Evolutionarily conserved cysteines in plant cytosolic seryl-tRNA synthetase are important for its resistance to oxidation.

We have previously identified a unique disulfide bond in the crystal structure of Arabidopsis cytosolic seryl-tRNA synthetase involving cysteines evolutionarily conserved in all green plants. Here, we discovered that both cysteines are important for protein stability, but with opposite effects, and that their microenvironment may promote disulfide bond formation in oxidizing conditions. The crystal structure of the C244S mutant exhibited higher rigidity and an extensive network of noncovalent interactions correlating with its higher thermal stability. The activity of the wild-type showed resistance to oxidation with H2 O2 , while the activities of cysteine-to-serine mutants were impaired, indicating that the disulfide link may enable the protein to function under oxidative stress conditions which can be beneficial for an efficient plant stress response.

Zn(II) halide coordination compounds with imidazole and 2-methylimidazole. Structural and computational characterization of intermolecular interactions and disorder.

Novel zinc(II) coordination compounds with imidazole (Im) and 2-methylimidazole (2-MeIm) were prepared and characterized: [ZnX2(Im)2] (X = Cl (1a), Br (1b), I (1c)) and [ZnX2(2-MeIm)2] (X = Cl (2a), Br (2b), I (2c)). Coordination compounds 1a-c were prepared mechanochemically by neat grinding while 2a-c were prepared by solution synthesis. The complexes were characterized by FT-IR and NMR spectroscopy and by powder X-ray diffraction. Crystal and molecular structures were determined by the single crystal X-ray diffraction. The characteristic of all structures is a distorted tetrahedral coordination of zinc consisting of two halide atoms and two nitrogen atoms from the imidazole (or 2-methylimidazole) ligand. Molecules in 1a-c are interconnected by hydrogen bonds into 3D structures. Structures of 1b and 1c were found to have similar unit cells and similar crystal packing and hydrogen bonding. Introduction of the 2-methylimidazole substituent introduced disorder in the crystal structures of 2a-c. Because of the very small size of the crystals data were collected by synchrotron radiation. For the disordered 2a , 2b and 2c fixed geometry was used in refining of the structures. Crystal structures of 2a-c are characterized by chains of molecules connected by hydrogen bonds of the type N-H⋅⋅⋅X, with weak π⋅⋅⋅π and van der Waals interactions between the chains. The QTAIM, RDG and NCI computational analysis of 1a and 2a-c confirmed the presence of weak attractive intermolecular interactions that can be attributed to weak N-H⋅⋅⋅X and van der Waals interactions.

Copper Binding and Oligomerization Studies of the Metal Resistance Determinant CrdA from Helicobacter pylori.

Within this research, the CrdA protein from Helicobacter pylori (HpCrdA), a putative copper-binding protein important for the survival of bacterium, was biophysically characterized in a solution, and its binding affinity toward copper was experimentally determined. Incubation of HpCrdA with Cu(II) ions favors the formation of the monomeric species in the solution. The modeled HpCrdA structure shows a conserved methionine-rich region, a potential binding site for Cu(I), as in the structures of similar copper-binding proteins, CopC and PcoC, from Pseudomonas syringae and from Escherichia coli, respectively. Within the conserved amino acid motif, HpCrdA contains two additional methionines and two glutamic acid residues (MMXEMPGMXXMXEM) in comparison to CopC and PcoC but lacks the canonical Cu(II) binding site (two His) since the sequence has no His residues. The methionine-rich site is in a flexible loop and can adopt different geometries for the two copper oxidation states. It could bind copper in both oxidation states (I and II), but with different binding affinities, micromolar was found for Cu(II), and less than nanomolar is proposed for Cu(I). Considering that CrdA is a periplasmic protein involved in chaperoning copper export and delivery in the H. pylori cell and that the affinity of the interaction corresponds to a middle or strong metal-protein interaction depending on the copper oxidation state, we conclude that the interaction also occurs in vivo and is physiologically relevant for H. pylori.

Binding of dipeptidyl peptidase III to the oxidative stress cell sensor Kelch-like ECH-associated protein 1 is a two-step process.

This work is about synergy of theory and experiment in revealing mechanism of binding of dipeptidyl peptidase III (DPP III) and Kelch-like ECH-associated protein 1 (KEAP1), the main cellular sensor of oxidative stress. The NRF2 ̶ KEAP1 signaling pathway is important for cell protection, but it is also impaired in many cancer cells where NRF2 target gene expression leads to resistance to chemotherapeutic drugs. DPP III competitively binds to KEAP1 in the conditions of oxidative stress and induces release of NRF2 and its translocation into nucleus. The binding is established mainly through the ETGE motif of DPP III and the Kelch domain of KEAP1. However, although part of a flexible loop, ETGE itself is firmly attached to the DPP III surface by strong hydrogen bonds. Using combined computational and experimental study, we found that DPP III ̶ Kelch binding is a two-step process comprising the endergonic loop detachment and exergonic DPP III ̶ Kelch interaction. Substitution of arginines, which keep the ETGE motif attached, decreases the work needed for its release and increases DPP III ̶ Kelch binding affinity. Interestingly, mutations of one of these arginine residues have been reported in cBioPortal for cancer genomics, implicating its possible involvement in cancer development. Communicated by Ramaswamy H. Sarma.

Phenylboronic Acids Probing Molecular Recognition against Class A and Class C ß-lactamases.

Worldwide dissemination of pathogens resistant to almost all available antibiotics represent a real problem preventing efficient treatment of infectious diseases. Among antimicrobial used in therapy, ß-lactam antibiotics represent 40% thus playing a crucial role in the management of infections treatment. We report a small series of phenylboronic acids derivatives (BAs) active against class A carbapenemases KPC-2 and GES-5, and class C cephalosporinases AmpC. The inhibitory profile of our BAs against class A and C was investigated by means of molecular docking, enzyme kinetics and X-ray crystallography. We were interested in the mechanism of recognition among class A and class C to direct the design of broad serine ß-Lactamases (SBLs) inhibitors. Molecular modeling calculations vs GES-5 and crystallographic studies vs AmpC reasoned, respectively, the ortho derivative 2 and the meta derivative 3 binding affinity. The ability of our BAs to protect ß-lactams from BLs hydrolysis was determined in biological assays conducted against clinical strains: Fractional inhibitory concentration index (FICI) tests confirmed their ability to be synergic with ß-lactams thus restoring susceptibility to meropenem. Considering the obtained results and the lack of cytotoxicity, our derivatives represent validated probe for the design of SBLs inhibitors.

Arabidopsis seryl-tRNA synthetase: the first crystal structure and novel protein interactor of plant aminoacyl-tRNA synthetase.

The rules of the genetic code are established by aminoacyl-tRNA synthetases (aaRSs) enzymes, which covalently link tRNA with the cognate amino acid. Many aaRSs are involved in diverse cellular processes beyond translation, acting alone, or in complex with other proteins. However, studies of aaRS noncanonical assembly and functions in plants are scarce, as are structural studies of plant aaRSs. Here, we have solved the crystal structure of Arabidopsis thaliana cytosolic seryl-tRNA synthetase (SerRS), which is the first crystallographic structure of a plant aaRS. Arabidopsis SerRS displays structural features typical of canonical SerRSs, except for a unique intrasubunit disulfide bridge. In a yeast two-hybrid screen, we identified BEN1, a protein involved in the metabolism of plant brassinosteroid hormones, as a protein interactor of Arabidopsis SerRS. The SerRS:BEN1 complex is one of the first protein complexes of plant aaRSs discovered so far, and is a rare example of an aaRS interacting with an enzyme involved in primary or secondary metabolism. To pinpoint regions responsible for this interaction, we created truncated variants of SerRS and BEN1, and identified that the interaction interface involves the SerRS globular catalytic domain and the N-terminal extension of BEN1 protein. BEN1 does not have a strong impact on SerRS aminoacylation activity, indicating that the primary function of the complex is not the modification of SerRS canonical activity. Perhaps SerRS performs as yet unknown noncanonical functions mediated by BEN1. These findings indicate that - via SerRS and BEN1 - a link exists between the protein translation and steroid metabolic pathways of the plant cell. DATABASE: Structural data are available in the PDB under the accession number PDB ID 6GIR.

Structural characterization of FlgE2 protein from Helicobacter pylori hook.

The Helicobacter pylori flagellum is a complex rotatory nanomachine fundamental for the bacterium's survival in the human stomach. Protein FlgE is a component of the hook, a flexible junction exposed on the cell surface. In the H. pylori genome two different genes are present in different positions coding for hypothetical FlgE. The first protein, FlgE1, is the actual component of the flagellum hook, whilst the second, FlgE2, shares only 26% of the sequence identity with the other and its physiological function is still undefined. We have cloned, purified and crystallized FlgE2, whose structure, determined by the single-wavelength anomalous diffraction method, shows that in overall organization, the protein is composed of three distinct domains, two of them relatively similar to those of FlgE from other Gram-negative bacteria, whilst the third is peculiar to H. pylori. The crystal structure, along with the detected interaction with the regulatory cap protein FlgD, suggests a complementary function of FlgE1 and FlgE2 in the H. pylori flagellum, possibly typical of polar flagella, confirming the role of both proteins in the flagellar hook organization. Although some general features are shared with other Gram-negative bacteria, the presence of two different hook proteins indicates that the molecular organization of H. pylori flagellum has its own peculiarities. DATABASE: Atomic coordinates and structural factors have been deposited in the Protein Data Bank as 5NPY.