The significance of the flexible loop in the azurin (Az-iso2) from the obligate methylotroph Methylomonas sp. strain J

The obligate methylotroph Methylomonas sp. strain J produces two azurins (Az-iso1 and Az-iso2) as candidates for electron acceptor from methylamine dehydrogenase (MADH) in the electron-transfer process involving the oxidation of methylamine to formaldehyde and ammonia. The X-ray crystallographic study indicated that Az-iso2 gives two types of crystals (form I and form II) with polyethylene glycol (PEG4000) and ammonium sulfate as the precipitants, respectively. Comparison between the two Az-iso2 structures in forms I and II reveals the remarkable structural changes at the top surface of the molecule around the copper atom. Az-iso2 possesses Gly43 instead of Val43 or Ala43, which is unique among all other azurins around the copper ligand His46, inducing the remarkable structural change in the loop region from Gly37 to Gly43. When the structure of Az-iso2 is superimposed on that of amicyanin in the ternary complex composed of MADH, amicyanin, and cytochrome c(551), the loop of Az-iso2 deeply overlaps with the light subunit of MADH. However, the Az-iso2 molecule is probably able to avoid any steric hindrance with the cognate MADH to form the complex for intermolecular electron-transfer reaction, since the loop containing Gly43 is flexible. We discuss why the electron-transfer activity of Az-iso2 is fivefold higher than that of Az-iso1.     

Amine free crystal structure: the crystal structure of d(CGCGCG)2 and methylamine complex crystal

We succeeded in the crystallization of d(CGCGCG)2 and methylamine Complex. The crystal was clear and of sufficient size to collect the X-ray crystallographic data up to 1.0 A resolution using synchrotron radiation. As a result of X-ray crystallographic analysis of 2Fo-Fc map was much clear and easily traced. It is the first time monoamine co-crystallizes with d(CGCGCG)2. However, methylamine was not found from the complex crystal of d(CGCGCG)2 and methylamine. Five Mg ions were found around d(CGCGCG)2 molecules. These Mg ions neutralized the anion of 10 values of the phosphate group of DNA with five Mg2+. DNA stabilized only by a metallic ion and there is no example of analyzing the X-ray crystal structure like this. Mg ion stabilizes the conformation of Z-DNA. To use monoamine for crystallization of DNA, we found that we can get only d(CGCGCG)2 and Mg cation crystal. Only Mg cation can stabilize the conformation of Z-DNA. The method of using the monoamine for the crystallization of DNA can be applied to the crystallization of DNA of long chain of length in the future like this.     

Spectroscopic and electrochemical properties of heteroleptic cationic copper complexes bis-(diphenylphosphino)alkane-(2,2′-biquinoline)copper(I). Crystal structure of bis(diphenylphosphino)ethane-(2,2′-biquinoline)copper(I) perchlorate

A series of [Cu^(I)(2,2′-biquinoline)(L)](ClO₄) complexes (L = bis(diphenylphosphino)methane (bppm), 1,2-bis(diphenylphosphino)ethane (bppe), 1,4-bis(diphenylphosphino)butane (bppb)) have been synthesized and characterized by elemental analysis, conductivity, ESI-mass, NMR and UV-Vis spectroscopies, cyclic voltammetry, X-ray diffraction ([Cu^(I)(2,2′-biquinoline)(bppe)](ClO₄)) and DFT calculations. These compounds are monometallic species in a distorted tetrahedral arrangement, in contrast with related compounds found as dinuclear according to diffraction studies. The spectroscopic properties are not directly correlated with the length of alkyl chain bridge between the bis-diphenylphosphine groups. In this way, the chemical shift of some 2,2′-biquinoline protons and the metal to ligand charge transfer (Cu to 2,2′-biquinoline) follows the order [Cu(2,2′-biquinoline)(bppm)](ClO₄), [Cu(2,2′-biquinoline)(bppb)](ClO₄), [Cu(2,2′-biquinoline)(bppe)](ClO₄). The same dependence is followed by the potentials to Cu(II)/Cu(I) couple. These results are discussed in terms of inter-phosphorus alkane chain length and tetrahedral distortions on copper.     

Blue phosphorescent iridium complexes based on 2-(fluoro substituted phenyl)-4-methylpyridines: Synthesis, crystal structure, and photophysics

A series blue phosphorescent emitting materials based on 2-(fluoro substituted phenyl)-4-methylpyridine as the cyclometalated ligands have been synthesized and characterized. The complexes have the general structure (C^{^}N)₂Ir(pic), where C^{^}N is a monoanionic cyclometalating ligand (e.g., 2-(2,4-difluorophenyl)-4-methylpyridine (24f₂pmpyH), 2-(3,4-difluorophenyl)-4-methylpyridine (34f₂pmpyH), 2-(3,5-difluorophenyl)-4-methylpyridine (35f₂pmpyH), and 2-(3,4,5-trifluorophenyl)-4-methyl-pyridine (345f₃pmpyH)), pic is 2-picolinic acid. The absorption, emission, cyclic voltammetry and thermostability of the complexes were systematically investigated. The (46f₂pmpy)₂Ir(pic) has been characterized using X-ray crystallography and the electronic ground state calculated using B3LYP density functional theory. HOMO levels are a mixture of Ir and 2-(fluoro phenyl)-4-methylpyridine ligand orbitals, while the LUMO is predominantly pic ligand based. Introduction of fluorine atoms and methyl group into ppy ligand and changing in position of F substituents in phenyl ring can finely tune emission of the complexes, showing bright blue-to-green luminescence at a wavelength of 463-501 nm at room temperature in CH₂Cl₂.     

Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1 at 2.0A resolution

Sphingomonas sp. A1 possesses a high molecular mass (average 25,700 Da) alginate uptake system mediated by a novel pit-dependent ABC transporter. The X-ray crystallographic structure of AlgQ2 (57,200 Da), an alginate-binding protein in the system, was determined by the multiple isomorphous replacement method and refined at 2.0 A resolution with a final R-factor of 18.3% for 15 to 2.0 A resolution data. The refined structure of AlgQ2 was comprised of 492 amino acid residues, 172 water molecules, and one calcium ion. AlgQ2 was composed of two globular domains with a deep cleft between them, which is expected to be the alginate-binding site. The overall structure is basically similar to that of maltose/maltodextrin-binding protein, except for the presence of an N2-subdomain. The entire calcium ion-binding site is similar to the site in the EF-hand motif, but comprises a ten residue loop. This calcium ion-binding site is about 40 A away from the alginate-binding site.     

Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1

Biphenyl dioxygenase is the enzyme that catalyzes the stereospecific dioxygenation of the aromatic ring. This enzyme has attracted the attention of researchers due to its ability to oxidize polychlorinated biphenyls, which is one of the serious environmental contaminants. We determined the crystal structure of the terminal oxygenase component of the biphenyl dioxygenase (BphA1A2) derived from Rhodococcus strain sp. RHA1 in substrate-free and complex forms. These crystal structures revealed that the substrate-binding pocket makes significant conformational changes upon substrate binding to accommodate the substrate into the pocket. Our analysis of the crystal structures suggested that the residues in the substrate-binding pocket can be classified into three groups, which, respectively, seem to be responsible for the catalytic reaction, the orientation/conformation of the substrate, and the conformational changes of the substrate-binding pocket. The cooperative actions of residues in the three groups seem to determine the substrate specificity of the enzyme.     

Crystal structure of a novel fold protein Gp72 from the freshwater cyanophage Mic1

Cyanophages, widespread in aquatic systems, are a class of viruses that specifically infect cyanobacteria. Though they play important roles in modulating the homeostasis of cyanobacterial populations, little is known about the freshwater cyanophages, especially those hypothetical proteins of unknown function. Mic1 is a freshwater siphocyanophage isolated from the Lake Chaohu. It encodes three hypothetical proteins Gp65, Gp66, and Gp72, which share an identity of 61.6% to 83%. However, we find these three homologous proteins differ from each other in oligomeric state. Moreover, we solve the crystal structure of Gp72 at 2.3 Å, which represents a novel fold in the α + β class. Structural analyses combined with redox assays enable us to propose a model of disulfide bond mediated oligomerization for Gp72. Altogether, these findings provide structural and biochemical basis for further investigations on the freshwater cyanophage Mic1.     

Crystal structure, optical, magnetic, and photochemical properties of the complex pentakis(dimethyl sulfoxide)nitrosylchromium(2+) hexafluorophosphate

The nitrosyl complex [Cr(dmso)₅(NO)](PF₆)₂ (1) (dmso = dimethyl sulfoxide) has been prepared by the solvolysis of [Cr(NCCH₃)₅(NO)](PF₆)₂ in neat dmso. The optical absorption spectrum of 1 in dmso shows maxima at 734, 567, 450, 413, and 337 nm. Continuous photolysis of 1 with λ = 365-580 nm light in dmso solution results in a release of NO with quantum yield, Φ, in the range 0.034-0.108 mol Einstein⁻¹. Irradiation of a deoxygenated CH₃CN solution of [Cr(NCCH₃)₅(NO)](PF₆)₂ in the presence of excess of [Fe(S₂CNEt₂)₂] results in a transfer of NO to the iron centre as shown from the characteristic EPR spectrum of [Fe(S₂CNEt₂)₂(NO)] with A_iso(¹⁴N) = 12.2 × 10⁻⁴ cm⁻¹. The EPR parameters of 1 were determined: g_iso, g_‖ and g_⊥ : 1.96725, 1.91881(4) and 1.992763(2); A_iso(⁵³Cr), A_‖ (⁵³Cr) and A_⊥(⁵³Cr): 22.8 × 10⁻⁴, 39 × 10⁻⁴ and 15.8 × 10⁻⁴ cm⁻¹; A_iso(¹⁴N), A_‖ (¹⁴N) and A_⊥(¹⁴N): 5.9 × 10⁻⁴, 2 × 10⁻⁴ and 7.540(4) × 10⁻⁴ cm⁻¹.     

Crystal structure of the kinase domain of serum and glucocorticoid-regulated kinase 1 in complex with AMP PNP

Serum and glucocorticoid-regulated kinase 1 (SGK1) is a serine/threonine protein kinase of the AGC family which participates in the control of epithelial ion transport and is implicated in proliferation and apoptosis. We report here the 1.9 A crystal structure of the catalytic domain of inactive human SGK1 in complex with AMP-PNP. SGK1 exists as a dimer formed by two intermolecular disulfide bonds between Cys258 in the activation loop and Cys193. Although most of the SGK1 structure closely resembles the common protein kinase fold, the structure around the active site is unique when compared to most protein kinases. The alphaC helix is not present in this inactive form of SGK1 crystal structure; instead, the segment corresponding to the C helix forms a beta-strand that is stabilized by the N-terminal segment of the activation loop through a short antiparallel beta-sheet. Since the differences from other kinases occur around the ATP binding site, this structure can provide valuable insight into the design of selective and highly potent ATP-competitive inhibitors of SGK1 kinase.     

Cobalt(II) coordination compounds with acetate and 2-aminopyridine ligands: Synthesis, characterization, structures and magnetic properties of two polymorphic forms

The synthesis and characterization of two polymorphic modifications of new cobalt coordination compound with 2-aminopyridine are reported. The modifications were prepared by the reaction of a solution of cobalt acetate tetrahydrate and 2-aminopyridine. The crystal structures of both polymorphic modifications have been determined by single-crystal X-ray diffraction analysis. The structures of both modifications are quite similar. In both of them the Co²⁺ is six coordinated by four O atoms from two bidentate chelate acetate ligands and by two N atoms from two 2-aminopyridine molecules. Acetate and 2-aminopyridine ligands are lying cis about the metal centre. The most important difference is in asymmetry of acetate ligand chelate bonding and in H-bonding network. Compounds exhibit an extensive system of intra and intermolecular hydrogen bonding. Magnetic properties of both modifications were studied between 2 K and 300 K giving the result μ_eff = 4.6 BM for modification I and μ_eff = 4.7 BM for modification II in paramagnetic region.     

Synthesis, and characterization of cobalt(III) complexes with Schiff bases derived from 2-hydroxynaphthaldehyde, (naph)2dien and (naph)2dpt, and monodentate amine ligands: Crystal structure, spectral and redox properties

Two series of complexes of the type [Co^III{(naph)₂dien}(amine)]BPh₄ {(naph)₂dien = bis-(2-hydroxy-1-naphthaldimine)-N-diethylenetriamine dianion, and amine = piperidine (pprdn) (1), pyrrolidine (prldn) (2), pyridine (py) (3), N-methylimidazole (N-MeIm) (4)}, and [Co^III{(naph)₂dpt}(amine)]BPh₄ {(naph)₂dpt = bis-(2-hydroxy-1-naphthaldimine)-N-dipropylenetriamine dianion, and amine = piperidine (pprdn) (5), 3-methylpyridine (3-Mepy) (6)} have been synthesized and characterized by elemental analyses, IR, UV-Vis, and ¹H NMR spectroscopy. The crystal structures of (2) and (6) have been determined by X-ray diffraction. The redox potentials of the central cobalt ion show a relatively good correlation with the σ-donor ability of the axial ligands. The spectroscopic and electrochemical properties of these complexes are also influenced by the mutual steric hindrance between the pentadentate Schiff base and the ancillary ligands.     

Mixed-solvothermal syntheses, structures and luminescence properties of two new Zn(II) phosphonates with layered and 3D framework structures

Two new zinc phosphonates with 2-hydroxyphosphonoacetic acid (HPAA) and 1-hydroxyethylidenediphosphonic acid (hedpH₄), [Zn₂{HO₃PCH(OH)CO₂}₃]·2NH₂(CH₃)₂·3H₂O (1) and [Zn₃{CH₃C(OH)(PO₃)₂}₂]·2NH₂(CH₃)₂·H₂O (2) have been synthesized under mixed-solvothermal conditions at 160 °C and structurally characterized by X-ray single-crystal diffraction, X-ray powder diffraction, infrared spectroscopy and elemental analysis. The structure of compound 1 comprises Zn1O₆ and Zn2O₆ octahedra connected by [HO₃PCH(OH)CO₂]²⁻ to form a 2D layered structure with one-dimensional channel system along c-axis direction, and the protonated dimethylamine cations are being located between two adjacent layers. Interestingly the layers of 1 arranged in an alternative sequence (ABAB). Compound 2 features a 3D framework structure with channels along the b- and c-axis, respectively. The charge-compensating protonated Hdma⁺ cations and solvate water molecules are located inside the channels along the c-axis. A notable feature for compound 2 is the presence of the alternate left- and right-handed helical chains in the structure. The luminescence properties of compounds 1 and 2 have also been studied.     

Synthesis and X-ray crystal structure of a polymeric copper(II) complex containing the novel ligand 4,4-(1,4-phenylene)bis[3-phenyl-5-(2-pyridyl)-4H-1,2,4-triazole]

The synthesis and X-ray crystal structure of the complex {[Cu^II(Ph₂PBPT)(bpy)](ClO₄)₂ · 2DMF}_∞ where Ph₂PBPT=4,4^′-(1,4-phenylene)bis[3-phenyl-5-(2-pyridyl)-4H-1,2,4-triazole], bpy=2,2^′-bipyridine and DMF=N,N-dimethylformamide are reported. In this one-dimensional coordination polymer the Cu²⁺ ions are in a distorted octahedral N₆ coordination environment made up of two Ph₂PBPT molecules, each chelating via one pyridine and one triazole nitrogen, and one bpy co-ligand. Within the zig-zag chain thus formed the shortest distance between two metal centres across the Ph₂PBPT ligand is 13.305(3) Å while it is 10.009(3) Å between two chains. This complex represents the first structurally characterised example of a coordination compound incorporating a chelating 4,4^′-bis(4H-1,2,4-triazole) as a ligand.     

Tridentate N(2)S ligand from 2,2'-dithiodibenzaldehyde and N,N-dimethylethylenediamine: Synthesis, structure, and characterization of a Ni(II) complex with relevance to Ni Superoxide Dismutase

Nickel Superoxide Dismutase (NiSOD) and the A-cluster of Carbon Monoxide Dehydrogenase/Acetyl Coenzyme A Synthase (CODH/ACS) both feature active sites with Ni coordinated by thiolate and amide donors. It is likely that the particular set of donors is important in tuning the redox potential of the Ni center(s). We report herein an expansion of our efforts involving the use of 2,2′-dithiodibenzaldehyde (DTDB) as a synthon for metal-thiolate complexes to reactions with Ni complexes of N,N-dimethylethylenediamine (dmen). In the presence of coordinating counterions, these reactions result in monomeric square-planar complexes of the tridentate N₂S donor ligand derived from the Schiff-base condensation of dmen and DTDB. In the absence of a coordinating counterion, we have isolated a Ni(II) complex with an asymmetric N₂S₂ donor set involving one amine and one imine N donor in addition to two thiolate donors. This latter complex is discussed with respect to its relevance to the active site of NiSOD.     

Characterization of an insertion sequence (IS891) of novel structure from the cyanobacterium Anabaena sp. strain M-131.

When recombinant plasmids that were transferred to the cyanobacterium Anabaena sp. strain M-131 were transferred back to Escherichia coli, some of the transformants contained inserts. One of the insertion sequences (ISs) was characterized by sequencing. This 1,351-base-pair IS contained an open reading frame that was capable of encoding a peptide of 310 amino acids and had terminal sequences with distinctive structures, but it lacked terminal inverted repeats and did not duplicate target DNA upon insertion. The element bore no significant sequence homology to any sequence stored in the GenBank data base. Restriction analysis of the genomes of Anabaena sp. strain M-131 and Anabaena sp. strain PCC 7120 showed those strains to be closely related. Sequences homologous to the IS element were also present in the DNA of Anabaena strain PCC 7120, but the copy numbers and chromosomal locations of such sequences differed in the two strains. The largest visualized plasmid was 425 kilobases (kb) in M-131 and 410 kb in PCC 7120; at least the former plasmid contained multiple copies of the element, as did a 115-kb plasmid in M-131.     

Regioselective synthesis of 4azido-Neu2en5,7Ac(2)1Me and its intramolecular transformation to 4azido-Neu2en5,9Ac(2)1Me

Methyl 5-N-acetyl-7-O-acetyl-4-azido-2,3-didehydro-2,4-dideoxy-neuraminic acid (4azido-Neu2en5,7 Ac(2)1Me) was synthesized regioselectively starting from 4azido-Neu2en5Ac1Me in high yield. The transformation of 4azido-Neu2en5,7Ac(2)1Me to the corresponding thermodynamically stable 4azido-Neu2en5,9Ac(2)1Me via intramolecular acetyl migration was confirmed by single-crystal X-ray diffraction analysis. The proposed rearrangement mechanism is discussed.     

Example of two novel thiocyanato bridged copper (II) complexes derived from substituted thiosemicarbazone ligand: structural elucidation,DNA/albumin binding,biological profile analysis,and molecular docking study

Two novel copper (II) substituted thiosemicarbazone Schiff base complexes [Cu(L₁)(µ-SCN)]_n(NO₃)₂ (1) and [Cu₂(µ-SCN)(SCN)(L₂)₂](NO₃) (2) have been synthesized by condensing substituted thiosemicarbazides like 4-methyl-3-thiosemicarbazide or 4-ethyl-3-thiosemicarbazide with 2-acetylpyridine. Both the metal complexes 1 and 2 are characterized using different spectroscopic techniques like IR, UV-Vis, ESR spectroscopy followed by elemental analysis, cyclic voltammetric measurement and single crystal X-ray structure analysis. X-ray crystal structure analysis reveal that complex 1 is polymeric while complex 2 is dimeric in nature. The coordination geometry around Cu(II) are square pyramidal in which thiosemicarbazone Schiff base ligand coordinate to the central Cu(II) atom in tridentate fashion. The prominent interaction patterns of 1 and 2 with CT-DNA were examined by employing electronic absorption and emission spectral titrations, cyclic voltammetry and viscosity measurements. All the results show that CT-DNA binds with both copper (II) complexes 1 and 2. Furthermore, protein binding ability in vitro of complexes 1 and 2 with both BSA and HSA were carried out using multispectroscopic techniques and a static quenching pattern was observed in both cases. Molecular docking study was employed to ascertain the exact mechanism of action of 1 and 2 with DNA and protein molecules (BSA and HSA). In vitro cytotoxicity activity of complexes 1 and 2 toward AGS and A549 was evaluated using MTT assay which demonstrates that both complexes 1 and 2 have superior prospectus to act as anticancer agents.

Communicated by Ramaswamy H. Sarma     

Nucleotide sequence and genetic structure of a novel carbaryl hydrolase gene (cehA) from Rhizobium sp. strain AC100

Rhizobium sp. strain AC100, which is capable of degrading carbaryl (1-naphthyl-N-methylcarbamate), was isolated from soil treated with carbaryl. This bacterium hydrolyzed carbaryl to 1-naphthol and methylamine. Carbaryl hydrolase from the strain was purified to homogeneity, and its N-terminal sequence, molecular mass (82 kDa), and enzymatic properties were determined. The purified enzyme hydrolyzed 1-naphthyl acetate and 4-nitrophenyl acetate indicating that the enzyme is an esterase. We then cloned the carbaryl hydrolase gene (cehA) from the plasmid DNA of the strain and determined the nucleotide sequence of the 10-kb region containing cehA. No homologous sequences were found by a database homology search using the nucleotide and deduced amino acid sequences of the cehA gene. Six open reading frames including the cehA gene were found in the 10-kb region, and sequencing analysis shows that the cehA gene is flanked by two copies of insertion sequence-like sequence, suggesting that it makes part of a composite transposon.     

Multinuclear magnetic resonance study of Pt(II) compounds with sulfoxide ligands and crystal structures of complexes of the types [Pt(R2SO)X3] and Pt(R2SO)2Cl2

Pt(II) complexes of the types K[Pt(R₂SO)X₃], NR₄[Pt(R₂SO)X₃] and Pt(R₂SO)₂Cl₂ (where X = Cl or Br) were characterized by multinuclear magnetic resonance spectroscopy (¹⁹⁵Pt, ¹H and ¹³C). In ¹⁹⁵Pt NMR, the chloro ionic compounds have shown signals between −2979 and −3106 ppm, while the cis disubstituted complexes were observed at higher fields, between −3450 and −3546 ppm. The signal of the compound trans-Pt(DPrSO)₂Cl₂ was found at higher field (−3666 ppm) than its cis analogue (−3517 ppm), since π-back-donation is considerably less effective in the trans geometry. In ¹H NMR, a single signal was observed for the sulfoxide in [Pt(DMSO)Cl₃]⁻, but for the other more sterically hindered ligands, two series of resonances were observed for the protons in α and β positions. The coupling constant ³J(¹⁹⁵Pt-¹H) are between 15 and 33 Hz. The ¹³C NMR results were interpreted in relation to the concept of inversed polarization of the π sulfoxide bond. The ²J(¹⁹⁵Pt-¹³C) values vary between 35 and 66 Hz, while a few ³J(¹⁹⁵Pt-¹³C) couplings were observed (13-26 Hz). The crystal structures of five monosubstituted ionic compounds N(n-Bu)₄[Pt(TMSO)Cl₃], N(Me)₄[Pt(DPrSO)Cl₃], K[Pt(EMSO)Cl₃], K[Pt(TMSO)Br₃] · H₂O and N(Et)₄[Pt(DPrSO)Br₃] and one disubstituted complex cis-Pt(DBuSO)₂Cl₂ were determined. The trans influence of the different ligands is discussed.