room temperature (< 400K) and after annealing (773K). The resistivity of the films was measured using the four-point probe method. The microstrain profile obtained from XRD thanks to the Williamson-Hall method shows an increase with increasing copper content.

scholarly journals Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Aron Broom ◽  
Rojo V. Rakotoharisoa ◽  
Michael C. Thompson ◽  
Niayesh Zarifi ◽  
Erin Nguyen ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Protein Design ◽  
Active Site ◽  
Room Temperature ◽  
De Novo ◽  
Conformational Ensemble ◽  
Enzyme Design ◽  
X Ray ◽  
Conformational Ensembles ◽  
X Ray Crystallography

Abstract The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M−1s−1). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M−1s−1) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.

scholarly journals Структурные, магнитные и тепловые свойства соединения Tb-=SUB=-0.8-=/SUB=-Sm-=SUB=-0.2-=/SUB=-Fe-=SUB=-2-=/SUB=- cо структурой фаз Лавеса

2019 ◽  
Vol 61 (12) ◽  
pp. 2471
Author(s):  
Т.А. Алероева ◽  
И.С. Терешина ◽  
Т.П. Каминская ◽  
З.С. Умхаева ◽  
А.В. Филимонов ◽  
...  
Keyword(s):  
Thermal Expansion ◽  
Wide Temperature Range ◽  
Room Temperature ◽  
Structural Features ◽  
Surface Topology ◽  
Magnetic Domains ◽  
X Ray Diffraction ◽  
X Ray ◽  
Temperature Range ◽  
Comprehensive Study

A comprehensive study of the structure, phase composition, features of the surface topology, the magnetostrictive and thermal properties of the Tb0.8Sm0.2Fe2 compound are performed. The structural features were established at micro- and nanoscale levels, and information on the magnetic domains structure at room temperature was obtained. The results of x-ray diffraction studies in a wide temperature range of 90–760 K, including Curie temperature, are represented. Experimental data on thermal expansion and magnetostriction in magnetic fields up to 12 kOe were obtained and analyzed. Anomalies were found in the thermal expansion curves dl/l (T) and magnetostriction λ (T) at low temperatures. It is established that in compound under study the value of the magnetostrictive effect remains almost unchanged in a wide temperature range 100–300 K in fields up to 3.5 kOe.

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