The structures and catalytic mechanisms of molybdenum centres in enzymes studied by e.p.r and X-ray spectroscopy

1984 ◽  
pp. 707-722 ◽  
Keyword(s):  
X Ray ◽  
Catalytic Mechanisms

scholarly journals Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhiwen Liu ◽  
Fanglong Zhao ◽  
Boyang Zhao ◽  
Jie Yang ◽  
Joseph Ferrara ◽  
...  
Keyword(s):  
High Resolution ◽  
Organic Synthesis ◽  
Indole Alkaloids ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Directed Mutagenesis ◽  
Computational Studies ◽  
X Ray ◽  
Evolutionary Branch ◽  
Catalytic Mechanisms

AbstractPrenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.

X-ray Structure of the ZnII β-Lactamase from Bacteroides fragilis in an Orthorhombic Crystal Form

1998 ◽  
Vol 54 (1) ◽  
pp. 47-57 ◽  
Author(s):  
Andrea Carfi ◽  
Emile Duée ◽  
Raquel Paul-Soto ◽  
Moreno Galleni ◽  
Jean-Marie Frère ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Catalytic Mechanism ◽  
Bacteroides Fragilis ◽  
Crystal Form ◽  
Water Molecules ◽  
Orthorhombic Crystal ◽  
X Ray ◽  
Class B ◽  
Catalytic Mechanisms ◽  
Zn Ions

β-Lactamases are extracellular or periplasmic bacterial enzymes which confer resistance to β-lactam antibiotics. On the basis of their catalytic mechanisms, they can be divided into two major groups: active-site serine enzymes (classes A, C and D) and the ZnII enzymes (class B). The first crystal structure of a class B enzyme, the metallo-β-lactamase from Bacillus cereus, has been solved at 2.5 Å resolution [Carfi, Pares, Duée, Galleni, Duez, Frère & Dideberg (1995). EMBO J. 14, 4914–4921]. Recently, the crystal structure of the metallo-β-lactamase from Bacteroides fragilis has been determined in a tetragonal space group [Concha, Rasmussen, Bush & Herzberg (1996). Structure, 4, 823–836]. The structure of the metallo-β-lactamase from B. fragilis in an orthorhombic crystal form at 2.0 Å resolution is reported here. The final crystallographic R is 0.196 for all the 32 501 observed reflections in the range 10–2.0 Å. The refined model includes 458 residues, 437 water molecules, four zinc and two sodium ions. These structures are discussed with reference to Zn binding and activity. A catalytic mechanism is proposed which is coherent with metallo-β-lactamases being active with either one Zn ion (as in Aeromonas hydrophila) or two Zn ions (as in B. fragilis) bound to the protein.

Simulating the XANES of metalloenzymes – a case study

2002 ◽  
Vol 10 (1) ◽  
pp. 64-68 ◽  
Author(s):  
Ana Mijovilovich ◽  
Wolfram Meyer-Klaucke
Keyword(s):  
Data Analysis ◽  
Absorption Spectroscopy ◽  
Theory Development ◽  
Structural Models ◽  
Spectroscopy Data ◽  
X Ray ◽  
Catalytic Mechanisms ◽  
X Ray Absorption ◽  
Future Theory

The analysis of XANES patterns is very indicative for screening samples. Powerful X-ray absorption spectroscopy data-analysis programs can simulate these patterns. Here, a case study on two structural motifs is presented: a non-heme Fe site (2-His-1-carboxylate motif) and the metallo β-lactamase dinuclear Zn site. Simulations of the edge shapes for different structural models will be compared with experimental results, pointing out limitations and challenges. The influence of single neighbouring atoms in the first and second shell on the resulting XANES pattern is discussed. Insights into catalytic mechanisms and the requirements for future theory development are addressed.

scholarly journals C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Takahiro Mori ◽  
Takuto Kumano ◽  
Haibing He ◽  
Satomi Watanabe ◽  
Miki Senda ◽  
...  
Keyword(s):  
Bond Cleavage ◽  
Structural Basis ◽  
Electron Microscopic ◽  
Intestinal Microbes ◽  
X Ray ◽  
Sugar Moiety ◽  
Structural Details ◽  
Catalytic Mechanisms ◽  
Cleavage Reactions ◽  
Biochemical Analyses

AbstractC-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and the resulting aglycones exert various bioactivities. Although the enzymes responsible for the reactions have been identified, their catalytic mechanisms and the generality of the reactions in nature remain to be explored. Here, we present the identification and structural basis for the activation of xenobiotic C-glycosides by heterocomplex C-deglycosylation enzymes from intestinal and soil bacteria. They are found to be metal-dependent enzymes exhibiting broad substrate specificity toward C-glycosides. X-ray crystallographic and cryo-electron microscopic analyses, as well as structure-based mutagenesis, reveal the structural details of these enzymes and the detailed catalytic mechanisms of their remarkable C-C bond cleavage reactions. Furthermore, bioinformatic and biochemical analyses suggest that the C-deglycosylation enzymes are widely distributed in the gut, soil, and marine bacteria.

scholarly journals Synchrotron Radiation Based Study of the Catalytic Mechanism of Ag+ to Chalcopyrite Bioleaching by Mesophilic and Thermophilic Cultures

Minerals ◽  
2018 ◽  
Vol 8 (9) ◽  
pp. 382 ◽  
Author(s):  
Zhenyuan Nie ◽  
Weiwei Zhang ◽  
Hongchang Liu ◽  
Jinlan Xia ◽  
Wei Zhu ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Catalytic Mechanism ◽  
Copper Extraction ◽  
X Ray Diffraction ◽  
Edge Structure ◽  
Secondary Minerals ◽  
X Ray ◽  
Catalytic Mechanisms ◽  
X Ray Absorption ◽  
Insight Into

The catalytic mechanism of Ag+ for chalcopyrite bioleaching by mesophilic culture (at 30 °C) and thermophilic culture (at 48 °C) was investigated using synchrotron radiation-based X-ray diffraction (SR-XRD) and S K-edge and Fe L-edge X-ray absorption near edge structure (XANES) spectroscopy. Bioleaching experiments showed that copper extraction from chalcopyrite bioleaching by both cultures was promoted significantly by Ag+, with more serious corrosion occurring on the minerals surface. SR-XRD and XANES analyses showed that the intermediates S0, jarosite and secondary minerals (bornite, chalcocite and covellite) formed for all bioleaching experiments. For these secondary minerals, the formation of bornite and covellite was promoted significantly in the presence of Ag+ for both cultures, while Ag+ has almost no effect on the formation of chalcocite. These results provided insight into the catalytic mechanisms of Ag+ to chalcopyrite bioleaching by the mesophilic and thermophilic cultures, which are both probably due to the rapid formation of bornite by Ag+ and the conversion of bornite to covellite.

scholarly journals Perdeuteration, large crystal growth and neutron data collection ofLeishmania mexicanatriose-phosphate isomerase E65Q variant

2019 ◽  
Vol 75 (4) ◽  
pp. 260-269 ◽  
Author(s):  
Vinardas Kelpšas ◽  
Bénédicte Lafumat ◽  
Matthew P. Blakeley ◽  
Nicolas Coquelle ◽  
Esko Oksanen ◽  
...  
Keyword(s):  
Triose Phosphate Isomerase ◽  
Dihydroxyacetone Phosphate ◽  
Leishmania Mexicana ◽  
Large Crystal ◽  
Neutron Data ◽  
X Ray ◽  
Triose Phosphate ◽  
Catalytic Mechanisms ◽  
Crystal Volume ◽  
Neutron Crystallography

Triose-phosphate isomerase (TIM) catalyses the interconversion of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Two catalytic mechanisms have been proposed based on two reaction-intermediate analogues, 2-phosphoglycolate (2PG) and phosphoglycolohydroxamate (PGH), that have been used as mimics of thecis-enediol(ate) intermediate in several studies of TIM. The protonation states that are critical for the mechanistic interpretation of these structures are generally not visible in the X-ray structures. To resolve these questions, it is necessary to determine the hydrogen positions using neutron crystallography. Neutron crystallography requires large crystals and benefits from replacing all hydrogens with deuterium.Leishmania mexicanatriose-phosphate isomerase was therefore perdeuterated and large crystals with 2PG and PGH were produced. Neutron diffraction data collected from two crystals with different volumes highlighted the importance of crystal volume, as smaller crystals required longer exposures and resulted in overall worse statistics.

Space and Time Distribution of Hard X-Ray Emission in a Loop at the Beginning of a Flare

1994 ◽  
Vol 144 ◽  
pp. 275-277
Author(s):  
M. Karlický ◽  
J. C. Hénoux
Keyword(s):  
Time Distribution ◽  
Electron Bombardment ◽  
Spatial Evolution ◽  
Superthermal Electrons ◽  
Flare Loop ◽  
X Ray ◽  
Superthermal Electron ◽  
Flare Loops ◽  
Chromospheric Evaporation ◽  
Temporal And Spatial

AbstractUsing a new ID hybrid model of the electron bombardment in flare loops, we study not only the evolution of densities, plasma velocities and temperatures in the loop, but also the temporal and spatial evolution of hard X-ray emission. In the present paper a continuous bombardment by electrons isotropically accelerated at the top of flare loop with a power-law injection distribution function is considered. The computations include the effects of the return-current that reduces significantly the depth of the chromospheric layer which is evaporated. The present modelling is made with superthermal electron parameters corresponding to the classical resistivity regime for an input energy flux of superthermal electrons of 109erg cm−2s−1. It was found that due to the electron bombardment the two chromospheric evaporation waves are generated at both feet of the loop and they propagate up to the top, where they collide and cause temporary density and hard X-ray enhancements.

Some Problems in Understanding the Solar Corona

1994 ◽  
Vol 144 ◽  
pp. 1-9
Author(s):  
A. H. Gabriel
Keyword(s):  
Solar Corona ◽  
Solar Atmosphere ◽  
Theoretical Modelling ◽  
Total System ◽  
Major Advance ◽  
X Ray ◽  
Proper Perspective ◽  
Space Observations

The development of the physics of the solar atmosphere during the last 50 years has been greatly influenced by the increasing capability of observations made from space. Access to images and spectra of the hotter plasma in the UV, XUV and X-ray regions provided a major advance over the few coronal forbidden lines seen in the visible and enabled the cooler chromospheric and photospheric plasma to be seen in its proper perspective, as part of a total system. In this way space observations have stimulated new and important advances, not only in space but also in ground-based observations and theoretical modelling, so that today we find a well-balanced harmony between the three techniques.

White-Light Coronal Structures: Streamers and CMEs

1994 ◽  
Vol 144 ◽  
pp. 82
Author(s):  
E. Hildner
Keyword(s):  
Emission Line ◽  
Electron Density ◽  
White Light ◽  
Coronal Mass Ejections ◽  
X Rays ◽  
Solar Cycles ◽  
Temperature Function ◽  
X Ray ◽  
Eclipse Observations ◽  
Coronal Structures

AbstractOver the last twenty years, orbiting coronagraphs have vastly increased the amount of observational material for the whitelight corona. Spanning almost two solar cycles, and augmented by ground-based K-coronameter, emission-line, and eclipse observations, these data allow us to assess,inter alia: the typical and atypical behavior of the corona; how the corona evolves on time scales from minutes to a decade; and (in some respects) the relation between photospheric, coronal, and interplanetary features. This talk will review recent results on these three topics. A remark or two will attempt to relate the whitelight corona between 1.5 and 6 R⊙to the corona seen at lower altitudes in soft X-rays (e.g., with Yohkoh). The whitelight emission depends only on integrated electron density independent of temperature, whereas the soft X-ray emission depends upon the integral of electron density squared times a temperature function. The properties of coronal mass ejections (CMEs) will be reviewed briefly and their relationships to other solar and interplanetary phenomena will be noted.

Iron K-Line Emission from X-Ray Binaries

1988 ◽  
Vol 102 ◽  
pp. 47-50
Author(s):  
K. Masai ◽  
S. Hayakawa ◽  
F. Nagase
Keyword(s):  
Accretion Disk ◽  
Radiative Recombination ◽  
Characteristic Temperature ◽  
Line Emission ◽  
Ionization Front ◽  
Continuum Radiation ◽  
X Ray ◽  
Low Mass ◽  
X Ray Binaries

AbstractEmission mechanisms of the iron Kα-lines in X-ray binaries are discussed in relation with the characteristic temperature Txof continuum radiation thereof. The 6.7 keV line is ascribed to radiative recombination followed by cascades in a corona of ∼ 100 eV formed above the accretion disk. This mechanism is attained for Tx≲ 10 keV as observed for low mass X-ray binaries. The 6.4 keV line observed for binary X-ray pulsars with Tx> 10 keV is likely due to fluorescence outside the He II ionization front.

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