Search

Pseudomonas fluorescens strain KU-7 is a prototype microorganism that metabolizes 2-nitrobenzoate (2-NBA) via the formation of 3-hydroxyanthranilate (3-HAA), a known antioxidant and reductant. The initial two steps leading to the sequential formation of 2-hydroxy/aminobenzoate and 3-HAA are catalyzed by a NADPH-dependent 2-NBA nitroreductase (NbaA) and 2-hydroxylaminobenzoate mutase (NbaB), respectively. The 216-amino-acid protein NbaA is 78% identical to a plasmid-encoded hypothetical conserved protein of Polaromonas strain JS666; structurally, it belongs to the homodimeric NADH:flavin mononucleotide (FMN) oxidoreductase-like fold family. Structural modeling of complexes with the flavin, coenzyme, and substrate suggested specific residues contributing to the NbaA catalytic activity, assuming a ping-pong reaction mechanism. Mutational analysis supports the roles of Asn40, Asp76, and Glu113, which are predicted to form the binding site for a divalent metal ion implicated in FMN binding, and a role in NADPH binding for the 10-residue insertion in the [beta]5-[alpha]2 loop. The 181-amino-acid sequence of NbaB is 35% identical to the 4-hydroxylaminobenzoate lyases (PnbBs) of various 4-nitrobenzoate-assimilating bacteria, e.g., Pseudomonas putida strain TW3. Coexpression of nbaB with nbaA in Escherichia coli produced a small amount of 3-HAA from 2-NBA, supporting the functionality of the nbaB gene. We also showed by gene knockout and chemotaxis assays that nbaY, a chemoreceptor NahY homolog located downstream of the nbaA gene, is responsible for strain KU-7 being attracted to 2-NBA. NbaY is the first chemoreceptor in nitroaromatic metabolism to be identified, and this study completes the gene elucidation of 2-NBA metabolism that is localized within a 24-kb chromosomal locus of strain KU-7. doi:10.1128/JB.01098-06

The equilibrium geometries at 54 small molecules containing linear or near-linear N-H..N bonds (sample M) are optimized at the MP2/6-31G(d,p) level and the values of p' and p' of the parameters p(sub c) at the bond-critical points(p' in the N-H, p' in the H..N bond) are compounded from the results of the optimizations.

The equilibrium geometries of the isoelectronic Z[Ph.sup.0, [+ or -] 1.sub.4] (Z = B, C, N) molecules have been optimized, in [S.sub.4] and [D.sub.2d] symmetries, at the HF/6-31G(d,p) and B3LYP/6-31G(d,p) levels, with the phenyl rings constrained to be planar. The ground-state conformations of all three species are shown to be of [S.sub.4] symmetry, but the difference of the energies of the [S.sub.4] and the [D.sub.2d] conformations is estimated to amount to only ~1 kcal [mol.sup.-1], with a barrier to concerted rotational reorientation of the phenyl rings of ~5.0 kcal [mol.sup.-1] for B[Ph.sup.1.sub.4], ~6.4 kcal [mol.sup.-1] for C[Ph.sub.4], and ~7.9 kcal [mol.sup.-1] for N[Ph.sup.+.sub.4]. A redetermination of the crystal structure of C[Ph.sub.4] from -60[degrees]C X-ray data agrees with the results of previous determinations at ambient temperature; the C[Ph.sub.4] molecule in the crystal is slightly compressed along the [S.sub.4] axis relative to the free molecule, otherwise the geometries of the two are essentially the same. Correlations between the optimized geometric parameters of the Z[Ph.sup.0, [+ or -] 1.sub.4] molecules have been examined and analyzed in detail, as have the substitution-induced changes in the geometry of the phenyl ring. The results confirm and strengthen the conclusions from the statistical studies by Domenicano et al. on the geometry of benzene rings monosubstituted by atoms of elements from the first row of the Periodic system. Key words: tetraphenylborate, tetraphenylmethane, tetraphenylammonium, ab initio molecular geometries.

A study of the proline-catalyzed direct aldol reaction between acetone and acetaldehyde using density functional theory is presented. The results show that the aldol reaction between acetone and acetaldehyde, in which proline acts as an enzyme mimic illustrates the potential of small organic molecules to act as chiral catalysts in asymmetric synthesis and the complementary nature of theoretical calculations.

Trends exhibited in distance relationships and properties at the bond critical point (BCP) in linear or non-linear N-H...N hydrogen bonds are investigated by optimizing geometry of such bonds in a large number of suitable simple chemical species at the RHF/6-31G** level. Results obtained for several experimental parameters are discussed in detail along with the implications of the findings.

The cis-trans isomerization of N-acetylproline methylamide is investigated by using density functional theory. The study demonstrates the important role the intramolecular N... HN hydrogen bond plays in the cis-trans isomerization of proline-containing molecules and the catalytic possibilities of hydrogen bonding.

The equilibrium geometries of the isoelectronic ZPh[sub 4] [sup 0, ±1] (Z = B, C, N) molecules have been optimized, in S[sub 4] and D[sub 2] [sub d] symmetries, at the HF/6-31G(d,p) and B3LYP/6-31G(d,p) levels, with the phenyl rings constrained to be planar. The ground-state conformations of all three species are shown to be of S[sub 4] symmetry, but the difference of the energies of the S[sub 4] and the D[sub 2] [sub d] conformations is estimated to amount to only ~1 kcal mol[sup –1] , with a barrier to concerted rotational reorientation of the phenyl rings of ~5.0 kcal mol[sup –1] for BPh[sup –] [sub 4] , ~6.4 kcal mol[sup –1] for CPh[sub 4] , and ~7.9 kcal mol[sup –1] for NPh[sup +] [sub 4] . A redetermination of the crystal structure of CPh[sub 4] from –60°C X-ray data agrees with the results of previous determinations at ambient temperature; the CPh[sub 4] molecule in the crystal is slightly compressed along the S[sub 4] axis relative to the free molecule, otherwise the geometries of the two are essentially the same. Correlations between the optimized geometric parameters of the ZPh[sub 4] [sup 0, ±1] molecules have been examined and analyzed in detail, as have the substitution-induced changes in the geometry of the phenyl ring. The results confirm and strengthen the conclusions from the statistical studies by Domenicano et al. on the geometry of benzene rings monosubstituted by atoms of elements from the first row of the Periodic system.Key words: tetraphenylborate, tetraphenylmethane, tetraphenylammonium, ab initio molecular geometries.Opérant au niveau HF/6-31G(d,p) et B3LYP/6-31G(d,p) de la théorie et en contraignant les noyaux phényles à être plans, on a optimisé les géométries à l'équilibre des molécules isoélectroniques ZPh[sub 4] [sup 0, ±1] (Z = B, C, N) dans les symétries S[sub 4] et D[sub 2d] . On démontre que les conformations des trois espèces à l'état fondamental sont de symétrie S[sub 4] ; toutefois, on a évalué que la différence d'énergie entre les conformations S[sub 4] et D[sub 2d] n'est que d'environ 1 kcal mol[sup –1] alors que la barrière à la réorientation rotationnelle des noyaux phényles d'environ 5,0 kcal mol[sup –1] pour le BPh[sup –] [sub 4] , d'environ 6,4 kcal mol[sup –1] pour le CPh[sub 4] et d'environ 7,9 kcal mol[sup –1] pour le NPh[sup +] [sub 4] . Une redétermination de la structure cristalline du CPh[sub 4] à partir de données de rayons X obtenues à –60°C est en accord avec les déterminations antérieures à la température ambiante; par rapport à la molécule libre, la molécule de CPh[sub 4] dans le cristal est légèrement comprimée le long de l'axe S[sub 4] , mais autrement les géométries des deux sont essentiellement les mêmes. On a examiné les corrélations entre les paramètres géométriques optimisés des molécules de ZPh[sub 4] [sup 0, ±1] et on les a analysées en détail comme on l'a fait pour les changements dans la géométrie du noyau phényle induits par une substitution. Les résultats confirment et renforcent les conclusions obtenues par les études statistiques de Domenicano et ses collaborateurs sur les géométries des noyaux benzéniques monosubstitués par des atomes d'éléments de la première rangée du tableau périodique.Mots clés : tétraphénylborate, tétraphénylméthane, tétraphénylammonium, géométries moléculaires ab initio.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

Pseudomonas fluorescens strain KU-7 is a prototype microorganism that metabolizes 2-nitrobenzoate (2-NBA) via the formation of 3-hydroxyanthranilate (3-HAA), a known antioxidant and reductant. The initial two steps leading to the sequential formation of 2-hydroxy/aminobenzoate and 3-HAA are catalyzed by a NADPH-dependent 2-NBA nitroreductase (NbaA) and 2-hydroxylaminobenzoate mutase (NbaB), respectively. The 216-amino-acid protein NbaA is 78% identical to a plasmid-encoded hypothetical conserved protein of Polaromonas strain JS666; structurally, it belongs to the homodimeric NADH:flavin mononucleotide (FMN) oxidoreductase-like fold family. Structural modeling of complexes with the flavin, coenzyme, and substrate suggested specific residues contributing to the NbaA catalytic activity, assuming a ping-pong reaction mechanism. Mutational analysis supports the roles of Asn40, Asp76, and Glu113, which are predicted to form the binding site for a divalent metal ion implicated in FMN binding, and a role in NADPH binding for the 10-residue insertion in the β5-α2 loop. The 181-amino-acid sequence of NbaB is 35% identical to the 4-hydroxylaminobenzoate lyases (PnbBs) of various 4-nitrobenzoate-assimilating bacteria, e.g., Pseudomonas putida strain TW3. Coexpression of nbaB with nbaA in Escherichia coli produced a small amount of 3-HAA from 2-NBA, supporting the functionality of the nbaB gene. We also showed by gene knockout and chemotaxis assays that nbaY, a chemoreceptor NahY homolog located downstream of the nbaA gene, is responsible for strain KU-7 being attracted to 2-NBA. NbaY is the first chemoreceptor in nitroaromatic metabolism to be identified, and this study completes the gene elucidation of 2-NBA metabolism that is localized within a 24-kb chromosomal locus of strain KU-7. [ABSTRACT FROM AUTHOR]