scholarly journals High-resolution neutron crystallography visualizes an OH-bound resting state of a copper-containing nitrite reductase

2020 ◽  
Vol 117 (8) ◽  
pp. 4071-4077 ◽  
Author(s):  
Yohta Fukuda ◽  
Yu Hirano ◽  
Katsuhiro Kusaka ◽  
Tsuyoshi Inoue ◽  
Taro Tamada
Keyword(s):  
Computational Chemistry ◽  
Structural Biology ◽  
Resting State ◽  
Catalytic Mechanism ◽  
Low Ph ◽  
Intramolecular Electron Transfer ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Electron Transfer Pathway ◽  
Neutron Structure

Copper-containing nitrite reductases (CuNIRs) transform nitrite to gaseous nitric oxide, which is a key process in the global nitrogen cycle. The catalytic mechanism has been extensively studied to ultimately achieve rational control of this important geobiochemical reaction. However, accumulated structural biology data show discrepancies with spectroscopic and computational studies; hence, the reaction mechanism is still controversial. In particular, the details of the proton transfer involved in it are largely unknown. This situation arises from the failure of determining positions of hydrogen atoms and protons, which play essential roles at the catalytic site of CuNIRs, even with atomic resolution X-ray crystallography. Here, we determined the 1.50 Å resolution neutron structure of a CuNIR from Geobacillus thermodenitrificans (trimer molecular mass of ∼106 kDa) in its resting state at low pH. Our neutron structure reveals the protonation states of catalytic residues (deprotonated aspartate and protonated histidine), thus providing insights into the catalytic mechanism. We found that a hydroxide ion can exist as a ligand to the catalytic Cu atom in the resting state even at a low pH. This OH-bound Cu site is unexpected from previously given X-ray structures but consistent with a reaction intermediate suggested by computational chemistry. Furthermore, the hydrogen-deuterium exchange ratio in our neutron structure suggests that the intramolecular electron transfer pathway has a hydrogen-bond jump, which is proposed by quantum chemistry. Our study can seamlessly link the structural biology to the computational chemistry of CuNIRs, boosting our understanding of the enzymes at the atomic and electronic levels.

scholarly journals Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques

Biomolecules ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 370 ◽  
Author(s):  
Linda Cerofolini ◽  
Marco Fragai ◽  
Enrico Ravera ◽  
Christoph A. Diebolder ◽  
Ludovic Renault ◽  
...  
Keyword(s):  
Structural Biology ◽  
Catalytic Mechanism ◽  
X Ray ◽  
X Ray Crystallography ◽  
X Ray Scattering ◽  
Protein Model ◽  
Pros And Cons ◽  
Transient Interactions ◽  
Single Technique ◽  
Nmr Restraints

With the recent technological and computational advancements, structural biology has begun to tackle more and more difficult questions, including complex biochemical pathways and transient interactions among macromolecules. This has demonstrated that, to approach the complexity of biology, one single technique is largely insufficient and unable to yield thorough answers, whereas integrated approaches have been more and more adopted with successful results. Traditional structural techniques (X-ray crystallography and Nuclear Magnetic Resonance (NMR)) and the emerging ones (cryo-electron microscopy (cryo-EM), Small Angle X-ray Scattering (SAXS)), together with molecular modeling, have pros and cons which very nicely complement one another. In this review, three examples of synergistic approaches chosen from our previous research will be revisited. The first shows how the joint use of both solution and solid-state NMR (SSNMR), X-ray crystallography, and cryo-EM is crucial to elucidate the structure of polyethylene glycol (PEG)ylated asparaginase, which would not be obtainable through any of the techniques taken alone. The second deals with the integrated use of NMR, X-ray crystallography, and SAXS in order to elucidate the catalytic mechanism of an enzyme that is based on the flexibility of the enzyme itself. The third one shows how it is possible to put together experimental data from X-ray crystallography and NMR restraints in order to refine a protein model in order to obtain a structure which simultaneously satisfies both experimental datasets and is therefore closer to the ‘real structure’.

Copper–oxygen Dynamics in Tyrosinase

2019 ◽  
Author(s):  
Nobutaka Fujieda ◽  
Sachiko Yanagisawa ◽  
Minoru Kubo ◽  
Genji Kurisu ◽  
Shinobu Itoh
Keyword(s):  
Catalytic Mechanism ◽  
Substrate Binding ◽  
Active Form ◽  
Copper Ion ◽  
Atomic Resolution ◽  
Oxygen Species ◽  
X Ray ◽  
Oxygen Dynamics ◽  
Insight Into ◽  
Copper Centre

To unveil the activation of dioxygen on the copper centre (Cu<sub>2</sub>O<sub>2</sub>core) of tyrosinase, we performed X-ray crystallograpy with active-form tyrosinase at near atomic resolution. This study provided a novel insight into the catalytic mechanism of the tyrosinase, including the rearrangement of copper-oxygen species as well as the intramolecular migration of copper ion induced by substrate-binding.<br>

scholarly journals Discovery of fungal surface NADases predominantly present in pathogenic species

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Øyvind Strømland ◽  
Juha P. Kallio ◽  
Annica Pschibul ◽  
Renate H. Skoge ◽  
Hulda M. Harðardóttir ◽  
...  
Keyword(s):  
Cell Death ◽  
Aspergillus Fumigatus ◽  
Neurospora Crassa ◽  
Binding Site ◽  
Host Cell ◽  
Nicotinamide Adenine Dinucleotide ◽  
Catalytic Mechanism ◽  
Pathogenic Species ◽  
X Ray ◽  
Cellular Bioenergetics

AbstractNicotinamide adenine dinucleotide (NAD) is a key molecule in cellular bioenergetics and signalling. Various bacterial pathogens release NADase enzymes into the host cell that deplete the host’s NAD+ pool, thereby causing rapid cell death. Here, we report the identification of NADases on the surface of fungi such as the pathogen Aspergillus fumigatus and the saprophyte Neurospora crassa. The enzymes harbour a tuberculosis necrotizing toxin (TNT) domain and are predominately present in pathogenic species. The 1.6 Å X-ray structure of the homodimeric A. fumigatus protein reveals unique properties including N-linked glycosylation and a Ca2+-binding site whose occupancy regulates activity. The structure in complex with a substrate analogue suggests a catalytic mechanism that is distinct from those of known NADases, ADP-ribosyl cyclases and transferases. We propose that fungal NADases may convey advantages during interaction with the host or competing microorganisms.

Design of a novel Peltier-based cooling device and its use in neutron diffraction data collection of perdeuterated yeast pyrophosphatase

2010 ◽  
Vol 43 (5) ◽  
pp. 1113-1120 ◽  
Author(s):  
Esko Oksanen ◽  
François Dauvergne ◽  
Adrian Goldman ◽  
Monika Budayova-Spano
Keyword(s):  
Data Collection ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Catalytic Mechanism ◽  
Inorganic Pyrophosphatase ◽  
Neutron Diffraction Data ◽  
Cooling Device ◽  
Data Set ◽  
X Ray ◽  
X Ray Crystallography

H atoms play a central role in enzymatic mechanisms, but H-atom positions cannot generally be determined by X-ray crystallography. Neutron crystallography, on the other hand, can be used to determine H-atom positions but it is experimentally very challenging. Yeast inorganic pyrophosphatase (PPase) is an essential enzyme that has been studied extensively by X-ray crystallography, yet the details of the catalytic mechanism remain incompletely understood. The temperature instability of PPase crystals has in the past prevented the collection of a neutron diffraction data set. This paper reports how the crystal growth has been optimized in temperature-controlled conditions. To stabilize the crystals during neutron data collection a Peltier cooling device that minimizes the temperature gradient along the capillary has been developed. This device allowed the collection of a full neutron diffraction data set.

The first proof of protonated anion tetrahedra in the tsumcorite-type compounds

2004 ◽  
Vol 68 (5) ◽  
pp. 757-767 ◽  
Author(s):  
T. Mihajlović ◽  
H. Effenberger
Keyword(s):  
Crystal Structure ◽  
Hydrothermal Synthesis ◽  
Single Crystal ◽  
Diffraction Data ◽  
Title Compound ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Synthetic Compounds ◽  
X Ray

AbstractHydrothermal synthesis produced the new compound SrCo2(AsO4)(AsO3OH)(OH)(H2O). The compound belongs to the tsumcorite group (natural and synthetic compounds with the general formula M(1)M(2)2(XO4)2(H2O,OH)2; M(1)1+,2+,3+ = Na, K, Rb, Ag, NH4, Ca, Pb, Bi, Tl; M(2)2+,3+ = Al, Mn3+, Fe3+, Co, Ni, Cu, Zn; and X5+,6+ = P, As, V, S, Se, Mo). It represents (1) the first Sr member, (2) the until now unknown [7]-coordination for the M(1) position, (3) the first proof of (partially) protonated arsenate groups in this group of compounds, and (4) a new structure variant.The crystal structure of the title compound was determined using single-crystal X-ray diffraction data. The compound is monoclinic, space group P21/a, with a = 9.139(2), b = 12.829(3), c = 7.522(2) Å, β = 114.33(3)°, V = 803.6(3) Å3, Z = 4 [wR2 = 0.065 for 3530 unique reflections]. The hydrogen atoms were located experimentally.

scholarly journals Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

2013 ◽  
Vol 6 (1) ◽  
pp. 308 ◽  
Author(s):  
Mikael Elias ◽  
Dorothee Liebschner ◽  
Jurgen Koepke ◽  
Claude Lecomte ◽  
Benoit Guillot ◽  
...  
Keyword(s):  
High Resolution ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Diffraction Structure

Bestimmung von innermolekularen Torsionswinkeln aus Hyperfeinstruktur-Aufspaltungen und g-Faktoren

1965 ◽  
Vol 20 (9) ◽  
pp. 1117-1121 ◽  
Author(s):  
K. Möbius
Keyword(s):  
Electron Diffraction ◽  
Aromatic Hydrocarbon ◽  
Aromatic Hydrocarbons ◽  
Small Amplitude ◽  
Membered Ring ◽  
Radical Ions ◽  
Hydrogen Atoms ◽  
Stereochemical Structure ◽  
X Ray ◽  
Phenyl Rings

The stereochemical structure of aromatic hydrocarbons in solution being overcrowded with hydrogen atoms is not known with certainty, because the conventional X-ray and electron diffraction methods are suitable only for samples in the crystalline and vapor phase. Using EPR spectroscopy for the aromatic hydrocarbon radicals biphenyl (—), phenanthrene (—) and pentaphenylcyclopentadienyl (PPCPD) innermolecular twist and bond angles could be determined by means of hfssplittings and g-factors. Stably solvated biphenyl radical ions are found to have twist angles of 38 ±2°; phenanthrene ions turn out to be planar but change their angles of hybridization at particular positions; in the PPCPD radical the phenyl rings oscillate with small amplitude around planes orthogonal to the five-membered ring.

Distinguishment of Weak Interactions of Hydrogen Atoms Bound to Carbon Atoms: X-Ray Crystal Structural and Hirshfeld Surface Analyses of 2-Hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene with the 2-Methoxylated Homologue

2021 ◽  
Vol 19 ◽  
Author(s):  
Kikuko Iida ◽  
Toyokazu Muto ◽  
Miyuki Kobayashi ◽  
Hiroaki Iitsuka ◽  
Kun Li ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Molecular Conformation ◽  
Weak Interactions ◽  
Carbonyl Oxygen ◽  
Hirshfeld Surface ◽  
Molecular Surface ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Classical Hydrogen Bond

Abstract: X-ray crystal and Hirshfeld surface analyses of 2-hydroxy-7-methoxy-3-(2,4,6-trimethylbenzoyl)naphthalene and its 2-methoxylated homologue show quantitatively and visually distinct molecular contacts in crystals and minute differences in the weak intermolecular interactions. The title compound has a helical tubular packing, where molecules are piled in a two-folded head-to-tail fashion. The homologue has a tight zigzag molecular string lined up behind each other via nonclassical intermolecular hydrogen bonds between the carbonyl oxygen atom and the hydrogen atom of the naphthalene ring. The dnorm index obtained from the Hirshfeld surface analysis quantitatively demonstrates stronger molecular contacts in the homologue, an ethereal compound, than in the title compound, an alcohol, which is consistent with the higher melting temperature of the former than the latter. Stabilization through the significantly weak intermolecular nonclassical hydrogen bonding interactions in the homologue surpasses the stability imparted by the intramolecular C=O…H–O classical hydrogen bonds in the title compound. The classical hydrogen bond places the six-membered ring in the concave of the title molecule. The hydroxy group opposingly disturbs the molecular aggregation of the title compound, as demonstrated by the distorted H…H interactions covering the molecular surface, owing to the rigid molecular conformation. The position of effective interactions predominate over the strength of the classical/nonclassical hydrogen bonds in the two compounds.

scholarly journals Electrochemical hydrogenation, lithiation and sodiation of the GdFe2–xMx and GdMn2–xMx intermetallics

2021 ◽  
pp. 139-149
Keyword(s):  
Electrode Materials ◽  
Electrochemical Impedance ◽  
Diffraction Method ◽  
Electrochemical Characteristics ◽  
Electrochemical Hydrogenation ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Cell Parameters ◽  
The Difference ◽  
Better Than

Electrochemical hydrogenation, lithiation and sodiation of the phases GdFe2–xMx and GdMn2–xMx (M=Mn, Co, Ni, Zn, and Mg) and the influence of doping components on electrochemical characteristics of electrode materials on their basis were studied using X-ray powder diffraction method, scanning electron microscopy, energy dispersive X-ray analysis, X-ray fluorescent spectroscopy, cyclic voltammetry and electrochemical impedance spectroscopy. Phase analysis showed a simple correspondence between unit cell parameters of the phases and atomic radii of doping elements. Electrode materials based on GdFe2 and GdMn2 doped with 2 at.% of Co, Ni and Mg demonstrated better hydrogen sorption properties than those doped with Mn and Zn. Corrosion resistance of the doped electrodes was also better than of the binary analogues (e.g. corrosion potential of the GdFe2-based electrode was –0.162 V whereas that of GdFe1.96Ni0.04 was –0.695 V). The capacity parameters were increased in the following ranges: Zn<Mn<Mg<Co<Ni and Zn<Fe<Mg<Co<Ni for GdFe2–xMx and GdMn2–xMx, respectively. After fifty cycles of charge/discharge, we observed the changes in surface morphology and composition of the electrode samples. In the structure of studied Laves type phases with MgCu2-type structure, the most suitable sites for hydrogen atoms are tetrahedral voids 8a. During lithiation and sodiation of the phases, the atoms of the M-component of the structure are replaced by the atoms of lithium, and the atoms of gadolinium are replaced by the atoms of sodium. This difference in interaction is due to the difference in atomic sizes of the atoms. No insertion of lithium or sodium into the structural voids of the phases was observed.

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