SOS3 (salt overly sensitive 3) from Arabidopsis thaliana: expression, purification, crystallization and preliminary X-ray analysis.

The salt-tolerance gene SOS3 (salt overly sensitive 3) of Arabidopsis thaliana encodes a calcium-binding protein that is able to sense the cytosolic calcium signal elicited by salt stress. SOS3 activates the SOS2 protein kinase, which activates various ion transporters. SOS3 was cloned into a plasmid and expressed in Escherichia coli, allowing purification of the protein to homogeneity. Two crystals with different additive contents were grown. Both diffract to 3.2 A resolution and belong to space group I4(1), with unit-cell parameters a = 93.65, c = 80.08 A and a = 91.79, c = 85.78 A, respectively. A promising molecular-replacement solution has been found using neuronal calcium-sensor 1 as the search model. Interestingly, no solution was found using AtCBL2 (A. thaliana calcineurin B-like protein) structure as a search model, although this protein belongs to the same family and displays 50% sequence identity.

Structure of bacteriocin AS-48: from soluble state to membrane bound state.

The bacteriocin AS-48 is a membrane-interacting peptide, which displays a broad anti-microbial spectrum against Gram-positive and Gram-negative bacteria. The NMR structure of AS-48 at pH 3 has been solved. The analysis of this structure suggests that the mechanism of AS-48 anti-bacterial activity involves the accumulation of positively charged molecules at the membrane surface leading to a disruption of the membrane potential. Here, we report the high-resolution crystal structure of AS-48 and sedimentation equilibrium experiments showing that this bacteriocin is able to adopt different oligomeric structures according to the physicochemical environment. The analysis of these structures suggests a mechanism for molecular function of AS-48 involving a transition from a water-soluble form to a membrane-bound state upon membrane binding.

Structural enzymology of Li(+)-sensitive/Mg(2+)-dependent phosphatases.

Li(+)-sensitive/Mg(2+)-dependent phosphatases have attracted considerable attention since they have been proposed as targets for lithium therapy in the treatment of manic-depressive patients. The members of this enzyme superfamily display low levels of sequence identity while possessing a common fold and active site. Extensive structural and biochemical data demonstrate the direct involvement of two metal ions in catalysis, and show that lithium exerts its inhibitory action by blocking the products at the active site. By exploiting the different inhibitory properties of magnesium and calcium, we have been able to solve the X-ray structures of the Li(+)-sensitive/Mg(2+)-dependent 3'-phosphoadenosine-5'-phosphatase in complex with its substrate and with its products. The structural comparison of these complexes provides a 3D picture of the different stages of the catalytic cycle. This gives new insights into the understanding of the biological function of this group of enzymes and their lithium inhibition, and should assist in the design of improved inhibitors of therapeutic value.

The X-ray structure of the FMN-binding protein AtHal3 provides the structural basis for the activity of a regulatory subunit involved in signal transduction.

BACKGROUND: The Arabidopsis thaliana HAL3 gene product encodes for an FMN-binding protein (AtHal3) that is related to plant growth and salt and osmotic tolerance. AtHal3 shows sequence homology to ScHal3, a regulatory subunit of the Saccharomyces cerevisae serine/threonine phosphatase PPz1. It has been proposed that AtHal3 and ScHal3 have similar roles in cellular physiology, as Arabidopsis transgenic plants that overexpress AtHal3 and yeast cells that overexpress ScHal3 display similar phenotypes of improved salt tolerance. The enzymatic activity of AtHal3 has not been investigated. However, the AtHal3 sequence is homologous to that of EpiD, a flavoprotein from Staphylococcus epidermidis that recognizes a peptidic substrate and subsequently catalyzes the alpha, beta-dehydrogenation of its C-terminal cysteine residue. RESULTS: The X-ray structure of AtHal3 at 2 A resolution reveals that the biological unit is a trimer. Each protomer adopts an alpha/beta Rossmann fold consisting of a six-stranded parallel beta sheet flanked by two layers of alpha helices. The FMN-binding site of AtHal3 contains all the structural requirements of the flavoenzymes that catalyze dehydrogenation reactions. Comparison of the amino acid sequences of AtHal3, ScHal3 and EpiD reveals that a significant number of residues involved in trimer formation, the active site, and FMN binding are conserved. This observation suggests that ScHal3 and EpiD might also be trimers, having a similar structure and function to AtHal3. CONCLUSIONS: Structural comparisons of AtHal3 with other FMN-binding proteins show that AtHal3 defines a new subgroup of this protein family that is involved in signal transduction. Analysis of the structure of AtHal3 indicates that this protein is designed to interact with another cellular component and to subsequently catalyze the alpha,beta-dehydrogenation of a peptidyl cysteine. Structural data from AtHal3, together with physiological and biochemical information from ScHal3 and EpiD, allow us to propose a model for the recognition and regulation of AtHal3/ScHal3 cellular partners.

X-ray structure of yeast Hal2p, a major target of lithium and sodium toxicity, and identification of framework interactions determining cation sensitivity.

The product of the yeast HAL2 gene (Hal2p) is an in vivo target of sodium and lithium toxicity and its overexpression improves salt tolerance in yeast and plants. Hal2p is a metabolic phosphatase which catalyses the hydrolysis of 3'-phosphoadenosine-5'-phosphate (PAP) to AMP. It is, the prototype of an evolutionarily conserved family of PAP phosphatases and the engineering of sodium insensitive enzymes of this group may contribute to the generation of salt-tolerant crops. We have solved the crystal structure of Hal2p in complex with magnesium, lithium and the two products of PAP hydrolysis, AMP and Pi, at 1.6 A resolution. A functional screening of random mutations of the HAL2 gene in growing yeast generated forms of the enzyme with reduced cation sensitivity. Analysis of these mutants defined a salt bridge (Glu238 ellipsis Arg152) and a hydrophobic bond (Va170 ellipsis Trp293) as important framework interactions determining cation sensitivity. Hal2p belongs to a larger superfamily of lithium-sensitive phosphatases which includes inositol monophosphatase. The hydrophobic interaction mutated in Hal2p is conserved in this superfamily and its disruption in human inositol monophosphatase also resulted in reduced cation sensitivity.

Pd(II) complexes with polydentate nitrogen ligands. Molecular recognition and dynamic behavior involving Pd-N bond rupture. X-ray molecular structures of [[Pd(C6HF4)2](bpzpm)] and [[Pd(eta 3-C4H7)]2(bpzpm)] (CF3SO3)2 [bpzpm = 4,6-bis(pyrazol-1-yl)pyrimidine].

The ligands 4,6-bis(pyrazol-1-yl)pyrimidine (bpzpm) and 4,6-bis(4-methylpyrazol-1-yl)pyrimidine (Me-bpzpm) were synthesized and their reactions with some palladium derivatives explored. Mononuclear or dinuclear neutral or cationic complexes were obtained by reaction of the ligands with 1 or 2 equiv of Pd(C6XF4)2(cod) (cod = 1,5-cyclooctadiene; X = F, H) or the palladium fragment [Pd(eta 3-2-Me-C3H4)(S)2]+ (S = acetone). The reaction of the dinuclear derivatives with 1 equiv of the respective free ligand immediately led to the regeneration of the mononuclear complexes. Except in the case of the synthesis of [[Pd(C6HF4)2][Pd(C6F5)2](bpzpm)], where two similar metallic groups are present, all attempts to obtain dinuclear asymmetric complexes with two different palladium fragments failed. Instead, the dinuclear symmetric complexes were formed. This result could be considered as an example of molecular recognition with the ligand acting as a ditopic receptor. This behavior is comparable to chemical symbiosis but in this case applied to the ligand rather than to the metal center as occurs normally. The polyfluorophenyl rings are situated on average in a perpendicular orientation with respect to the coordination plane. Their restricted rotation results in several atropoisomers for the complexes with m-C6HF4. Different cross-reaction experiments were carried out, and these showed the mobility of the metallic fragments, with the more difficult process being that involving the more strongly bonded polyfluorophenyl palladium groups. By means of 1H NMR variable temperature studies, the interconversion of the two isomers of [[Pd(eta 3-C4H7)]2-(bpzpm)]Tf2 (Tf = CF3SO3) was analyzed. In the case of [[Pd(eta 3-C4H7)](bpzpm)]Tf the existence of two processes, an intramolecular apparent allyl rotation and an intermolecular exchange of the allylpalladium fragments, has been demonstrated. Different delta Gc++ values at the coalescence temperatures have also been determined. An X-ray single-crystal analysis was carried out on [[Pd(eta 3-C4H7)]2(bpzpm)]Tf2, which crystallizes in the monoclinic system, space group I2/m, with a = 9.368(2), b = 16.191(3), c = 20.228(6) A, beta = 101.26(3), and Z = 4. Compound [[Pd(C6HF4)2](bpzpm)] crystallized in the triclinic system, space group P1, with a = 8.845(6), b = 12.6609(9), c = 12.826(3) A, alpha = 88.45(2), beta = 74.36(3), gamma = 89.32(2), and Z = 2.

Structural basis of increased resistance to thermal denaturation induced by single amino acid substitution in the sequence of beta-glucosidase A from Bacillus polymyxa.

The increasing development of the biotechnology industry demands the design of enzymes suitable to be used in conditions that often require broad resistance against adverse conditions. beta-glucosidase A from Bacillus polymyxa is an interesting model for studies of protein engineering. This is a well-characterized enzyme, belonging to glycosyl hydrolase family 1. Its natural substrate is cellobiose, but is also active against various artificial substrates. In its native state has an octameric structure. Its subunit conserves the general (alpha/beta)8 barrel topology of its family, with the active site being in a cavity defined along the axis of the barrel. Using random-mutagenesis, we have identified several mutations enhancing its stability and it was found that one them, the E96K substitution, involved structural changes. The crystal structure of this mutant has been determined by X-ray diffraction and compared with the native structure. The only difference founded between both structures is a new ion pair linking Lys96 introduced at the N-terminus of helix alpha2, to Asp28, located in one of the loops surrounding the active-site cavity. The new ion pair binds two segments of the chain that are distant in sequence and, therefore, this favorable interaction must exert a determinant influence in stabilizing the tertiary structure. Furthermore, analysis of the crystallographic isotropic temperature factors reveals that, as a direct consequence of the introduced ion pair, an unexpected decreased mobility of secondary structure units of the barrel which are proximal to the site of mutation is observed. However, this effect is observed only in the surrounding of one of the partners forming the salt bridge and not around the other. These results show that far-reaching effects can be achieved by a single amino acid replacement within the protein structure. Consequently, the identification and combination of a few single substitutions affecting stability may be sufficient to obtain a highly resistant enzyme, suitable to be used under extreme conditions.

Crystal structure of beta-glucosidase A from Bacillus polymyxa: insights into the catalytic activity in family 1 glycosyl hydrolases.

Family 1 glycosyl hydrolases are a very relevant group of enzymes because of the diversity of biological roles in which they are involved, and their generalized occurrence in all sorts of living organisms. The biological plasticity of these enzymes is a consequence of the variety of beta-glycosidic substrates that they can hydrolyze: disaccharides such as cellobiose and lactose, phosphorylated disaccharides, cyanogenic glycosides, etc. The crystal structure of BglA, a member of the family, has been determined in the native state and complexed with gluconate ligand, at 2.4 A and 2.3 A resolution, respectively. The subunits of the octameric enzyme display the (alpha/beta)8 barrel structural fold previously reported for other family 1 enzymes. However, significant structural differences have been encountered in the loops surrounding the active-center cavity. These differences make a wide and extended cavity in BglA, which seems to be able to accommodate substrates longer than cellobiose, its natural substrate. Furthermore, a third sub-site is encountered, which might have some connection with the transglycosylating activity associated to this enzyme and its certain activity against beta-1,4 oligosaccharides composed of more than two units of glucose. The particular geometry of the cavity which contains the active center of BglA must therefore account for both, hydrolytic and transglycosylating activities. A potent and well known inhibitor of different glycosidases, D-glucono-1,5-lactone, was used in an attempt to define interactions of the substrate with specific protein residues. Although the lactone has transformed into gluconate under crystallizing conditions, the open species still binds the enzyme, the conformation of its chain mimicking the true inhibitor. From the analysis of the enzyme-ligand hydrogen bonding interactions, a detailed picture of the active center can be drawn, for a family 1 enzyme. In this way, Gln20, His121, Tyr296, Glu405 and Trp406 are identified as determinant residues in the recognition of the substrate. In particular, two bidentate hydrogen bonds made by Gln20 and Glu405, could conform the structural explanation for the ability of most members of the family for displaying both, glucosidase and galactosidase activity.

Enantiomerically Pure alpha-Alkylidene beta-Amino Esters from Asymmetric Addition of Metal Dienolates to N-Sulfinylimines.

Lithium dienolate of 3-butenoic methyl ester was reacted with enantiomerically pure N-arylsulfinyl phenylimines (1 and 2) under different conditions. The reactions were completely regioselective-the C-C coupling occurs at the 2-position of dienolate-and highly stereoselective at the iminic carbon. In the presence of different Lewis acids (ZnCl(2), ZnBr(2), and ScTf(3)) mixtures of two alpha-vinyl, beta-arylsulfinylamino esters (epimers at C-alpha) were obtained, being the stereoselectivity depending on the nature of the aryl sulfinyl moiety and the Lewis acid used. Desulfinylation of these mixtures followed by isomerization of the double bond with Na(2)CO(3) allowed the synthesis of the optically pure (E)-alpha-ethylidene-beta-amino ester 10 in quite high overall yield. The addition of the lithium dienolate to sulfinylimines in the absence of the Lewis catalysts yielded mixtures containing important amounts of the optically pure N-arylsulfinyl alpha-ethylidene-beta-amino esters, which became the exclusive product of the reaction when N-2-methoxynaphthylsulfinyl phenylimine 2 was used as starting product.

Strain Effects in Protonated Carbonyl Compounds. An Experimental and ab Initio Treatment of Acyclic Carboxamides and Ketones.

Strain effects have been quantitatively evaluated for a set of 22 compounds including ketones (R(2)CO), carboxamides (RCONH(2)), and N,N-dimethylcarboxamides (RCONMe(2)), where R = Me, Et, i-Pr, t-Bu, 1-adamantyl (1-Ad), in their neutral and protonated forms. To this end, use was made of the gas-phase proton affinities and standard enthalpies of formation of these compounds in the gas phase, as determined by Fourier transform ion cyclotron resonance mass spectrometry (FT ICR) and thermochemical techniques, respectively. The structures of 1-AdCOMe and (1-Ad)(2)CO were determined by X-ray crystallography. Quantum-mechanical calculations, at levels ranging from AM1 to MP2/6-311+G(d,p)//6-31G(d), were performed on the various neutral and protonated species. Constrained space orbital variation (CSOV) calculations were carried out on selected protonated species to further assess the contributions of the various stabilizing factors. Taking neutral and protonated methyl ketones as references, we constructed isodesmic reactions that provided, seemingly for the first time, quantitative measures of strain in the protonated species. A combination of these data with the results of theoretical calculations (which also included several "computational experiments") lead to a unified, conceptually satisfactory, quantitative description of these effects and their physical link to structural properties of the neutral and protonated species.

Crystallization and preliminary X-ray diffraction analysis of a type I beta-glucosidase encoded by the bgIA gene of Bacillus polymyxa.

The enzyme encoded by the bgIA gene of Bacillus polymyxa, a type I beta-glucosidase belonging to family I of glycosyl hydrolases, has been purified to homogeneity from an Escherichia coli culture which overexpressed the gene, and crystallized. The crystals, which diffract to 3.0 A resolution, belong to the orthorhombic space group C222(1). The cell dimensions are a = 155.4 A, b = 209.4 A, c = 209.7 A.

N-substituted pyrazino[2,3-c][1,2,6]thiadiazine 2,2-dioxides. A new class of diuretics.

The synthesis and evaluation of a new class of diuretic agents derived from the pyrazino[2,3-c][1,2,6]thiadiazine 2,2-dioxide ring system are described. Preliminary structure-activity relationships indicate that the nature and location of the substituents at different positions of the heterocycle are crucial for activity. Thus, a novel synthetic methodology has been developed to selectively introduce the desired substituents at different positions. From the study of the pharmacological properties (dose-response curves, duration of action, and acute toxicity) of the most active compounds, 4-amino-1,7-diethyl-6-methylpyrazino[2,3-c][1,2,6]thiadiazine++ + 2,2-dioxide (9) was selected for further investigation. Compound 9 (C10H15N5O2S) crystallizes in space group P21/a with unit cell dimensions a = 16.482 (1), b = 9.3484 (3), c = 8.333 (3) A, beta = 103.003 (3) degrees, Z = 4.