scholarly journals Phosphate-binding protein fromPolaromonasJS666: purification, characterization, crystallization and sulfur SAD phasing

2017 ◽  
Vol 73 (6) ◽  
pp. 342-346 ◽  
Author(s):  
Vanessa R. Pegos ◽  
Louis Hey ◽  
Jacob LaMirande ◽  
Rachel Pfeffer ◽  
Rosalie Lipsh ◽  
...  
Keyword(s):  
Binding Mode ◽  
Binding Activity ◽  
X Ray Diffraction ◽  
Phosphate Binding ◽  
X Ray ◽  
Sad Phasing ◽  
Binding Residues ◽  
Phosphate Binding Protein ◽  
Binding Cleft ◽  
Aspartate Residue

Phosphate-binding proteins (PBPs) are key proteins that belong to the bacterial ABC-type phosphate transporters. PBPs are periplasmic (or membrane-anchored) proteins that capture phosphate anions from the environment and release them to the transmembrane transporter. Recent work has suggested that PBPs have evolved for high affinity as well as high selectivity. In particular, a short, unique hydrogen bond between the phosphate anion and an aspartate residue has been shown to be critical for selectivity, yet is not strictly conserved in PBPs. Here, the PBP fromPolaromonasJS666 is focused on. Interestingly, this PBP is predicted to harbor different phosphate-binding residues to currently known PBPs. Here, it is shown that the PBP fromPolaromonasJS666 is capable of binding phosphate, with a maximal binding activity at pH 8. Its structure is expected to reveal its binding-cleft configuration as well as its phosphate-binding mode. Here, the expression, purification, characterization, crystallization and X-ray diffraction data collection to 1.35 Å resolution of the PBP fromPolaromonasJS666 are reported.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of human phosphate-binding protein

2005 ◽  
Vol 62 (1) ◽  
pp. 67-69 ◽  
Author(s):  
Carlos Contreras-Martel ◽  
Philippe Carpentier ◽  
Renaud Morales ◽  
Frédérique Renault ◽  
Marie-Laure Chesne-Seck ◽  
...  
Keyword(s):  
Diffraction Analysis ◽  
Binding Protein ◽  
X Ray Diffraction ◽  
Phosphate Binding ◽  
X Ray ◽  
Phosphate Binding Protein

scholarly journals Crystallization and preliminary X-ray diffraction analysis of the phosphate-binding protein PhoX fromXanthomonas citri

2014 ◽  
Vol 70 (12) ◽  
pp. 1604-1607 ◽  
Author(s):  
Vanessa R. Pegos ◽  
Francisco Javier Medrano ◽  
Andrea Balan
Keyword(s):  
Binding Protein ◽  
Structural Data ◽  
Citrus Canker ◽  
Economic Losses ◽  
X Ray Diffraction ◽  
Phosphate Binding ◽  
Canker Disease ◽  
X Ray ◽  
Periplasmic Binding Proteins ◽  
Phosphate Binding Protein

Xanthomonas axonopodispv.citri(X. citri) is an important bacterium that causes citrus canker disease in plants in Brazil and around the world, leading to significant economic losses. Determination of the physiology and mechanisms of pathogenesis of this bacterium is an important step in the development of strategies for its containment. Phosphate is an essential ion in all microrganisms owing its importance during the synthesis of macromolecules and in gene and protein regulation. Interestingly,X. citrihas been identified to present two periplasmic binding proteins that have not been further characterized: PstS, from an ATP-binding cassette for high-affinity uptake and transport of phosphate, and PhoX, which is encoded by an operon that also contains a putative porin for the transport of phosphate. Here, the expression, purification and crystallization of the phosphate-binding protein PhoX and X-ray data collection at 3.0 Å resolution are described. Biochemical, biophysical and structural data for this protein will be helpful in the elucidation of its function in phosphate uptake and the physiology of the bacterium.

scholarly journals Optimization in S-SAD phasing - difference between solved and unsolved structure

2014 ◽  
Vol 70 (a1) ◽  
pp. C613-C613
Author(s):  
Jan Stránský ◽  
Tomáš Kovaľ ◽  
Lars Østergaard ◽  
Jarmila Dušková ◽  
Tereza Skálová ◽  
...  
Keyword(s):  
Data Processing ◽  
De Novo ◽  
Protein Structures ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Sad Phasing ◽  
Optimal Values ◽  
Grant Agency ◽  
Intensity Reading

Development of X-ray diffraction technologies have made de novo phasing of protein structures by single-wavelength anomalous dispersion by sulphur (S-SAD) more common. As anomalous differences in the sulphur atomic factors are in the order of errors of measurement, careful intensity reading and data processing are crucial. S-SAD was used for de novo phasing of a small 12 kDa protein with 4 sulphur atoms per molecule at 2.3 Å, where the data did not enable a straightforward structure solution. Data processing was performed using XDS [1] and scaling using XSCALE. The sulphur substructure was determined by SHELXD [2] and phases were obtained from SHELXE [2]. Both algorithms strongly depend on input parameters and default values did not lead to the correct phases. Therefore a systematic search of optimal values of several parameters was used to find a solution. This method helped to confirm sulphur substructure and to differentiate the handedness of the solutions. Moreover, a script for comfortable conversion of SHELX outputs to MTZ format was developed, using programmes included in the CCP4 package [3]. The previously unsolvable protein structure was successfully resolved with the described procedure. This work was supported by the Grant Agency of the Czech Technical University in Prague, (SGS13/219/OHK4/3T/14), the Czech Science Foundation (P302/11/0855), project BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF.

scholarly journals Formation of Tetranuclear Nickel(II) Complexes with Schiff-Bases: Crystal Structures and Magnetic Properties

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 592 ◽  
Author(s):  
Zhonglu You ◽  
Yingying Luo ◽  
Susan Herringer ◽  
Yanmin Li ◽  
Silvio Decurtins ◽  
...  
Keyword(s):  
Bond Angle ◽  
Binding Mode ◽  
Ferromagnetic Behavior ◽  
X Ray Diffraction ◽  
Schiff Base Ligands ◽  
X Ray ◽  
Structural Correlation ◽  
Magnetization Data ◽  
Coupling Parameters ◽  
Nonzero Spin

The cubane-type structure is a typical representative of tetranuclear coordination compounds. In this work, two anionic Schiff-base ligands, (L1)2− and (L2)2−, each offering an O^N^O coordination pocket, ligate four NiII ions into a [Ni4O4] cubane core. The ligands are H2L1 = 2−[[(3-ethoxy-2−hydroxyphenyl) methylene]amino]benzenemethanol and H2L2 = 2−[[(5-fluoro-2−hydroxyphenyl)methylene]amino]benzenemethanol. In both compounds, [Ni4(L1)4(EtOH)4] (1) and [Ni4(L2)4(MeOH)4] (2), alkoxy oxygens of the ligands act in a bridging μ3-O binding mode. Magnetic susceptibility and magnetization data for compounds 1 and 2 are presented. The Ni–O–Ni bond angles of the cubane core determined from single crystal X-ray diffraction data play a key role for a magneto-structural correlation. Dominant intracube ferromagnetic behavior is observed, and the coupling parameters were determined for both compounds, leading to nonzero spin ground states in accordance with the broadly accepted bond angle guideline.

The effect of coordinated water on the connectivity of uranium(IV) sulfatex-hydrate: [U(SO4)2(H2O)5]·H2O and [U(SO4)2(H2O)6]·2H2O, and a comparison with other known structures

2014 ◽  
Vol 70 (7) ◽  
pp. 726-731 ◽  
Author(s):  
Alexander D. Burns ◽  
Brian O. Patrick ◽  
Anita E. Lam ◽  
David Dreisinger
Keyword(s):  
Raman Spectroscopy ◽  
Binding Mode ◽  
Three Dimensions ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
Anhydrous Compound ◽  
Coordinated Water ◽  
Ir And Raman ◽  
Sulfate Complexes

Two new solid-state uranium(IV) sulfatex-hydrate complexes (wherexis the total number of coordinated plus solvent waters), namelycatena-poly[[pentaaquauranium(IV)]-di-μ-sulfato-κ4O:O′] monohydrate], {[U(SO4)2(H2O)5]·H2O}n, and hexaaquabis(sulfato-κ2O,O′)uranium(IV) dihydrate, [U(SO4)2(H2O)6]·2H2O, have been synthesized, structurally characterized by single-crystal X-ray diffraction and analyzed by vibrational (IR and Raman) spectroscopy. By comparing these structures with those of four other known uranium(IV) sulfatex-hydrates, the effect of additional coordinated water molecules on their structures has been elucidated. As the number of coordinated water molecules increases, the sulfate bonds are displaced, thus changing the binding mode of the sulfate ligands to the uranium centre. As a result, uranium(IV) sulfatex-hydrate changes from being fully crosslinked in three dimensions in the anhydrous compound, through sheet and chain linking in the tetra- and hexahydrates, to fully unlinked molecules in the octa- and nonahydrates. It can be concluded that coordinated waters play an important role in determining the structure and connectivity of UIVsulfate complexes.

scholarly journals Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution

2018 ◽  
Vol 122 (24) ◽  
pp. 6371-6376 ◽  
Author(s):  
Rui Qi ◽  
Zhifeng Jing ◽  
Chengwen Liu ◽  
Jean-Philip Piquemal ◽  
Kevin N. Dalby ◽  
...  
Keyword(s):  
Binding Protein ◽  
Binding Mode ◽  
Phosphate Binding ◽  
Buffer Solution ◽  
Critical Effect ◽  
Phosphate Binding Protein

scholarly journals Isonitrile-Based Multicomponent Synthesis of β-Amino Boronic Acids as β-Lactamase Inhibitors

Antibiotics ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 249 ◽  
Author(s):  
Emanuele Bassini ◽  
Stefano Gazzotti ◽  
Filomena Sannio ◽  
Leonardo Lo Presti ◽  
Jacopo Sgrignani ◽  
...  
Keyword(s):  
Multicomponent Reactions ◽  
Inhibitory Concentration ◽  
Binding Mode ◽  
Antimicrobial Activities ◽  
X Ray Diffraction ◽  
Multicomponent Synthesis ◽  
X Ray ◽  
Class D ◽  
11B Nmr ◽  
Van Leusen Reaction

The application of various isonitrile-based multicomponent reactions to protected (2-oxoethyl)boronic acid (as the carbonyl component) is described. The Ugi reaction, both in the four components and in the four centers–three components versions, and the van Leusen reaction, proved effective at providing small libraries of MIDA-protected β-aminoboronic acids. The corresponding free β-aminoboronic acids, quantitatively recovered through basic mild deprotection, were found to be quite stable and were fully characterized, including by 11B-NMR spectroscopy. Single-crystal X-ray diffraction analysis, applied both to a MIDA-protected and a free β-aminoboronic acid derivative, provided evidence for different conformations in the solid-state. Finally, the antimicrobial activities of selected compounds were evaluated by measuring their minimal inhibitory concentration (MIC) values, and the binding mode of the most promising derivative on OXA-23 class D β-lactamase was predicted by a molecular modeling study.

scholarly journals Structural and Functional Analysis of the Complex between Citrate and the Zinc Peptidase Carboxypeptidase A

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
Daniel Fernández ◽  
Ester Boix ◽  
Irantzu Pallarès ◽  
Francesc X. Avilés ◽  
Josep Vendrell
Keyword(s):  
Oral Delivery ◽  
Binding Mode ◽  
Competitive Inhibitor ◽  
Zinc Ion ◽  
X Ray Diffraction ◽  
Carboxypeptidase A ◽  
X Ray ◽  
Citrate Complex ◽  
First Time ◽  
Catalytic Zinc

A high-resolution carboxypeptidase-Zn2+-citrate complex was studied by X-ray diffraction and enzyme kinetics for the first time. The citrate molecule acts as a competitive inhibitor of this benchmark zinc-dependent peptidase, chelating the catalytic zinc ion in the active site of the enzyme and inducing a conformational change such that carboxypeptidase adopts the conformation expected to occur by substrate binding. Citrate adopts an extended conformation with half of the molecule facing the zinc ion, while the other half is docked in the S1′ hydrophobic specificity pocket of the enzyme, in contrast with the binding mode expected for a substrate like phenylalanine or a peptidomimetic inhibitor like benzylsuccinic acid. Combined structural and enzymatic analysis describes the characteristics of the binding of this ligand that, acting against physiologically relevant zinc-dependent proteases, may serve as a general model in the design of new drug-protecting molecules for the oral delivery of drugs of peptide origin.

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