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The survival and growth of the pathogen Helicobacter pylori in the gastric acidic environment is ensured by the activity of urease, an enzyme containing two essential Ni2+ ions in the active site. The metallo-chaperone UreE facilitates in vivo Ni2+ insertion into the apo-enzyme. Crystals of apo-HpUreE and its Ni2+ and Zn2+ bound forms were obtained from protein solutions in the absence and presence of the metal ions. The crystal structures of the homodimeric protein, determined at 2.00 Å (apo), 1.59 Å (Ni) and 2.52 Å (Zn) resolution, show the conserved proximal and solvent-exposed His102 residues from two adjacent monomers invariably involved in metal binding. The C-terminal regions of the apo-protein are disordered in the crystal, but acquire significant ordering in the presence of the metal ions due to the binding of His152. The analysis of X-ray absorption spectral data obtained on solutions of Ni2+- and Zn2+-HpUreE provided accurate information of the metal ion environment in the absence of solid-state effects. These results reveal the role of the histidine residues at the protein C-terminus in metal ion binding, and the mutual influence of protein framework and metal ion stereo-electronic properties in establishing coordination number and geometry leading to metal selectivity.

PNA is a promising molecule for antisense therapy of trinucleotide repeat disorders. We present the first crystal structures of RNA–PNA duplexes. They contain CUG repeats, relevant to myotonic dystrophy type I, and CAG repeats associated with poly-glutamine diseases. We also report the first PNA–PNA duplex containing mismatches. A comparison of the PNA homoduplex and the PNA–RNA heteroduplexes reveals PNA's intrinsic structural properties, shedding light on its reported sequence selectivity or intolerance of mismatches when it interacts with nucleic acids. PNA has a much lower helical twist than RNA and the resulting duplex has an intermediate conformation. PNA retains its overall conformation while locally there is much disorder, especially peptide bond flipping. In addition to the Watson–Crick pairing, the structures contain interesting interactions between the RNA's phosphate groups and the Π electrons of the peptide bonds in PNA.

RNA transcripts that include expanded CCUG repeats are associated with myotonic dystrophy type 2. Crystal structures of two CCUG-containing oligomers show that the RNA strands associate into slipped duplexes that contain noncanonical C-U pairs that have apparently undergone tautomeric transition or protonation resulting in an unusual Watson-Crick-like pairing. The overhanging ends of the duplexes interact forming U-U pairs, which also show tautomerism. Duplexes consisting of CCUG repeats are thermodynamically less stable than the trinucleotide repeats involved in the TRED genetic disorders, but introducing LNA residues increases their stability and raises the melting temperature of the studied oligomers by ∼10°C, allowing detailed crystallographic studies. Quantum mechanical calculations were performed to test the possibility of the tautomeric transitions or protonation within the noncanonical pairs. The results indicate that tautomeric or ionic shifts of nucleobases can manifest themselves in biological systems, supplementing the canonical "rules of engagement."

Disufide-bond isomerase (DsbC) plays a crucial role in folding periplasmically excreted bacterial proteins. The crystal structure of the reduced form of DsbC is presented. The pair of thiol groups from Cys98 and Cys101 that form the reversible disulfide bond in the enzymatic active site are 3.1 A apart and the electron density clearly shows that the S atoms do not form a covalent bond. The other pair of Cys residues (141 and 163) in DsbC form a disulfide bond. This is different from the previously reported crystal form of DsbC (McCarthy et al., 2000), in which both Cys pairs are oxidized. Specific hydrogen-bond interactions are identified that stabilize the active site in the reactive reduced state with the special participation of hydrogen bonds between the active-site cysteine residues (98 and 101) and threonine residues 94 and 182. The present structure also differs in the orientation of the catalytic domains within the protein dimer. This is evidence of flexibility within the protein that probably plays a role in accommodating the substrates in the cleft between the catalytic domains.

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Energy and biomass production in cancer cells are largely supported by aerobic glycolysis in what is called the Warburg effect. The process is regulated by key enzymes, among which phosphofructokinase PFK‐2 plays a significant role by producing fructose‐2,6‐biphosphate; the most potent activator of the glycolysis rate‐limiting step performed by phosphofructokinase PFK‐1. Herein, the synthesis, biological evaluation and structure–activity relationship of novel inhibitors of 6‐phosphofructo‐2‐kinase/fructose‐2,6‐biphosphatase 3 (PFKFB3), which is the ubiquitous and hypoxia‐induced isoform of PFK‐2, are reported. X‐ray crystallography and docking were instrumental in the design and optimisation of a series of N‐aryl 6‐aminoquinoxalines. The most potent representative, N‐(4‐methanesulfonylpyridin‐3‐yl)‐8‐(3‐methyl‐1‐benzothiophen‐5‐yl)quinoxalin‐6‐amine, displayed an IC50 of 14 nm for the target and an IC50 of 0.49 μm for fructose‐2,6‐biphosphate production in human colon carcinoma HCT116 cells. This work provides a new entry in the field of PFKFB3 inhibitors with potential for development in oncology.