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Eukaryotic protein kinases contain an Asp-Phe-Gly (DFG) motif, the conformation of which is involved in controlling the catalytic activity, at the N-terminus of the activation segment. The motif can be switched between active-state (DFG-in) and inactive-state (DFG-out) conformations: however, the mechanism of conformational change is poorly understood, partly because there are few reports of the DFG-out conformation. Here, a novel crystal structure of nonphosphorylated human mitogen-activated protein kinase kinase 1 (MEK1; amino acids 38–381) complexed with ATP-γS is reported in which MEK1 adopts the DFG-out conformation. The crystal structure revealed that the structural elements (the αC helix and HRD motif) surrounding the active site are involved in the formation/stabilization of the DFG-out conformation. The ATP-γS molecule was bound to the canonical ATP-binding site in a different binding mode that has never been found in previously determined crystal structures of MEK1. This novel ATP-γS binding mode provides a starting point for the design of high-affinity inhibitors of nonphosphorylated inactive MEK1 that adopts the DFG-out conformation.

The thermostable endo-1,5-α-L-arabinanase fromBacillus thermodenitrificansTS-3 (ABN-TS) hydrolyzes the α-1,5-L-arabinofuranoside linkages of arabinan. In this study, the crystal structures of inactive ABN-TS mutants, D27A and D147N, were determined in complex with arabino-oligosaccharides. The crystal structures revealed that ABN-TS has at least six subsites in the deep V-shaped cleft formed across one face of the propeller structure. The structural features indicate that substrate recognition is profoundly influenced by the remote subsites as well as by the subsites surrounding the active center. The `open' structure of the substrate-binding cleft of the endo-acting ABN-TS is suitable for the random binding of several sugar units in polymeric substrates.

application/pdf, Article, FEBS Letter, 2018, 592, p.1378-1388

Isoniazid (INH) is one of the most effective antibiotics against tuberculosis. INH is a prodrug that is activated by KatG. Although extensive studies have been performed in order to understand the mechanism of KatG, even the binding site of INH in KatG remains controversial. In this study, we determined the crystal structure of KatG from Synechococcus elongatus PCC7942 (SeKatG) in a complex with INH at 2.12-A resolution. Three INH molecules were bound to the molecular surface. One INH molecule was bound at the entrance to the e-edge side of heme (designated site 1), another was bound at the entrance to the γ-edge side of heme (site 2), and another was bound to the loop structures in front of the heme propionate side chain (site 3). All of the interactions between KatG and the bound INH seemed to be weak, being mediated mainly by van der Waals contacts. Structural comparisons revealed that the identity and configuration of the residues in site 1 were very similar among SeKatG, Burkholderia pseudomallei KatG, and Mycobacterium tuberculosis KatG. In contrast, sites 2 and 3 were structurally diverse among the three proteins. Thus, site 1 is probably the common KatG INH-binding site. A static enzymatic analysis and thermal shift assay suggested that the INH-activating reaction does not proceed in site 1, but rather that this site may function as an initial trapping site for the INH molecule. Database The atomic coordinates and structure factors have been deposited in the Protein Data Bank under the accession number 3WXO.

Mitogen-activated protein kinase kinase 4 (MAP2K4) plays a crucial role in the stress-activated signal cascade and is enzymatically regulated by ligand or substrate binding, and/or post-translational modification. Crystal structures combined with small-angle X-ray scattering experiments revealed that the apo form of non-phosphorylated MAP2K4 (npMAP2K4) exists in a transient state which has a longer conformation compared with the typical kinase folding. Upon ATP-binding, the transient conformation adopted the configuration of typical kinase folding. In the absence of ATP-binding, the transient state of apo npMAP2K4 may shift to a state of aggregation via non-particular hydrophobic interactions as a result of the exposed hydrophobic residues.

Bimolecular fluorescence complementation (BiFC) assay has been used widely to visualize protein-protein interactions in cells. However, there is a problem that fluorescent protein fragments have an ability to associate with each other independent of an interaction between proteins fused to the fragments. To facilitate the BiFC assay, we have attempted to determine the structure and characteristics of reassembled fluorescent protein, Venus. The anion-exchange chromatography showed an oligomer and a monomer of reassembled Venus. Our results suggested that the oligomer was formed by β-strands swapping without any serious steric clashes and was converted to the monomer. Crystal structure of reassembled Venus had an 11-stranded β-barrel fold, typical of GFP-derived fluorescent proteins. Based on the structural features, we have mutated to β-strand 7 and measured T(m) values. The results have revealed that the mutation influences the thermal stability of reassembled fluorescent complex.

A novel scorpion venom peptide, La1 fromLiocheles australasiae, with a molecular weight of 7.8 kDa, is presumed to possess a single von Willebrand factor type C (VWC) domain, a common protein module, based on the position of eight Cys residues in its sequence. The biological function of La1 is still unknown. Deciphering its three-dimensional structure will be helpful in understanding its biological function. La1 was crystallized by the sitting-drop vapour-diffusion method using magnesium sulfate as a precipitant. The crystals belonged to the monoclinic space groupC2, with unit-cell parametersa= 63.0,b= 30.2,c= 32.3 Å, β = 108.5°, and diffracted to 1.9 Å resolution. The calculatedVMbased on one molecule per asymmetric unit was 1.87 Å3 Da−1. The solvent content was 34.1%.

MKK4 activates both JNKs and p38s. We determined the crystal structures of human non-phosphorylated MKK4 kinase domain (npMKK4) complexed with AMP-PNP (npMKK4/AMP) and a ternary complex of npMKK4, AMP-PNP and p38α peptide (npMKK4/AMP/p38). These crystal structures revealed that the p38α peptide-bound npMKK4 at the allosteric site rather than at the putative substrate binding site and induced an auto-inhibition state. While the activation loop of the npMKK4/AMP complex was disordered, in the npMKK4/AMP/p38 complex it configured a long α-helix, which prevented substrate access to the active site and αC-helix movement to the active configuration of MKK4.

To help resolve long-standing questions regarding the catalytic activity of the serine proteases the structure of porcine pancreatic elastase has been analyzed by high-resolution neutron (1.65 A resolution) and X-ray (0.94 A resolution) crystallography. In order to mimic the tetrahedral transition intermediate, a peptidic inhibitor was used. The neutron and X-ray data show that the hydrogen bond between His57 and Asp102 is not consistent with a low-barrier hydrogen which is predicted to have the hydrogen midway between the donor and acceptor atom. The neutron analysis also shows that the oxygen of the oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the “oxyanion hole” in stabilizing the tetrahedral intermediate in catalysis.

To help resolve long-standing questions regarding the catalytic activity of the serine proteases, the structure of porcine pancreatic elastase has been analyzed by high-resolution neutron and X-ray crystallography. To mimic the tetrahedral transition intermediate, a peptidic inhibitor was used. A single large crystal was used to collect room-temperature neutron data to 1.65 A resolution and X-ray data to 1.20 A resolution. Another crystal provided a low-temperature X-ray data set to 0.94 A resolution. The neutron data are to higher resolution than previously reported for a serine protease and the X-ray data are comparable with other studies. The neutron and X-ray data show that the hydrogen bond between His57 and Asp102 (chymotrypsin numbering) is 2.60 A in length and that the hydrogen-bonding hydrogen is 0.80-0.96 A from the histidine nitrogen. This is not consistent with a low-barrier hydrogen which is predicted to have the hydrogen midway between the donor and acceptor atom. The observed interaction between His57 and Asp102 is essentially a short but conventional hydrogen bond, sometimes described as a short ionic hydrogen bond. The neutron analysis also shows that the oxygen of the oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the "oxyanion hole" in stabilizing the tetrahedral intermediate in catalysis.

Extracellular signal-regulated kinase (ERK) is a member of the MAP kinase family, and can regulate several cellular responses. The isoforms ERK1 and ERK2 have markedly similar amino acid sequences, but exhibit distinctive physiological functions. As well as ERK2, ERK1 was auto- and mono-phosphorylated at Tyr204 in the activation loop during Escherichia coli production, resulting in basal level activity, approximately 500-fold less compared with fully-active ERK1 dual-phosphorylated at Thr202 and Tyr204. Crystal structure demonstrated that the mono-phosphorylated ERK1 kinase possessed a novel conformation distinguishable from the un-phosphorylated (inactive) and the dual-phosphorylated (full-active) forms. The characteristic structural features in both the C-helix and the activation loop likely contribute to the basal activity of the mono-phosphorylated ERK1. The structural dissection of ERK1 compared to ERK2 suggests that the structural differences in the D-motif binding site and in the backside binding site are putative targets for development of selective ERK1/ERK2 inhibitors.

Background: The major dog allergens, Can f 1 and Can f 2, are members of the lipocalin protein family. The characterization of both dog allergens is still not complete. Their deduced amino acid sequences indicate the presence of three cysteine residues, probably connected with a disulfide bridge. We compared the biochemical and immunological properties of Can f 1 with those of Can f 2 using gel filtration, electrophoresis, and immunological assays. Methods: The rCan f 1, rCan f 2 and dog salivary proteins containing natural Can f 1 and Can f 2 were analyzed by HPLC gel filtration. The recombinant Can f 1 (rCan f 1) and rCan f 2 were analyzed by native and sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) with or without reduction. The binding ability of rabbit IgG purified by protein G affinity chromatography from the antiserum against rCan f 1 and rCan f 2 was examined after a reduction in the recombinant allergens. The immunological cross-reaction between rCan f 1 and rCan f 2 was examined by an enzyme-linked immunosorbent assay (ELISA) using the rabbit IgG against rCan f 1 and rCan f 2. The cross-reaction of human IgE in the serum of a patient with dog allergy between rCan f 1 and rCan f 2 was also analyzed by competitive ELISA. Results: The molecular weights of rCan f 1 and of rCan f 2 were 18 and 21 kDa, respectively, using SDS-PAGE under reducing conditions, but the natural Can f 1 and Can f 2 were separated by HPLC gel filtration into fractions containing proteins of 31 and 34 kDa, respectively. rCan f 1 and rCan f 2 migrated as multiple bands (30–100 kDa) in native PAGE in the presence or absence of a reductant. The molecular weights of natural Can f 1 and of Can f 2 were 20 and 23 kDa, respectively, in SDS-PAGE under reducing conditions. The ability of rabbit IgG to bind to rCan f 1 and rCan f 2 increased after the reduction of the recombinant allergens. The rabbit IgG against rCan f 1 bound to rCan f 2. Cross-reaction of human IgE was observed between rCan f 1 and rCan f 2. Conclusions: In the native and recombinant forms, Can f 1 and Can f 2 possessed a dimer structure under natural (non-reduced) condition. The dimers of Can f 1 and of Can f 2 were not built with a disulfide bridge but by non-covalent association. Cleavage of a disulfide bond of rCan f 1 and rCan f 2 increased the ability of binding of rabbit IgG to the allergens. The cross-reactivity of rabbit IgG and human IgE between rCan f 1 and rCan f 2 indicates that the same epitope(s) was present in Can f 1 and Can f 2.

The tyrosine kinase Fyn is a member of the Src kinase family. Besides the role of Fyn in T cell signal transduction in concert with Lck, its excess activity in the brain is involved with conditions such as Alzheimer's and Parkinson's diseases. Therefore, inhibition of Fyn kinase may help counteract these nervous system disorders. Here, we solved the crystal structure of the human Fyn kinase domain complexed with staurosporine, a potent kinase inhibitor, at 2.8 A resolution. Staurosporine binds to the ATP-binding site of Fyn in a similar manner as in the Lck- and Csk-complexes. The small structural differences in the staurosporine-binding and/or -unbinding region among the three kinase domains may help obtaining the selective inhibitors against the respective kinases.

The crystal structure of NADP-dependent apo-glyceraldehyde-3-phosphate dehydrogenase (apo-GAPDH) from Synechococcus PCC 7942 is reported. The crystal structure was solved by molecular replacement and refined to an R of 21.7% and R(free) of 27.5% at 2.9 angstroms resolution. The structural features of apo-GAPDH are as follows. The S-loop has an extremely flexible conformation and the sulfate ion is only taken into the classical P(i) site. A structural comparison with holo-GAPDHs indicated that the S-loop fixation is essential in the discrimination of NADP and NAD molecules.

Porcine pancreatic elastase (PPE) was crystallized under new sulfate-free conditions containing 0.3 M NaCl and 50 mM tris(hydroxymethyl)aminomethane-HCl at pH 7.0. The crystal structure determined at 1.5 angstroms resolution had a unique conformation in four regions which contained loop portions. A chloride ion was bound near the catalytic triad instead of the sulfate ion in PDB entry 1qnj, a typical PPE crystal structure. However, the chloride ion did not affect the configuration of the catalytic triad. A tris(hydroxymethyl)aminomethane (Tris) molecule was bound to the S4 and S5 subsites in place of the adjacent molecule in the 1qnj crystal and played a significant role in the structural change of the region. The distortion in this region may subsequently have induced conformational changes in the other three regions. The fact that Tris and these four regions make a diagonal line in the ac plane may have affected the crystal-packing contraction along the a and c axes in the crystal compared with the typical crystal.

Thermostable pectate lyase 47 (PL 47) prepared from Bacillus sp. TS 47 was mutated by a random mutation with error-prone PCR. The mutated PL 47 gene was expressed in Escherichia coli and the variants were screened over the PL activity using a plate assay method. Three less-thermostable mutants were isolated and their enzymes (LT-PLs) were isolated and characterized. The LT-PLs were inferior to the PL 47 in their thermostability and thermoactivity. Analyses of the amino acids substituted in the LT-PLs suggested that Ala325 in the PL 47 contributes to its thermostability.

The reaction of a new donor molecule having a planar but largely bent skeleton, bis(methylthio)tetrathiafulvalenothioquinone-1,3-dithiocarbonatodithiolemethide (1), with CuBr(2) in CH(3)CN/CS(2) afforded a black-colored crystal with a formula of 1(4).CuBr(4).2CuBr(3). In the crystal 1 molecules are one-dimensionally stacked to form half-cut pipelike columns, which are arranged to construct two different shapes of channels included by a one-dimensional array of CuBr(4)(2)(-) ions and a bibromide-bridged linear chain of CuBr(3)(-) ions with a square-pyramidal geometry at the Cu atom, [CuBr(3)(-)](n)(), respectively. The room-temperature electrical conductivity on the single crystal of 1(4).CuBr(4).2CuBr(3) was 2.0 x 10(-)(2) S cm(-)(1), and the temperature dependence of electrical conductivity was semiconducting with a large activation energy of 160 meV. The interactions between the neighboring Cu(II) d spins in the one-dimensional S = 1/2 spin systems due to CuBr(4)(2)(-) ions and CuBr(3)(-) ions in [CuBr(3)(-)](n)() were both antiferromagnetic, and the magnitudes were moderate (Weiss temperature, THETAV; = -18 K) in the former spin system and fairly large (coupling constant, J/k(B) = -120 K) in the latter spin system, which was in marked contrast to a moderate and ferromagnetic [CuBr(3)(-)](n)() chain in the cyclohexylammonium salt already known.

Ascorbate peroxidase (APX) is a heme-containing protein that plays a central role in scavenging H(2)O(2) in higher plants. The structure of stromal APX (sAPX) was determined at 1.6 A to an R-factor of 19.1% and an R-free-factor of 22.3%. The electrostatic potential of the gamma-channel that connects the molecular surface of sAPX to the gamma-edge of heme was more positive than that of cytosolic APX (cAPX) from pea, so sAPX might bind more easily with ascorbate than cAPX. The overall structure of sAPX was similar to those of cAPX from pea and cytochrome c peroxidase (CCP) from yeast, with a substantial difference in a loop structure located in the vicinity of the heme. The side chain of Arg169 in sAPX corresponding to His169 in cAPX and His181 in CCP extended in the opposite direction from the heme, forming two hydrogen bonds with carbonyl groups in the loop structure. The rapid inactivation of sAPX might be due to the characteristic conformation of Arg169 owing to the loop structure of sAPX.

The crystal structure of porcine pancreatic elastase (PPE) complexed with a potent peptidyl inhibitor, FR136706, was solved at 2.2 A resolution. FR136706 fits snugly into the extended active site pocket. The benzene moiety of FR136706 induced dramatic movement of the side chain moiety of Arg217 and both moieties formed a π–π interaction, which has never been found previously in structures of PPE complexed with inhibitors. This novel interaction mode may lead to design of new types of inhibitors.

Plant β-galactosidases play important roles in carbohydrate-reserve mobilization, cell-wall expansion and degradation, and turnover of signalling molecules during ripening. Tomato β-galactosidase 4 (TBG4) not only has β-galactosidase activity but also has exo-β-(1,4)-galactanase activity, and prefers β-(1,4)-galactans longer than pentamers as its substrates; most other β-galactosidases only have the former activity. Recombinant TBG4 protein expressed in the yeastPichia pastoriswas crystallized by the sitting-drop vapour-diffusion method using PEG 10 000 as a precipitant. The crystals belonged to the orthorhombic space groupP212121, with unit-parametersa= 92.82,b= 96.30,c= 159.26 Å, and diffracted to 1.65 Å resolution. Calculation of the Matthews coefficient suggested the presence of two monomers per asymmetric unit (VM= 2.2 Å3 Da−1), with a solvent content of 45%.

By the reaction of a new donor molecule, ethylenedithiotetrathiafulvalenoquinone-1,3-dithiolemethide (1) with FeBr3, GaBr3 or FeCl3 in CH3CN/CS2 charge transfer (CT) salts of 1 with counteranions of FeBr4−, GaBr4− or FeCl4− (12·FeBr4, 12·GaBr4 and 12·FeCl4) as plate crystals were obtained. Their crystal structures are apparently similar to each other, in which 1 molecules are dimerized in the parallel direction of their molecular long axes, and the dimers are stacked with changing the direction of the molecular long axes alternately to form a one- dimensional column. The counteranions intervene between the 1-stacked columns and are aligned in a zigzag manner. The room-temperature electrical conductivities of 12·FeBr4 and 12·GaBr4 are fairly high (10–15 S cm−1), but a small value (0.8 S cm−1) is obtained for 12·FeCl4. For all CT salts, temperature dependences of electrical conductivity are semiconducting in spite of very small activation energies (30–90 meV). Based on the comparison between their electrical conducting and magnetic properties, it is suggested that the d spins of FeBr4− or FeCl4− ions exert almost no influence on the π conducting electrons in the 1-stacked column.

Summary Plant β-galactosidases hydrolyze cell wall β-(1,4)-galactans to play important roles in cell wall expansion and degradation, and turnover of signaling molecules, during ripening. Tomato β-galactosidase 4 (TBG4) is an enzyme responsible for fruit softening through the degradation of β-(1,4)-galactan in the pericarp cell wall. TBG4 is the only enzyme among TBGs 1–7 that belongs to the β-galactosidase/exo-β-(1,4)-galactanase subfamily. The enzyme can hydrolyze a wide range of plant-derived (1,4)- or 4-linked polysaccharides, and shows a strong ability to attack β-(1,4)-galactan. To gain structural insight into its substrate specificity, we determined crystal structures of TBG4 and its complex with β-d-galactose. TBG4 comprises a catalytic TIM barrel domain followed by three β-sandwich domains. Three aromatic residues in the catalytic site that are thought to be important for substrate specificity are conserved in GH35 β-galactosidases derived from bacteria, fungi and animals; however, the crystal structures of TBG4 revealed that the enzyme has a valine residue (V548) replacing one of the conserved aromatic residues. The V548W mutant of TBG4 showed a roughly sixfold increase in activity towards β-(1,6)-galactobiose, and ~0.6-fold activity towards β-(1,4)-galactobiose, compared with wild-type TBG4. Amino acid residues corresponding to V548 of TBG4 thus appear to determine the substrate specificities of plant β-galactosidases towards β-1,4 and β-1,6 linkages.

We have developed three monoclonal antibodies against spinach chloroplastic (chl-mAb3 and chl-mAb6) and cytosolic (cyt-mAb1) ascorbate peroxidase (APX) isoenzymes to analyze the cross-reactivity and the structure of the epitopes for each monoclonal antibody. All three antibodies reacted specifically with their respective isoenzymes, but none cross-reacted with the others. Immunoreactive fragments in proteolytic recombinant APX isoenzymes were detected by means of the absorption on the corresponding immunoaffinity column. The cyt-mAb1 reacted with a peptide fragment containing the distal His region obtained by the lysyl endopeptidase digestion. The chl-mAb6 was capable of binding to the fragment, D-I-K-E-K-R, which is consistent with an inherent region of chloroplastic isoenzymes. No fragments reacting to the chl-mAb3 could be found in this study, suggesting that the chl-mAb3 recognizes a conformationally constituted epitope of the chloroplastic APX molecule, which may be destroyed by the enzymatic cleavage. We concluded that the peptides identified as epitopes are characteristic evidence of monoclonal antibodies.

The reaction of dimethylthio- (1) and ethylenedithio-tetrathiafulvalenothioquinone-1,3-dithiolemethides (2) with CuCl2 afforded the corresponding CuCl4 salts, (1)2·CuCl4 and (2)3·CuCl4. For (1)2·CuCl4 the 1 molecules are stacked to form a one-dimensional column, and in each column the neighboring 1 molecules are dimerized. On the other hand, the 2 molecules in (2)3·CuCl4 are stacked one-dimensionally in a triad unit. The CuCl4 ions intervene between the 1- or 2-stacked columns in each case. The electrical resistivities (ρ) for single crystals of (1)2·CuCl4 and (2)3·CuCl4 were 3 × 104 and 0.6 Ω cm at room temperature, respectively. The ρ value of (2)3·CuCl4 increased continuously on cooling, and its activation energy was 0.15 eV, which became gradually smaller with increasing applied pressure. For (1)2·CuCl4 the Cu(II) spins on the CuCl4 ions were only present whilst (2)3·CuCl4 involved both conducting π electrons on the 2-stacked column and localized Cu(II) spins on the CuCl4 ions which did not interact with each other between 300 and ca. 170 K, but below ca. 170 K the conducting π electrons disappeared, presumably as a result of interaction with the localized d spins.

X-ray crystal structure analysis of FR901277, a novel inhibitor of human leukocyte elastase, was performed and revealed that the lipophilic side chains are located towards the outside of the molecule. Binding simulation using computational methods showed that these lipophilic moieties could bind to the hydrophobic binding pockets of HLE.

N-Alkylated analogs (C 1 -C 3 ) of an N-arylcarbamoylpyrazoline were prepared. The introduction of these alkyl groups completely changed the crystal structure in respect of the torsion angle of the amide C-N bond of the non-alkyl compound. The introduction of methyl and ethyl groups slightly, and that of an isopropyl group markedly, decreased insecticidal activity against American cockroaches and house flies. Conformational analyses of the compounds suggested that the insecticidally active conformer of this class of compounds is in the anti-position regarding the N'-C(=O) and N-aryl bonds in which the non-alkyl compound is energetically the most stable. The most stable conformers of the alkylated compounds are in the syn-position, and these compounds would interact with target sites in the less stable anti-form.

The 1:2 mixed tetramethylammonium (NMe 4 + ) ( 1 ) and tetramethylphosphonium (PMe 4 + ) salts ( 2 ) of 2,5-dimethyltetracyano-quinodimethane (DMTCNQ) and its radical anion (DMTCNQ −⋅ ) were prepared, which exhibited both ferromagnetic behavior and high electrical conductivity at room temperature. The crystal structure of 2 showed a composition of two different DMTCNQ/DMTCNQ −⋅ (1:1) and DMTCNQ −⋅ columns, which have significant contact with each other.

The spinach stromal, thylakoid-bound, and cytosolic ascorbate peroxidase isozymes (EC 1.11.1.11) were overexpressed in Escherichia coli, and their enzymatic properties were compared with the respective native isozymes. The purification of the recombinant stromal and cytosolic ascorbate peroxidases using the conventional column chromatography yielded 0.73 and 2.2 mg of protein/liter of bacteria culture with enzyme activities of 800 and 486 micromol min-1 mg protein-1, respectively. In every respect, the recombinant stromal, thylakoid-bound, and cytosolic ascorbate peroxidase isozymes exhibited identical enzymatic properties with each native isozyme. Specifically, the recombinant stromal and thylakoid-bound ascorbate peroxidase isozymes showed high utilization of ascorbate as an electron donor and had a very short lifetime in ascorbate-depleted medium. Polyclonal antibodies raised against both purified recombinant stromal and cytosolic ascorbate peroxidase isozymes were prepared. Both antibodies showed a cross-reaction with the recombinant and native ascorbate peroxidase isozymes.

The crystal structure of catalase-peroxidase from Synechococcus elongatus PCC7942 (SeKatG) was solved by molecular replacement and refined to an R work of 16.8% and an R free of 20.6% at 2.2 A resolution. The asymmetric unit consisted of only one subunit of the catalase-peroxidase molecule, including a protoporphyrin IX haem moiety and two sodium ions. A typical KatG covalent adduct was formed, Met248–Tyr222–Trp94, which is a key structural element for catalase activity. The crystallographic equivalent subunit was created by a twofold symmetry operation to form the functional dimer. The overall structure of the dimer was quite similar to other KatGs. One sodium ion was located close to the proximal Trp314. The location and configuration of the proximal cation site were very similar to those of typical peroxidases such as ascorbate peroxidase. These features may provide a structural basis for the behaviour of the radical localization/delocalization during the course of the enzymatic reaction.

(Z)-2-(2-aminothiazol-4-yl)-N-(2-hydroxyethyl)-2-(hydroxyimino)acetamide (HL) has been employed as a model compound for an orally active cephalosporin antibiotic, Cefdinir (CFDN). A binuclear copper(II) complex Cu2L4 (1) has been obtained from an aqueous solution containing CuCl2 and HL, and its structure determined by means of X-ray crystallography: monoclinic, P2/c, a = 11.954(3) A, b = 10.661(3) A, c = 16.969(7) A, β = 108.13(3)°, Z = 2. The molecular structure of 1 is a dimeric copper(II) complex consisting of two copper(II) complex units CuL2, where the two molecules of L (La and Lb) are coordinated to the copper atom through their thiazole and oximate nitrogen atoms. La is also coordinated to the copper atom of the other CuL2 unit through the oximate oxygen atom, namely, the two complex units are bound to each other by forming a pair of oximate NO bridges of the two La molecules. The coordination environment of the copper atom is a distorted trigonal bipyramid. In addition, based on the molecular structure, the coordination property of CFDN to copper(II) in water has been clarified by means of spectrophotometry and titration. Both copper(II) (0.05 mM)-HL (0.1 mM) and copper(II) (0.05 mM)-CFDN (0.1 mM) aqueous solutions gave broad d-d bands at ca. 720 nm above pH 6, corresponding to that observed in the diffuse reflectance spectrum of the crystals of 1. The results indicate that CFDN also forms a binuclear copper(II) complex, Cu2(CFDN)4, corresponding to Cu2L4 as the main species in water above pH 7. Stability constants are as follows: log β110 = 11.12, log β240 = 41.13 for copper(II)-L complexes. The theoretical species distribution diagram as a function of pH for the copper(II) (0.05 mM)-HL (0.1 mM) system shows that Cu2L4 exists as the main species above pH 7. The titration results are consistent with the spectral data. The spectral and titration studies indicate that not only HL, but also CFDN forms a binuclear complex Cu2(CFDN)4 corresponding to Cu2L4 as the main species under the neutral and basic conditions. In addition, the stability constants of CFDN complexes should be as large as those of CuL complexes, although titrations for copper(II)-CFDN systems could not be carried out due to precipitation of copper(II)-CFDN complexes.

A new ternary uranium-based intermetallic compound U3Ni5Al19 has been synthesized. It crystallizes in the unique flat orthorhombic structure. Uranium atoms occupy two crystallographic 4c and 8f sites of quite similar local chemical environments. The temperature dependence of the magnetic susceptibility χ ( T ) demonstrates peculiar magnetic anisotropy; χ ( T ) along the b- and c-axis obeys the Curie–Weiss law above 23 K, while χ ( T ) along a-axis is small and temperature independent. At 23 K, only χ c shows a sharp cusp corresponding to an antiferromagnetic ordering, while χ b remains paramagnetic down to 2 K. From the crystallographical structure we suggest that only uranium atoms at the 8c site order antiferromagnetically at T N = 23 K , while those occupying the 4c site do not order down to 50 mK.

The open reading frame of tomato β-galactosidase 1 was expressed in yeast, and the enzymatic properties and substrate specificity were investigated. The enzyme had peak activity at pH 5.0 and 40-50°C. TBG1 was active on β-(1,3)- and β-(1,6)-galactobiose and lactose. TBG1 released galactose from lupin galactan, tomato fruit alkali soluble pectin, arabinogalactan, gum arabic and methyl β-(1,6)-galactohexaoside, but not from labeled β-(1,4)-galactoheptaose. TBG1 was assessed for its ability to degrade three galactosyl-containing cell wall fractions purified from different development and ripening stages of tomato fruit. TBG1 released galactose from all of the fractions from all of the stages tested. TBG1 activity was highest on the hemicellulose fraction at the 10 and 20d after pollination stage. This result is not correlated the with TBG1 expression pattern. TBG1 might act on a small but specific set of polysaccharide containing galactose.

The formation constant (KZnL), enthalpy and entropy changes (ΔH and ΔS), and deprotonation constant (Ka) of coordinated water for hydrated zinc(II)–triamine (1 : 1) complexes (N3–Zn-(OH2)n (N3 = diethylenetriamine (dien), N-(2-aminoethyl)-1,3-propanediamine (epd), dipropylenetriamine (dpt), cis,cis-1,3,5-triaminocyclohexane (tach), and 1,5,9-triazacyclododecane ([12]aneN3)) were determined by potentiometry. The pKa linearly increased along with an increase in -ΔH, and was explained in terms of a ligand–ligand interaction through the N3–Zn-O bond on the bases of a thermodynamic analysis and strain-energy calculation (MM2). The zinc(II) complex-promoted hydrolysis of 2,4-dinitrophenyl diethyl phosphate was investigated in 1% (v/v) methanol–water; the rate constants linearly increased along with decreases of pKa and −ΔH. This fact indicates that the hydrolysis proceeds via a concerted direct nucleophilic attacking mechanism of the coordinated hydroxide ion, in which the phosphate ester coordinates to the zin...

Cefdinir (CFDN) is an orally active, semisynthetic cephalosporin antibiotic and its structure is characterized by an oxyimino side chain which is able to form complexes with various metal ions. We observed that bioavailability of CFDN in dogs was reduced when it was co-administered with iron(II) salts. To assess possible effects of extraneous iron such as iron supplements on the bioavailability of CFDN, stability constants of the complexes formed between CFDN and iron(II) and iron(III) have been determined in aqueous solution by potentiometric and spectrophotometric titration methods. The stability constants were as follows : log β110=7.53, log β120=14.44, log β130=18.33 for the iron(II) complexes and log β110=10.43, log β120=20.40 and log β130=27.54 for the iron(III) complexes. Theoretical species distribution diagrams as a function of pH for solutions of metal (M) (0.1 mM) and ligand (L) (0.3 mM) showed that M1L1H0 and M1L2H0 existed as major species for the iron(II) system and M1L2H0 and M1L3H0 were main species for the iron(III) system under neutral conditions. From these results it is believed that complex formation in the digestive tract is involved in the reduction of the bioavailability of CFDN in dogs. In addition, spectrophotometric studies indicated that iron(II) coordinated to CFDN via the thiazole-ring and deprotonated oxime nitrogen atoms and iron(III) coordinated via the amide and deprotonated oxime oxygen atoms.

The influence of magnetic field on the crystallization process has been examined in Cs 2 TCNQ 3 (TCNQ=tetracyanoquinodimethane), a strongly Coulomb-correlated organic semiconductor. The crystal structure is unaffected by the magnetic field, while the electric, magnetic and optical properties change markedly if the magnetic field higher than a threshold (∼4 T) is applied during the crystal growth. The high-field crystals exhibit a very weak but distinct spontaneous magnetization with the exceedingly high Curie temperature of ∼420 K. The infrared and visible spectroscopy data show that this novel ferromagnetism concurs with the renormalization of the π ∗ state of TCNQ radical anions, TCNQ − .

Cholix toxin (ChxA) is a recently discovered exotoxin in Vibrio cholerae which has been characterized as a third member of the eukaryotic elongation factor 2-specific ADP-ribosyltransferase toxins, in addition to exotoxin A of Pseudomonas aeruginosa and diphtheria toxin of Corynebacterium diphtheriae . These toxins consist of three characteristic domains for receptor binding, translocation, and catalysis. However, there is little information about the prevalence of chxA and its genetic variations and pathogenic mechanisms. In this study, we screened the chxA gene in a large number ( n = 765) of V. cholerae strains and observed its presence exclusively in non-O1/non-O139 strains (27.0%; 53 of 196) and not in O1 ( n = 485) or O139 ( n = 84). Sequencing of these 53 chxA genes generated 29 subtypes which were grouped into three clusters designated chxA I, chxA II, and chxA III. chxA I belongs to the prototype, while chxA II and chxA III are newly discovered variants. ChxA II and ChxA III had unique receptor binding and catalytic domains, respectively, in comparison to ChxA I. Recombinant ChxA I (rChxA I) and rChxA II but not rChxA III showed variable cytotoxic effects on different eukaryotic cells. Although rChxA II was more lethal to mice than rChxA I when injected intravenously, no enterotoxicity of any rChxA was observed in a rabbit ileal loop test. Hepatocytes showed coagulation necrosis in rChxA I- or rChxA II-treated mice, seemingly the major target for ChxA. The present study illustrates the potential of ChxA as an important virulence factor in non-O1/non-O139 V. cholerae , which may be associated with extraintestinal infections rather than enterotoxicity.

Intracellular proteins can have free cysteines that may contribute to their structure, function, and stability; however, free cysteines can lead to chemical instabilities in solution because of oxidation-driven aggregation. The MAP kinase, c-Jun N-terminal kinase 1 (JNK1), possesses seven free cysteines and is an important drug target for autoimmune diseases, cancers, and apoptosis-related diseases. To characterize the role of cysteine residues in the structure, function, and stability of JNK1, we prepared and evaluated wild-type JNK1 and seven cysteine-deficient JNK1 proteins. The nonreduced sodium dodecyl sulfate-polyacrylamide gel electrophoresis experiments showed that the chemical stability of JNK1 increased as the number of cysteines decreased. The contribution of each cysteine residue to biological function and thermal stability was highly susceptible to the environment surrounding the particular cysteine mutation. The mutations of solvent-exposed cysteine to serine did not influence biological function and increased the thermal stability. The mutation of the accessible cysteine involved in the hydrophobic pocket did not affect biological function, although a moderate thermal destabilization was observed. Cysteines in the loosely assembled hydrophobic environment moderately contributed to thermal stability, and the mutations of these cysteines had a negligible effect on enzyme activity. The other cysteines are involved in the tightly filled hydrophobic core, and mutation of these residues was found to correlate with thermal stability and enzyme activity. These findings about the role of cysteine residues should allow us to obtain a stable JNK1 and thus promote the discovery of potent JNK1 inhibitors.

Mitogen-activated protein kinase kinase 6 (MAP2K6) plays a crucial role in the p38 MAP kinase signal cascade that regulates various stress-induced responses and is associated with pathological conditions. The crystal structure of human non-phosphorylated MAP2K6 (npMAP2K6) complexed with an ATP analogue was determined at 2.6 A resolution and represents an auto-inhibition state of MAP2K6. Three characteristics of short α-helices configured in the activation loop region, termed activation helices (AH1, AH2 and AH3), are important in controlling the auto-inhibition mechanism. AH1 displaces the αC-helix, a component essential for forming the active configuration, away from the active site. AH1 and AH2 were found to enclose the γ-phosphate, the leaving group of ATP. A comparison with the related enzymes, MAP2K1 and MAP2K4 reveals that MAP2K6 has the unique auto-inhibition mechanism mediated by the three activation helices.

The detailed understanding of the molecular features of a ligand binding to a target protein, facilitates the successful design of potent and selective inhibitors. We present a case study of ATP-competitive kinase inhibitors that include a pyradine moiety. These compounds have similar chemical structure, except for distinct terminal hydrophobic cyclopentyl or isopropyl groups, and block kinase activity of casein kinase 2 subunit α (CK2α), which is a target for several diseases, such as cancer and glomerulonephritis. Although these compounds display similar inhibitory potency against CK2α, the crystal structures reveal that the cyclopentyl derivative gains more favorable interactions compared with the isopropyl derivative, because of the additional ethylene moiety. The structural observations and biological data are consistent with the thermodynamic profiles of these inhibitors in binding to CK2α, revealing that the enthalpic advantage of the cyclopentyl derivative is accompanied with a lower entropic loss. Computational analyses indicated that the relative enthalpic gain of the cyclopentyl derivative arises from an enhancement of a wide range of van der Waals interactions from the whole complex. Conversely, the relative entropy loss of the cyclopentyl derivative arises from a decrease in the molecular fluctuation and higher conformational restriction in the active site of CK2α. These structural insights, in combination with thermodynamic and computational observations, should be helpful in developing potent and selective CK2α inhibitors.

We previously described five arabinanolytic enzymes secreted by Penicillium chrysogenum 31B into the culture medium. Here, we describe a sixth such enzyme, termed AbnS1. Analysis of the reaction products of debranched arabinan revealed that AbnS1 cleaved the substrate in an endo manner. The optimum temperature of AbnS1 was 60°C, which was much higher than that of a cold-adapted endo-arabinanase (Abnc) produced by this strain. The abns1 cDNA gene encoding AbnS1 was isolated by in vitro cloning. The deduced amino acid sequence of AbnS1 had 70% identity with that of Abnc. Pfam analysis revealed a Glyco_hydro_43 domain at positions 28 to 318 of AbnS1. Semi-quantitative reverse transcription-polymerase chain reaction analysis indicated that the abns1 gene was constitutively expressed in P. chrysogenum 31B at a low level, although the expression was only slightly induced with arabinose and arabinan. In contrast, expression of the abnc gene encoding Abnc was strongly induced by arabinose, arabinitol, and arabinan. Using debranched arabinan as substrate, recombinant AbnS1 (rAbnS1) accumulated arabinobiose and arabinotriose as the major products. Recombinant Abnc (rAbnc) released mainly arabinotriose and lesser amounts of arabinose and arabinobiose than did rAbnS1. Branched arabinan was completely degraded to arabinose by the action of rAbnS1 or rAbnc in combination with α-L: -arabinofuranosidase.

Fructose-1,6-/sedoheptulose-1,7-bisphosphatase of Synechococcus PCC 7942, overexpressed from Escherichia coli, has been purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as a precipitant. The crystals were monoclinic, with unit-cell parameters a = 80.1, b = 84.2, c = 104.3 A, beta = 101.7 degrees. They belonged to space group P2(1) and diffracted to at least 2.2 A resolution. The calculated V(M) value, based on a tetramer in the asymmetric unit, was 2.2 A(3) Da(-1).

Arabinanase Abnx from Penicillium chrysogenum 31B, which belongs to the GH93 family, releases arabinobiose from the nonreducing terminus of α-1,5-L-arabinan, which is distributed in the primary cell walls of higher plants. Crystal structures of Abnx and of its complex with arabinobiose were determined at the high resolutions of 1.14 Å to an R(work) of 10.7% (R(free) = 12.8%) and 1.04 Å to an R(work) of 10.4% (R(free) = 12.5%). Abnx has a six-bladed β-propeller fold with a typical ring-closure mode called `Velcro', in which the last four-stranded β-sheet is completed by the incorporation of a strand from the N-terminus. Catalytic residues which act as a nucleophile and an acid/base were proposed from the structures and confirmed by site-directed mutagenesis. The substrate-binding groove is enclosed at one end by two residues, Glu64 and Tyr66, which contribute to the recognition of the nonreducing chain end of the polysaccharide. A comparison with the related enzyme Arb93A which has a quite similar overall structure suggested that Abnx has different mechanisms to funnel substrates to the active site and/or to stabilize the transition state.

A monodentate phosphine, 8-diphenylphosphino-8'-methoxy-1, 1'-binaphthyl, was shown to be active as a ligand in palladium-catalyzed reactions, including the reduction of allylic carbonates with formic acid, hydrosilylation of a terminal olefin, and hydroboration of but-1-en-3-yne, even though it has a highly hindered lone pair.

Fyn-related kinase (Frk) was first identified using human breast cancer cells. It shares 51% identity with c-Src. Like all members of the Src family, Frk is thought to cause several cancers via dysregulations in signal transduction from cell-surface receptors. The excess activity of Frk on beta-cells has a crucial role in type-I diabetes. A silent mutation at Ile229 conferred a bacterial expression system on the kinase domains of Frk, which allowed for the quick expression and purification of one unphosphorylated and two mono-phosphorylated kinase domains. The C-terminal catalytic segment of the human Frk kinase conjugating hexahistidine purification tag (His-tag) was expressed in Escherichia coli. After first-step purification utilizing the His-tag, an anion-exchange chromatogram yielded three major peaks that had distinguishable phosphorylation characteristics as judged by Western blot analysis and measurement of kinase activity. This result of active protein production should promote drug discovery studies, including highthrough-put screening and structure-based drug design.

Two hydrates (tetrahydrate, I, and monohydrate, II) of a new antiallergic, sodium 5-(4-oxo-phenoxy-4H-quinolizine-3-carbox-amide)-tetrazolate (FR71021), were prepared and characterized by means of infrared spectrometry, thermal analysis, and power X-ray diffraction spectrometry. While I was confirmed to dehydrate readily resulting in an anhydrate form (noncrystalline form) below its critical relative humidity for dehydration, I was also transformed into II under humid conditions. The transformation kinetics from I to II were investigated under varying temperature and humidity conditions by a powder X-ray diffraction technique. The transformation mechanism followed a zero-order reaction, and the apparent transformation rate constant (k) could be described as a function of water vapor pressure (P), temperature (T), and the interaction orders between water vapor pressure and the samples (s) :k = A · exp(−Ea/ RT) ·Ps, where Ea is the activation energy and R is the gas constant.