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Lon proteases are distributed in all kingdoms of life and are required for survival of cells under stress. Lon is a tandem fusion of an AAA+ molecular chaperone and a protease with a serine-lysine catalytic dyad. We report the 2.0-Å resolution crystal structure of Thermococcus onnurineus NA1 Lon (TonLon). The structure is a three-tiered hexagonal cylinder with a large sequestered chamber accessible through an axial channel. Conserved loops extending from the AAA+ domain combine with an insertion domain containing the membrane anchor to form an apical domain that serves as a gate governing substrate access to an internal unfolding and degradation chamber. Alternating AAA+ domains are in tight- and weak-binding nucleotide states with different domain orientations and intersubunit contacts, reflecting intramolecular dynamics during ATP-driven protein unfolding and translocation. The bowl-shaped proteolytic chamber is contiguous with the chaperone chamber allowing internalized proteins direct access to the proteolytic sites without further gating restrictions. [ABSTRACT FROM AUTHOR]

BldD is a central regulator of the developmental process in Streptomyces coelicolor. The 1.8 Å resolution structure of the DNA-binding domain of BldD (BldDN) reveals that BldDN forms a compact globular domain composed of four helices (α1–α4) containing a helix-turn-helix motif (α2–α3) resembling that of the DNA-binding domain of lambda repressor. The BldDN/DNA complex model led us to design a series of mutants, which revealed the important role of α3 and the ‘turn’ region between α2 and α3 for DNA recognition. Based on the fact that BldD occupies two operator sites of bldN and whiG and shows significant disparity in the affinity toward the two operator sites when they are disconnected, we propose a model of cooperative binding, which means that the binding of one BldD dimer to the high affinity site facilitates that of the second BldD dimer to the low affinity site. In addition, structural and mutational investigation reveals that the Tyr62Cys mutation, found in the first-identified bldD mutant, can destabilize BldD structure by disrupting the hydrophobic core. [ABSTRACT FROM AUTHOR]

The emergence and dissemination of extended-spectrum (ES) β-lactamases induce therapeutic failure and a lack of eradication of clinical isolates even by third-generation β-lactam antibiotics like ceftazidime. CMY-10 is a plasmid-encoded class C β-lactamase with a wide spectrum of substrates. Unlike the well-studied class C ES β-lactamase from Enterobacter cloacae GC1, the Ω-loop does not affect the active site conformation and the catalytic activity of CMY-10. Instead, a three-amino-acid deletion in the R2-loop appears to be responsible for the ES activity of CMY-10. According to the crystal structure solved at 1.55 Å resolution, the deletion significantly widens the R2 active site, which accommodates the R2 side-chains of β-lactam antibiotics. This observation led us to demonstrate the hydrolysing activity of CMY-10 towards imipenem with a long R2 substituent. The forced mutational analyses of P99 β-lactamase reveal that the introduction of deletion mutations into the R2-loop is able to extend the substrate spectrum of class C non-ES β-lactamases, which is compatible with the isolation of natural class C ES enzymes harbouring deletion mutations in the R2-loop. Consequently, the opening of the R2 active site by the deletion of some residues in the R2-loop can be considered as an operative molecular strategy of class C β-lactamases to extend their substrate spectrum. [ABSTRACT FROM AUTHOR]

The B30.2/SPRY domain is present in ∼700 eukaryotic (∼150 human) proteins, including medically important proteins such as TRIM5α and Pyrin. Nonetheless, the functional role of this modular domain remained unclear. Here, we report the crystal structure of an SPRY-SOCS box family protein GUSTAVUS in complex with Elongins B and C, revealing a highly distorted two-layered β-sandwich core structure of its B30.2/SPRY domain. Ensuing studies identified one end of the β-sandwich as the surface interacting with an RNA helicase VASA with a 40 nM dissociation constant. The sequence variation in TRIM5α responsible for HIV-1 restriction and most of the mutations in Pyrin causing familial Mediterranean fever map on this surface, implicating the corresponding region in many B30.2/SPRY domains as the ligand-binding site. The amino acids lining the binding surface are highly variable among the B30.2/SPRY domains, suggesting that these domains are protein-interacting modules, which recognize a specific individual partner protein rather than a consensus sequence motif. [ABSTRACT FROM AUTHOR]

Nickel ions serve in the correct folding and function of microbial enzymes implicated in metabolic processes. Although nickel ions are indispensable for the survival of cells, the intracellular level of nickel ions needs to be properly maintained as excessive levels of nickel ions are toxic. Nur, a nickel-uptake regulator belonging to the Fur family, is a nickel-responsive transcription factor that controls nickel homeostasis and antioxidative response in Streptomyces coelicolor. Nur was purified and crystallized at 295 K. A 2.4 Å native data set and a 3.0 Å Ni-MAD data set were collected using synchrotron radiation. The Nur crystals belong to space group P31, with unit-cell parameters a = b = 78.17, c = 50.39 Å. Assuming the presence of two molecules in the asymmetric unit, the solvent content is estimated to be about 54.7%. [ABSTRACT FROM AUTHOR]

The N-terminal DNA-binding domain of BldD from Streptomyces coelicolor A3(2) was crystallized by the hanging-drop vapour-diffusion method at 296 K. A 1.8 Å data set has been collected using synchrotron radiation at Pohang Light Source, South Korea. The crystal belongs to the monoclinic space group C2, with unit-cell parameters a = 77.2, b = 31.8, c = 33.6 Å, β = 105.1°. Analysis of the packing density shows that the asymmetric unit probably contains one molecule, with a solvent content of 43.6%. [ABSTRACT FROM AUTHOR]

Studies the crystallization and preliminary X-ray crystallographic analyses of CMY-1 and CMY-10, plasmidic class C Β-lactamases with extended substrate spectrum. Potential of the enzymes as targets for developing agents against pathogens isolated from patients suffering from wound infection, urinary tract infection or pneumonia.

Investigates the crystallization and preliminary X-ray crystallographic analysis of a ytfG gene product from Escherichia coli. Unit-cell parameters of the crystal which belongs to the primitive trigonal system; Analysis of the packing density showing that the asymmetric unit probably contains one monomer, with a solvent content of 48.8 percent.