Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4.

Commensal bacterium Clostridium paraputrificum J4 produces several extracellular chitinolytic enzymes including a 62 kDa chitinase Chit62J4 active toward 4-nitrophenyl N,N'-diacetyl-ß-d-chitobioside (pNGG). We characterized the crude enzyme from bacterial culture fluid, recombinant enzyme rChit62J4, and its catalytic domain rChit62J4cat. This major chitinase, securing nutrition of the bacterium in the human intestinal tract when supplied with chitin, has a pH optimum of 5.5 and processes pNGG with Km = 0.24 mM and kcat = 30.0 s-1. Sequence comparison of the amino acid sequence of Chit62J4, determined during bacterial genome sequencing, characterizes the enzyme as a family 18 glycosyl hydrolase with a four-domain structure. The catalytic domain has the typical TIM barrel structure and the accessory domains-2x Fn3/Big3 and a carbohydrate binding module-that likely supports enzyme activity on chitin fibers. The catalytic domain is highly homologous to a single-domain chitinase of Bacillus cereus NCTU2. However, the catalytic profiles significantly differ between the two enzymes despite almost identical catalytic sites. The shift of pI and pH optimum of the commensal enzyme toward acidic values compared to the soil bacterium is the likely environmental adaptation that provides C. paraputrificum J4 a competitive advantage over other commensal bacteria.

Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer.

Unlike any protein studied so far, the active site of bilirubin oxidase from Myrothecium verrucaria contains a unique type of covalent link between tryptophan and histidine side chains. The role of this post-translational modification in substrate binding and oxidation is not sufficiently understood. Our structural and mutational studies provide evidence that this Trp396-His398 adduct modifies T1 copper coordination and is an important part of the substrate binding and oxidation site. The presence of the adduct is crucial for oxidation of substituted phenols and it substantially influences the rate of oxidation of bilirubin. Additionally, we bring the first structure of bilirubin oxidase in complex with one of its products, ferricyanide ion, interacting with the modified tryptophan side chain, Arg356 and the active site-forming loop 393-398. The results imply that structurally and chemically distinct types of substrates, including bilirubin, utilize the Trp-His adduct mainly for binding and to a smaller extent for electron transfer.

Domain structure of HelD, an interaction partner of Bacillus subtilis RNA polymerase.

The HelD is a helicase-like protein binding to Bacillus subtilis RNA polymerase (RNAP), stimulating transcription in an ATP-dependent manner. Here, our small angle X-ray scattering data bring the first insights into the HelD structure: HelD is compact in shape and undergoes a conformational change upon substrate analog binding. Furthermore, the HelD domain structure is delineated, and a partial model of HelD is presented. In addition, the unique N-terminal domain of HelD is characterized as essential for its transcription-related function but not for ATPase activity, DNA binding, or binding to RNAP. The study provides a topological basis for further studies of the role of HelD in transcription.

Highly stable single-strand-specific 3'-nuclease/nucleotidase from Legionella pneumophila.

The Gram-negative bacterium Legionella pneumophila is one of the known opportunistic human pathogens with a gene coding for a zinc-dependent S1-P1 type nuclease. Bacterial zinc-dependent 3'-nucleases/nucleotidases are little characterized and not fully understood, including L. pneumophila nuclease 1 (Lpn1), in contrast to many eukaryotic representatives with in-depth studies available. To help explain the principle properties and role of these enzymes in intracellular prokaryotic pathogens we have designed and optimized a heterologous expression protocol utilizing E. coli together with an efficient purification procedure, and performed detailed characterization of the enzyme. Replacement of Ni2+ ions by Zn2+ ions in affinity purification proved to be a crucial step in the production of pure and stable protein. The production protocol provides protein with high yield, purity, stability, and solubility for structure-function studies. We show that highly thermostable Lpn1 is active mainly towards RNA and ssDNA, with pH optima 7.0 and 6.0, respectively, with low activity towards dsDNA; the enzyme features pronounced substrate inhibition. Bioinformatic and experimental analysis, together with computer modeling and electrostatics calculations point to an unusually high positive charge on the enzyme surface under optimal conditions for catalysis. The results help explain the catalytic properties of Lpn1 and its substrate inhibition.

Tetranuclear Copper(I) Iodide Complexes: A New Class of X-ray Phosphors.

We report intensive visible light radioluminescence upon X-ray irradiation of archetypal tetranuclear copper(I) iodide complexes containing triphenylphosphine or pyridine ligands in the solid state. These properties, attractive for the design of X-ray responsive materials, can be attributed to the heavy {Cu4I4} cubane-like core, the absence of oxygen quenching of the emissive triplet states, and the high photoluminescence quantum yields. Radioluminescence originates from the same emissive triplet states as those produced by ultraviolet excitation as confirmed by the observed radioluminescence thermochromism. The radioluminescence properties are also preserved after incorporation of these complexes into polystyrene films, making them appealing for the development of plastic scintillators.

Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.

The single-strand-specific S1 nuclease from Aspergillus oryzae is an archetypal enzyme of the S1-P1 family of nucleases with a widespread use for biochemical analyses of nucleic acids. We present the first X-ray structure of this nuclease along with a thorough analysis of the reaction and inhibition mechanisms and of its properties responsible for identification and binding of ligands. Seven structures of S1 nuclease, six of which are complexes with products and inhibitors, and characterization of catalytic properties of a wild type and mutants reveal unknown attributes of the S1-P1 family. The active site can bind phosphate, nucleosides, and nucleotides in several distinguished ways. The nucleoside binding site accepts bases in two binding modes-shallow and deep. It can also undergo remodeling and so adapt to different ligands. The amino acid residue Asp65 is critical for activity while Asn154 secures interaction with the sugar moiety, and Lys68 is involved in interactions with the phosphate and sugar moieties of ligands. An additional nucleobase binding site was identified on the surface, which explains the absence of the Tyr site known from P1 nuclease. For the first time ternary complexes with ligands enable modeling of ssDNA binding in the active site cleft. Interpretation of the results in the context of the whole S1-P1 nuclease family significantly broadens our knowledge regarding ligand interaction modes and the strategies of adjustment of the enzyme surface and binding sites to achieve particular specificity.

Crystallization of nepenthesin I using a low-pH crystallization screen.

Nepenthesins are aspartic proteases secreted by carnivorous pitcher plants of the genus Nepenthes. They significantly differ in sequence from other plant aspartic proteases. This difference, which provides more cysteine residues in the structure of nepenthesins, may contribute to their unique stability profile. Recombinantly produced nepenthesin 1 (rNep1) from N. gracilis in complex with pepstatin A was crystallized under two different crystallization conditions using a newly formulated low-pH crystallization screen. The diffraction data were processed to 2.9 and 2.8 Šresolution, respectively. The crystals belonged to space group P212121, with unit-cell parameters a = 86.63, b = 95.90, c = 105.40 Å, α = ß = γ = 90° and a = 86.28, b = 97.22, c = 103.78 Å, α = ß = γ = 90°, respectively. Matthews coefficient and solvent-content calculations suggest the presence of two molecules of rNep1 in the asymmetric unit. Here, the details of the crystallization experiment and analysis of the X-ray data are reported.

X-ray Inducible Luminescence and Singlet Oxygen Sensitization by an Octahedral Molybdenum Cluster Compound: A New Class of Nanoscintillators.

Newly synthesized octahedral molybdenum cluster compound (n-Bu4N)2[Mo6I8(OOC-1-adamantane)6] revealed uncharted features applicable for the development of X-ray inducible luminescent materials and sensitizers of singlet oxygen, O2((1)Δg). The compound exhibits a red-NIR luminescence in the solid state and in solution (e.g., quantum yield of 0.76 in tetrahydrofuran) upon excitation by UV-vis light. The luminescence originating from the excited triplet states is quenched by molecular oxygen to produce O2((1)Δg) with a high quantum yield. Irradiation of the compound by X-rays generated a radioluminescence with the same emission spectrum as that obtained by UV-vis excitation. It proves the formation of the same excited triplet states regardless of the excitation source. By virtue of the described behavior, the compound is suggested as an efficient sensitizer of O2((1)Δg) upon X-ray excitation. The luminescence and radioluminescence properties were maintained upon embedding the compound in polystyrene films. In addition, polystyrene induced an enhancement of the radioluminescence intensity via energy transfer from the scintillating polymeric matrix. Sulfonated polystyrene nanofibers were used for the preparation of nanoparticles which form stable dispersions in water, while keeping intact the luminescence properties of the embedded compound over a long time period. Due to their small size and high oxygen diffusivity, these nanoparticles are suitable carriers of sensitizers of O2((1)Δg). The presented results define a new class of nanoscintillators with promising properties for X-ray inducible photodynamic therapy.

Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme.

Tomato multifunctional nuclease TBN1 belongs to the type I nuclease family, which plays an important role in apoptotic processes and cell senescence in plants. The newly solved structure of the N211D mutant is reported. Although the main crystal-packing motif (the formation of superhelices) is conserved, the details differ among the known structures. A phosphate ion was localized in the active site of the enzyme. The binding of the surface loop to the active centre is stabilized by the phosphate ion, which correlates with the observed aggregation of TBN1 in phosphate buffer. The conserved binding of the surface loop to the active centre suggests biological relevance of the contact in a regulatory function or in the formation of oligomers.

Crystal structure, spectroscopic and theoretical studies on two Schiff base compounds of 2,6-dichlorobenzylidene-2,4-dichloroaniline and 2,4-dichlorobenzylidene-2,4-dichloroaniline.

The crystal structures of two Schiff base compounds, 2,6-dichlorobenzylidene-2,4-dichloroaniline (1) and 2,4-dichlorobenzylidene-2,4-dichloroaniline (2) have been determined from single-crystal X-ray diffraction and characterized by FT-IR and (1)H NMR spectroscopy. The electronic structures of compounds 1 and 2 in the gas phase were computed by the density functional theory (DFT) method. The obtained theoretical results were supported by the crystallographic data. In addition, theoretical configurations of the title compounds were relaxed and studied in terms of the combined analysis of HOMO-LUMO energy gap, total density of states (DOS), molecular electrostatic potential (MEP), NMR spectra and harmonic vibrational frequencies.

A novel amido-pyrophosphate Mn(II) chelate complex with the synthetic ligand O{P(O)[NHC(CH3)3]2}2 (L): [Mn(L)2{OC(H)N(CH3)2}2]Cl2·2H2O.

The title complex, trans-bis(dimethylformamide-κO)bis{N,N'-N'',N'''-tetra-tert-butyl[oxybis(phosphonic diamide-κO)]}manganese(II) dichloride dihydrate, [Mn(C16H40N4O3P2)2(C3H7NO)2]Cl2·2H2O, is the first example of a bis-chelate amido-pyrophosphate (pyrophosphoramide) complex containing an O[P(O)(NH)2]2 fragment. Its asymmetric unit contains half of the complex dication, one chloride anion and one water molecule. The Mn(II) atom, located on an inversion centre, is octahedrally coordinated, with a slight elongation towards the monodentate dimethylformamide ligand. Structural features of the title complex, such as the P=O bond lengths and the planarity of the chelate ring, are compared with those of previously reported complexes with six-membered chelates involving the fragments C(O)NHP(O), (X)NP(O) [X = C(O), C(S), S(O)2 and P(O)] and O[P(O)(N)2]2. This analysis shows that the six-membered chelate rings are less puckered in pyrophosphoramide complexes containing a P(O)OP(O) skeleton, such as the title compound. The extended structure of the title complex involves a linear aggregate mediated by N-H...O and N-H...Cl hydrogen bonds, in which the chloride anion is an acceptor in two additional O-H...Cl hydrogen bonds.

A comparative study of the redox and excited state properties of (nBu4N)2[Mo6X14] and (nBu4N)2[Mo6X8(CF3COO)6] (X = Cl, Br, or I).

The excited-state dynamics, luminescence, and redox properties of a series of hexanuclear molybdenum cluster complexes, (nBu4N)2[Mo6X14] and (nBu4N)2[Mo6X8(CF3COO)6] (X = Cl, Br, or I), were investigated. Substitution of the apical halogen ligands for the trifluoroacetate ligands increased the oxidation potentials and induced a blue shift in the absorption and luminescence bands as well as a considerable increase in the luminescence quantum yields for heavy inner ligands. Time-resolved transient absorption measurements showed that the intersystem crossing from the excited singlet states is ultrafast with time constants ranging between <120 fs and 1.68 ps and leads to hot triplet states. The following cooling occurred at a ps time scale and was assigned to electronic redistribution within the emissive triplet state sublevels. The formation of singlet oxygen, O2((1)Δg), suggested earlier on the basis of photooxidation experiments for some complexes, was revised by direct measurements of O2((1)Δg) phosphorescence. We showed the effects of the attached ligands on key physico-chemical and photophysical parameters of the title complexes. The synthesis and structural characterisation of a new cluster complex, (nBu4N)2[Mo6Br8(CF3COO)6], completed the series. Our results demonstrated that the complexes with heavy inner ligands (Br, I) and apical trifluoroacetate ligands were photochemically and electrochemically stable, highly luminescent, and good sensitisers of O2((1)Δg).

4-[(E)-(4-Eth-oxy-phen-yl)imino-meth-yl]phenol.

In the title compound, C(15)H(15)NO(2), the dihedral angle between the benzene rings is 52.04 (5)° and the mol-ecule has an E conformation about the central C=N bond. In the crystal, mol-ecules are connected by O-H⋯N hydrogen bonds, forming zigzag chains along the b axis. The crystal packing also features weak C-H⋯O inter-actions.

[N,N'-Bis(2,3,4-trimeth-oxy-benzyl-idene)-ethane-1,2-diamine-κ(2)N,N']dibromido-mercury(II).

In the title compound, [HgBr(2)(C(22)H(28)N(2)O(6))], the Hg(II) ion is bonded to two Br(-) ions and two N atoms of the chelating Schiff base ligand in a distorted tetra-hedral geometry. The Schiff base ligand adopts an E,E conformation. The dihedral angle between the planes of the two halves of the central N,N'-dimethyl-ethylenediamine part of the ligand is 2.3 (11)°. The crystal studied was twinned by pseudomerohedry [twin law (0-10/-100/00-1)]; the contribution of the minor twin component refined to 0.208 (3).

1,3-Dinitro-soimidazolidine.

The title compound, C(3)H(6)N(4)O(2), exhibits partial disorder with the refined occupancy ratios of the two components being 0.582 (5):0.418 (5). In the major component, the nitroso groups have a relative syn spatial arrangement [O=N⋯N=O pseudo-torsion angle = 1.1 (4)°], whereas the other component has an anti disposition [177.6 (1)°]. The N-N=O moieties are almost coplanar with a dihedral angle of 5.3 (3)°, while in the minor occupied set of atoms, this angle is 8 (1)°. In both components, the imidazolidine ring adopts a twisted conformation on the C-C bond and the crystal structure shows the strain of this ring according to the N-CH(2)-CH(2)-N torsion angles [25.9 (5) and -23.8 (7)°]. In the crystal, molecules are linked by weak C-H⋯O hydrogen bonds.

2-[(4-Meth-oxy-2-nitro-phen-yl)imino-meth-yl]phenol.

The crystal structure of the title compound, C(14)H(12)N(2)O(4), contains four crystallographically independent mol-ecules in the asymmetric unit. All the mol-ecules have similar conformations; the dihedral angles between the aromatic rings are 33.1 (1), 33.76 (9), 31.41 (9) and 32.56 (10)°. Intra-molecular O-H⋯N hydrogen bonds form S(6) ring motifs in each molecule. In the crystal, there are two pairs of pseudo-inversion-related mol-ecules. Along the c axis, mol-ecules are stacked with π-π inter-actions between the 2-hy-droxy-phenyl and 4-meth-oxy-2-nitro-phenyl rings [centroid-centroid distances = 3.5441 (12)-3.7698 (12) Å].

(E)-4-[(4-Bromo-phen-yl)imino-meth-yl]-2-meth-oxy-phenol.

In the crystal structure of the title compound, C(14)H(12)BrNO(2), the dihedral angle between the rings is 37.87 (10)° and the mol-ecule has an E conformation about the central C=N bond. In the crystal, mol-ecules are connected by inter-molecular O-H⋯N hydrogen bonds into zigzag chains running parallel to the b axis. The packing also features C-H⋯O inter-actions.

[4-Bromo-N-(pyridin-2-yl-methyl-idene)aniline-κ(2)N,N']iodido(triphenyl-phosphane-κP)copper(I).

In the title compound, [CuI(C(12)H(9)BrN(2))(C(18)H(15)P)], the Cu(I) ion is bonded to one I atom, one triphenyl-phosphane P atom and two N atoms of the diimine ligand in a distorted tetra-hedral geometry. The Schiff base acts as a chelating ligand and coordinates to the Cu(I) atom via two N atoms. In the diimine ligand, the dihedral angle between the pyridine and bromo-phenyl rings is 19.2 (2)°. In the crystal, mol-ecules are connected by π-π stacking inter-actions between inversion-related pyridine rings [centroid-centroid distance = 3.404 (3) Å].

[N,N'-Bis(2,6-dichloro-benzyl-idene)propane-1,3-diamine-κ(2)N,N']dibromidozinc.

In the title compound, [ZnBr(2)(C(17)H(14)Cl(4)N(2))], the Zn(II) ion is bonded to two bromide ions and two N atoms of the diimine ligand and displays a moderately distorted tetra-hedral coordination geometry. The Schiff base ligand acts as a chelating ligand and coordinates to the Zn(II) atom via two N atoms.

6H,13H-5,12:7,14-Dimethano-dinaphtho-[2,3-d:2,3-i][1,3,6,8]tetra-azecine.

In the title compound, C(24)H(20)N(4), obtained through the condensation of naphthalene-2,3-diamine with formaldehyde in methanol, the mol-ecule is located on a special position of site symmetry -4. Due to symmetry considerations, the aromatic rings are strictly perpendicular to each other. In the crystal, mol-ecules are linked by pairs of C-H⋯π inter-actions into columns along [110].