A Puzzling Protein from Variovorax paradoxus Has a PLP Fold Type IV Transaminase Structure and Binds PLP without Catalytic Lysine

Effective biocatalysts for the synthesis of optically pure amines from keto precursors are highly required in organic synthesis. Transaminases are a large group of PLP-dependent enzymes, which can be utilized for production of chiral amines or amino acids. The bioinformatic approach previously made to search for promising transaminases with unusual characteristics surprisingly revealed mysterious genes in some Gram-negative bacteria, which products were annotated as aminotransferases, but they lacked the key catalytic lysine residue required for covalent binding of the PLP-cofactor. To address the question of which products these genes encode, we obtained the first structure of such a type of protein from the bacterium Variovorax paradoxus (VP5454) and provided its comprehensive analysis. We demonstrated that VP5454 has a typical aminotransferase fold and architecture of the active site, where substitution of the catalytic lysine with asparagine was observed. Despite that no covalent adduct can be formed between PLP and asparagine residue, using X-ray analysis and molecular dynamic (MD) simulation, we demonstrated that VP5454 is able to bind the PLP molecule in the transaminase in a specific manner, with PLP coordinated via its phosphate moiety. Taking into account a number of sequences homologous to VP5454 with a substituted catalytic lysine found in the genomes of various bacteria, we speculate that the proteins encoded by these sequences may have hidden functional roles.

Choosing the adequate thermodynamic reference state: The evolution of pyrophosphate bioenergetics as an example

The use of the thermodynamic formalism in the investigation of biochemical reactions constitutes one of the key analysis in bioenergetics, and the first step in such analysis is the selection of the adequate reference state. For biochemistry majors, thermodynamic analysis based on the chemical reference state is used in Physical Chemistry courses, while the biological and biochemical reference states are used in Biochemistry courses. As these definitions are introduced in different courses, it is difficult that students can understand the need to select a reference state as a first step in the energy analysis of a system. The lack of suitable examples in textbooks to illustrate the importance of the adequate selection of the reference state in a thermodynamic analysis, promoted the present analysis of the energetic role of pyrophosphate (PPi) in comparison with adenosine-triphosphate in different ambient conditions, namely, the early PPi world (better described by the chemical reference state), the enclosed systems like the cells (better described by the biological reference state), and the actual thioester world (better described by the biochemical reference state). This example not only provides a new interesting point of view on the evolution of two biochemical fuels but also represents a biochemical example in which the use of different reference states can illustrate a single process from different points of views.

Fluorescence detection of phosphonates in water by a naphthalimide-based receptor and its derived cryopolymers

The concentration of compound M in cryopolymers has a dramatic influence on the fluorescence response in the presence of phosphonates.

The synergistic effect of nickel-iron-foam and tripolyphosphate for enhancing the electro-Fenton process at circum-neutral pH

A composite nickel-iron-foam (Ni-Fe-F) electrode was used as a cathode in the electro-Fenton (EF) process at circum-neutral pH in the presence of sodium tripolyphosphate (TPP) as supporting electrolyte. It was found that phenol degradation was dramatically improved by the synergistic effect of Ni-Fe-F and TPP, reaching 100% removal in 40 min, with k_app = (8.90 ± 0.12) × 10^-2 min^-1, which was about 18 times higher than that of Ni-Fe-F with sulfate as conventional electrolyte at pH 3.00 (k_app = (5.00 ± 0.14) × 10^-3 min^-1). A (75.00 ± 1.67)% mineralization yield was attained after 4-h treatment time. Ni-Fe-F proved capable of providing the Fe²⁺ ions necessary to catalyze the Fenton's reaction via a controlled chemical/electrochemical redox process. In addition, Ni-Fe-F promoted the chemical and electrochemical generation of H₂O₂. With respect to TPP, its chelation with Fe ions prevented iron precipitation at neutral and higher pH values, extending the pH range of the Fenton's reaction. Furthermore, the TPP ligand promoted the activation of molecular O₂ for the chemical production of OH, enhancing the process efficiency. By overcoming these common limitations of conventional EF in K₂SO₄ electrolyte, the Ni-Fe-F/TPP system represents a more sustainable alternative for practical application of EF. A degradation pathway for phenol mineralization with homogeneous and heterogeneous OH produced by the EF Ni-Fe-F/TPP system is proposed based on the identification of the oxidation by-products.

Chemical Transformations in Proto-Cytoplasmic Media. Phosphorus Coupling in the Silica Hydrogel Phase

It has been proposed that prebiotic chemical studies on the emergence of primitive life would be most relevant when performed in a hydrogel, rather than an aqueous, environment. In this paper we describe the ambient temperature coupling of phosphorus oxyacids [Pi] mediated by Fe(II) under aerobic conditions within a silica hydrogel (SHG) environment. We have chosen to examine SHGs as they have considerable geological precedence as key phases in silicification en route to rock formation. Following a description of the preparation and characterization studies on our SHG formulations, coupling experiments between Pi species are described across multiple permutations of (i) Pi compound; (ii) gel formulation; (iii) metal salt additive; and (iv) pH-modifying agent. The results suggest that successful Pi coupling, indicated by observation of pyrophosphate [PPi(V)] via ³¹P-NMR spectroscopy, takes place when the following components are present: (i) a mixture of mixture of Pi(III) and Pi(V) or pure PPi(III– V); (ii) Fe(II); (iii) acetic or formic acid (not hydrochloric acid); (iv) aerobic conditions or the presence of H₂O₂ as an oxidant; and (v) the presence of a gel system. On the basis of these, and aqueous control reactions, we suggest mechanistic possibilities.

Recent Trends in Nucleotide Synthesis

Focusing on the recent literature (since 2000), this review outlines the main synthetic approaches for the preparation of 5'-mono-, 5'-di-, and 5'-triphosphorylated nucleosides, also known as nucleotides, as well as several derivatives, namely, cyclic nucleotides and dinucleotides, dinucleoside 5',5'-polyphosphates, sugar nucleotides, and nucleolipids. Endogenous nucleotides and their analogues can be obtained enzymatically, which is often restricted to natural substrates, or chemically. In chemical synthesis, protected or unprotected nucleosides can be used as the starting material, depending on the nature of the reagents selected from P(III) or P(V) species. Both solution-phase and solid-support syntheses have been developed and are reported here. Although a considerable amount of research has been conducted in this field, further work is required because chemists are still faced with the challenge of developing a universal methodology that is compatible with a large variety of nucleoside analogues.

Recent advances in H-phosphonate chemistry. Part 1. H-phosphonate esters: synthesis and basic reactions

This review covers recent progress in the preparation of H-phosphonate mono- and diesters, basic studies on mechanistic and stereochemical aspects of this class of phosphorus compounds, and their fundamental chemistry in terms of transformation of P-H bonds into P-heteroatom bonds. Selected recent applications of H-phosphonate derivatives in basic organic phosphorus chemistry and in the synthesis of biologically important phosphorus compounds are also discussed.