New Zinc Coordination Compound with Simple Salicylato and Pyridine Ligands: Synthesis, Crystal Structure and Hirshfeld Surface Analysis

A novel mononuclear zinc coordination compound with formula [Zn(Hsal)2(Py)2] (H2sal = salicylic acid, Py = pyridine) was prepared by mixing aqueous solutions of sodium salicylate and zinc sulfate in 1:1 molar ratio, and to the resulting solution pyridine was added dropwise. The obtained compound was characterized by elemental analysis, IR spectroscopy, and its crystal structure was determined by single-crystal X-ray diffraction method. X-ray structure analysis has shown that the central zinc ion is four-coordinated by two monodentate salicylato ligands and two pyridine molecules, forming a distorted tetrahedron. Since the asymmetric unit consists of two halves of coordination molecules, orthorhombic Ibca space group symmetry leads to two coordination molecules with slightly different geometry. The comparison between the two is given in terms of interatomic distances and angles, and also in terms of differences in intermolecular interactions obtained as a result of Hirshfeld surface analysis. With the assistance of C−H…O interactions, the adjacent molecules are linked into chains and further connected into three-dimensional network.

Crystal structure and physical properties of a new two-dimensional zinc coordination polymer based on 1,4-bis(4-(imidazole-1-yl)benzyl)piperazine and benzophenone-2,4′-dicarboxylate ligands

A new 2-dimensional (2D) zinc(II) coordination polymer based on a flexible bis(imidazole) ligand, namely, [Zn2(BIBP)(BPDC)2·DMF] n (1) BIBP is 1,4-bis(4-(imidazole-1-yl)benzyl)piperazine and H2BPDC is benzophenone-2,4′-dicarboxylic acid), has been synthesized and characterized through single-crystal X-ray diffraction, infrared (IR) spectroscopy, and elemental and thermal gravimetric analysis. Complex 1 exhibits a 2D framework oriented parallel to [0 2 1] based on [Zn(BPDC)] n chains. The fluorescence and catalytic properties of complex 1 for the photodegradation of methylene blue were investigated.

E3 ubiquitin ligase RNF213 employs a non-canonical zinc finger active site and is allosterically regulated by ATP

RNF213 is a giant E3 ubiquitin ligase and a major susceptibility factor of Moyamoya disease, a cerebrovascular disorder that can result in stroke or death. In the cell, RNF213 is involved in lipid droplet formation, lipotoxicity, hypoxia, and NF-κB signaling, but its exact function in these processes is unclear. Structural characterization has revealed the presence of a dynein-like ATPase module and an unprecedented but poorly understood E3 module. Here, we demonstrate that RNF213 E3 activity is dependent on ATP binding, rather than ATP hydrolysis, and is particularly responsive to the ATP/ADP/AMP ratio. Biochemical and activity-based probe analyses identify a non-canonical zinc finger domain as the E3 active site, which utilizes the strictly conserved Cys4462, not involved in zinc coordination, as the reactive nucleophile. The cryo-EM structure of the trapped RNF213:E2~Ub intermediate reveals RNF213 C-terminal domain as the E2 docking site, which positions the ubiquitin-loaded E2 proximal to the catalytic zinc finger, facilitating nucleophilic attack of Cys4462 on the E2~Ub thioester. Our findings show that RNF213 represents an undescribed type of a transthiolation E3 enzyme and is regulated by adenine nucleotide concentration via its ATPase core, possibly allowing it to react to changing metabolic conditions in the cell.

Association of Sonic Hedgehog with the extracellular matrix requires its zinc-coordination center

Background Sonic Hedgehog (Shh) has a catalytic cleft characteristic for zinc metallopeptidases and has significant sequence similarities with some bacterial peptidoglycan metallopeptidases defining a subgroup within the M15A family that, besides having the characteristic zinc coordination motif, can bind two calcium ions. Extracellular matrix (ECM) components in animals include heparan-sulfate proteoglycans, which are analogs of bacterial peptidoglycan and are involved in the extracellular distribution of Shh. Results We found that the zinc-coordination center of Shh is required for its association to the ECM as well as for non-cell autonomous signaling. Association with the ECM requires the presence of at least 0.1 μM zinc and is prevented by mutations affecting critical conserved catalytical residues. Consistent with the presence of a conserved calcium binding domain, we find that extracellular calcium inhibits ECM association of Shh. Conclusions Our results indicate that the putative intrinsic peptidase activity of Shh is required for non-cell autonomous signaling, possibly by enzymatically altering ECM characteristics.

Transcription factor allosteric regulation through substrate coordination to zinc

The development of new synthetic biology circuits for biotechnology and medicine requires deeper mechanistic insight into allosteric transcription factors (aTFs). Here we studied the aTF UxuR, a homodimer of two domains connected by a highly flexible linker region. To explore how ligand binding to UxuR affects protein dynamics we performed molecular dynamics simulations in the free protein, the aTF bound to the inducer D-fructuronate or the structural isomer D-glucuronate. We then validated our results by constructing a sensor plasmid for D-fructuronate in Escherichia coli and performed site-directed mutagenesis. Our results show that zinc coordination is necessary for UxuR function since mutation to alanines prevents expression de-repression by D-fructuronate. Analyzing the different complexes, we found that the disordered linker regions allow the N-terminal domains to display fast and large movements. When the inducer is bound, UxuR can sample an open conformation with a more pronounced negative charge at the surface of the N-terminal DNA binding domains. In opposition, in the free and D-glucuronate bond forms the protein samples closed conformations, with a more positive character at the surface of the DNA binding regions. These molecular insights provide a new basis to harness these systems for biological systems engineering.