1H, 15N and 13C NMR assignments of mouse methionine sulfoxide reductase B2

A recombinant mouse methionine-r-sulfoxide reductase 2 (MsrB2ΔS) isotopically labeled with ¹⁵N and ¹⁵N/¹³C was generated. We report here the ¹H, ¹⁵N, and ¹³C NMR assignments of the reduced form of this protein. An erratum to this article can be found at     

Biosynthesis of [1-<Superscript>15</Superscript>N] <Emphasis Type="SmallCaps">l</Emphasis>-tryptophan from <Superscript>15</Superscript>N labeled anthranilic acid by fermentation of <Emphasis Type="Italic">Candida utilis</Emphasis> mutant

A new method for synthesizing the labeled l-tryptophan is described in this work. l-Tryptophan, labeled with 98% ¹⁵N at position 1 was synthesized from the labeled anthranilic acid using Candida utilis mutants. The conversion ratio of ¹⁵N of 50% was achieved. The labeled anthranilic acid was synthesized by [¹⁵N] phthalimide that was prepared by 99.34% [¹⁵N] urea and phthalic anhydride in ortho-xylene medium at 140°C and under atmospheric pressure.     

Bacterial siderophores: structure elucidation, and 1H, 13C and 15N two-dimensional NMR assignments of azoverdin and related siderophores synthesized by Azomonas macrocytogenes ATCC 12334

Two major azoverdins were isolated from the cultures of Azomonas macrocytogenes ATCC 12334 grown in irondeficient medium. Their structures have been established using fast atom bombardment-mass spectroscopy, homonuclear and heteronuclear two-dimensional ¹⁵N, ¹³C and ¹H NMR, and circular dichroism techniques. These siderophores are chromopeptides possessing at the N-terminal end of their peptide chain the chromophore derived from 2,3-diamino-6,7-dihydroxyquinoline common to pyoverdins. The linear peptide chain (l)-Hse-(d)-AcOHOrn-(d)-Ser-(l)-AcOHOrn-(d)-Hse-(l)-CTHPMD has at its C-terminal end a new natural amino acid which is the result of the condensation of 1 mol of homoserine and 1 mol of 2,4-diaminobutyric acid forming a cyclic amidine belonging to the tetrahydropyrimidine family: 2-homoseryl-4-carboxyl-3,4,5,6-tetrahydropyrimidine. The azoverdins differ only by a substitutent bound to the nitrogen on C-3 of the chromophore: azoverdin, the most abundant one, possesses a succinamide moiety, whereas azoverdin A bears a succinic acid moiety. ¹⁵N-labelled azoverdin afforded readily, after the complete assignment of the ¹⁵N spectrum of the siderophore, a sequence determination of the peptidic part of the molecule and gave evidence for the presence of two tetrahydropyrimidine groups on the molecule: one on the chromophore and the second at the C-terminal end of the siderophore.     

1H, 15N, 13C resonance assignment of the AlgE6R1 subunit from the Azotobacter vinelandii mannuronan C5-epimerase

Isotopically labelled, ¹³C/¹⁵N from of recombinant subunit of the first R-module from alginate C5-epimerase 6 (AlgE6R1) from Azotobacter vinelandii mannuronan C5-epimerase was produced. We report here the ¹H, ¹⁵N, ¹³C resonance assignment of this subunit from AlgE6 epimerase.     

Hydroxyurea,a natural metabolite and an intermediate in d-cycloserine biosynthesis in streptomyces garyphalus

It was found that hydroxyurea, l-arginine and l-citrulline respectively significantly stimulated the formation of d-cycloserine in Streptomyces garyphalus. The formation of [¹⁴C]-hydroxyurea by washed cells was demonstrated after incubation with l-[guanido-¹⁴C]-arginine and l-[ureido-¹⁴C]-citrulline. The ¹⁵N of H₂NCO¹⁵NHOH was incorporated to 40% in d-cycloserine. The mass spectrum as well as the ¹⁵N NMR spectrum of labelled N,2-dicarbobenzyloxy-d-cycloserine derived from [¹⁵N]-hydroxyurea showed that hydroxyurea was the source of the heterocyclic nitrogen in the biosynthesis of d-cycloserine.     

Backbone and sidechain 1H, 15N and 13C assignments of the human G-actin binding protein profilin IIa

The resonance assignment of the human profilin IIa have been determined, based on triple-resonance experiments using uniformly [¹³C,¹⁵N]-labeled protein. These assignments facilitate further studies of interactions between profilin IIa and its poly-l-proline rich ligands.     

1H, 13C and 15N resonances of the AlgE62 subunit from Azotobacter vinelandii mannuronan C5-epimerase

The 17.7 kDa R2 module from Azotobacter vinelandii mannronan C5-epimerase AlgE6 has been isotopically labeled (¹³C,¹⁵N) and recombinantly expressed. Here we report the ¹H, ¹³C, ¹⁵N resonance assignment of AlgE6R2.     

Rapid corepressor exchange from the trp-repressor/operator complex: An NMR study of [ul-13C/15N]-l-tryptophan

Summary [ul-¹³C/¹⁵N]-l-tryptophan was prepared biosynthetically and its dynamic properties and intermolecular interaction with a complex of Escherichia coli trp-repressor and a 20 base-pair operator DNA were studied by heteronuclear isotope-edited NMR experiments. The resonances of the free and bound corepressor (l-Trp) were unambiguously identified from gradient-enhanced ¹⁵N–¹H HSQC, ¹³C–¹H HSQC, ¹³C-and ¹⁵N-edited 2D NOESY spectra. The exchange off-rate of the corepressor between the bound and free states was determined to be 3.4±0.52 s^–1 at 45°C, almost three orders of magnitude faster than the dissociation of the protein-DNA complex. Examination of the experimental NOE buildup curves indicates that it may be desirable to use longer mixing times than would normally be used for a large molecule, in order to detect weak intermolecular NOEs in the presence of exchange. Intermolecular NOEs from bound corepressor to trp-repressor and DNA were analyzed with respect to the mechanism of ligand exchange. This analysis suggests that, in order for the ligand to diffuse out of the complex, there must be significant movement or breathing of the protein and/or DNA.Abbreviations NOESY nuclear Overhauser enhancement spectroscopy - HSQC heteronuclear single-quantum coherence - PFG pulsed field gradient - l-Trp l-tryptophan     

1H, 13C, and 15N NMR assignments of the actinoporin Sticholysin I

Sticholysin I is an actinoporin, a pore forming toxin, of 176 aminoacids produced by the sea anemone Stichodactyla heliantus. Isotopically labelled ¹³C/¹⁵N recombinant protein was produced in E. coli. Here we report the complete NMR ¹⁵N, ¹³C and ¹H chemical shifts assignments of Stn I at pH 4.0 and 25°C (BMRB No. 15927).     

NMR assignments of 1H, 13C and 15N resonances of the C-terminal subunit from Azotobacter vinelandii mannuronan C5-epimerase 6 (AlgE6R3)

The 19.9 kDa C-terminal module (R3) from Azotobacter vinelandii mannronan C5-epimerase AlgE6 has been ¹³C, ¹⁵N isotopically labelled and recombinantly expressed. We report here the ¹H, ¹³C, ¹⁵N resonance assignment of AlgE6R3.     

1H, 15N and 13C resonance assignments,secondary structure,and the conformation of substrate in the binary folate complex of Escherichia coli dihydrofolate reductase

Summary By using fully ¹⁵N- and ¹⁵N/¹³C-labeled Escherichia coli dihydrofolate reductase, the sequence-specific ¹H and ¹⁵N NMR assignments were achieved for 95% of the backbone resonances and for 90% of the ¹³C resonances in the binary folate complex. These assignments were made through a variety of three-dimensional proton-detected ¹⁵N and ¹³C experiments. A smaller but significant subset of side-chain ¹H and ¹³C assignments were also determined. In this complex, only one ¹⁵N or ¹³C resonance was detected per ¹⁵N or ¹³C protein nucleus, which indicated a single conformation. Proton-detected ¹³C experiments were also performed with unlabeled DHFR, complexed with ¹³C-7/¹³C-9 folate to probe for multiple conformations of the substrate in its binary complex. As was found for the protein resonances, only a single bound resonance corresponding to a productive conformation could be detected for C-7. These results are consistent with an earlier report based on ¹H NMR data [Falzone, C.J. et al. (1990) Biochemistry, 29, 9667–9677] and suggest that the E. coli enzyme is not involved in any catalytically unproductive binding modes in the binary complex. This feature of the E. coli enzyme seems to be unique among the bacterial forms of DHFR that have been studied to date.     

Stable‐isotope comparisons between embryos and mothers of a placentatrophic shark species

Stable nitrogen (δ¹⁵N) and carbon (δ¹³C) isotopes of Atlantic sharpnose shark Rhizoprionodon terraenovae embryos and mothers were analysed. Embryos were generally enriched in ¹⁵N in all studied tissue relative to their mothers' tissue, with mean differences between mother and embryo δ¹⁵N (i.e. Δδ¹⁵N) being 1·4‰ for muscle, 1·7‰ for liver and 1·1‰ for cartilage. Embryo muscle and liver were enriched in ¹³C (both Δδ¹³C means = 1·5‰) and embryo cartilage was depleted (Δδ¹³C mean = ?1·01‰) relative to corresponding maternal tissues. While differences in δ¹⁵N and δ¹³C between mothers and their embryos were significant, muscle δ¹⁵N values indicated embryos to be within the range of values expected if they occupied a similar trophic position as their respective mothers. Positive linear relationships existed between embryo total length (L_T) and Δδ¹⁵N for muscle and liver and embryo L_T and Δδ¹³C for muscle, with those associations possibly resulting from physiological differences between smaller and larger embryos or differences associated with the known embryonic nutrition shift (yolk feeding to placental feeding) that occurs during the gestation of this placentatrophic species. Together these results suggest that at birth, the δ¹⁵N and δ¹³C values of R. terraenovae are likely higher than somewhat older neonates whose postpartum feeding habits have restructured their isotope profiles to reflect their postembryonic diet.     

Sequence-specific 1H, 15N and 13C resonance assignments of Art v 1: a proline-rich allergen of Artemisia vulgaris pollen

Art v 1 is the major allergen of Artemisia vulgaris. The IgE raised against Art v 1 not only can cross-react with other proteins from the Asteraceae family members but also with components of various forms of food. Art v 1 is an important target for immunotherapy strategies, including vaccination with hypoallergenic derivatives or chimeras. We report the ¹H, ¹³C, and ¹⁵N resonance assignments of the recombinant Art v 1 and identification of secondary structures based on ¹³C chemical shifts.     

Holocene palaeoenvironment in a former coastal lagoon of the arid south eastern Iberian Peninsula: salinization effects on δ<Superscript>15</Superscript>N

The palaeoenvironment of a former coastal lagoon in the south eastern Iberian Peninsula (San Rafael, Almeria, Spain) were inferred from one core analyzed for particulate organic matter content (POM) together with its C/N, δ¹³C, δ¹⁵N to depict the biogeochemical record from the Late Glacial to the Holocene. The results, complemented by previously reported pollen assemblages, indicate the appearance of a freshwater lagoon at 7300 b.p. (uncalibrated ¹⁴C age), its salinization at 6200 b.p. and its disappearance at 4400 b.p. The period of existence of the lagoon coincided with a period of wetter conditions as inferred from terrestrial vegetation. The lagoon’s salinization was not related to a decrease in precipitation but to a stronger maritime influence since there were no parallel changes in terrestrial vegetation. Salinization caused an increase in δ¹³C, associated with a higher relative presence of C₄ plants, and an increase in δ¹⁵N, due to a decrease in plant N demand. The late period of the lagoon, from about 5100 to 4400 b.p., shows a progressive drying and salinization not detected in isotopes but reflected in a decrease in POM, and in the pollen records. Increases in δ¹⁵N were related to increases in salinity within the lagoon, and are indicative of a more open N cycle, because the absence of changes in terrestrial vegetation rules out changes in the catchment area as the cause for changes in δ¹⁵N.     

An investigation of d-{1-13C} xylose metabolism in Pichia stipitis under aerobic and anaerobic conditions

Summary The uptake of d-{1-¹³C} xylose, the accumulation of intermediates and the distribution of the label in ethanol in Pichia stipitis under aerobic and anaerobic conditions were investigated by nuclear magnetic resonance spectroscopy. The rate-limiting step of d-xylose metabolism under aerobic conditions appeared to be uptake, whereas under anaerobic conditions it was the conversion of xylitol to xylulose. The yeast showed no preference to either the alpha-or beta-forms of d-xylose. Under anaerobic conditions only {2-¹³C{ ethanol was detected and this suggests that NADH but not NADPH was used as cofactor in the conversion of xylose to xylitol. d-Xylose is most likely metabolised by the pentose phosphate pathway in this yeast.     

Conformational studies of diastereoisomeric cyclo(alanyl-phenylalanyl) with the coupling constants 1H–1H, 15N–1H, 13C–1H,and 13C–15N

The cyclodipeptides cyclo(L -alanyl-L -phenylalanyl) and cyclo(D -alanyl-L -phenylalanyl) were synthesized with various atoms substituted by the isotopes ¹⁵N and ¹³C. Thus, the coupling constants ¹⁵N–¹H, ¹³C–¹H, and ¹³C–¹⁵N could be obtained, in addition to the commonly used ¹H–¹H constants. The applicability of these coupling constants for obtaining conformational information on side chains and substituted 2,5-piperazinedione rings is discussed.     

Assignment of 1H, 13C, and 15N resonances of the RNA binding protein Snu13p from Saccharomyces cerevisiae

Snu13p is a highly conserved RNA binding protein from Saccharomyces cerevisiae required for both eukaryotic pre-mRNA splicing and pre-rRNA processing. The ¹H, ¹³C, and ¹⁵N assignments were determined from multidimensional, multinuclear NMR experiments conducted at 25°C.     

NMR assignment of the Rhodobacter sphaeroides fasciclin-1 domain protein (Fdp)

We report the almost complete assignment of ¹H, ¹³C and ¹⁵N nuclei in the 137-residue his-tagged fasciclin domain protein (Fdp) from Rhodobacter sphaeroides. Fdp is homologous to fasciclin I domains, including Drosophila FAS1 and M. tuberculosis MPB70 and plays a role in cell adhesion.     

1H, 15N, 13C and 13CO resonance assignments and secondary structure of villin 14T,a domain conserved among actin-severing proteins

Summary Sequence-specific assignments have been made for the ¹H, ¹⁵N, ¹³C and ¹³CO resonances of 14T, the 126-residue amino-terminal domain of the actin-severing protein villin. Villin is a member of a family of proteins that regulate cytoskeletal actin by severing, capping and nucleating actin filaments. Actin binding is dependent on calcium and disrupted by phosphatidyl inositol 4,5-bisphosphate. Actin-severing proteins are built from three or six repeats of a conserved domain, represented by 14T. Expression in Escherichia coli facilitated incorporation of ¹⁵N and ¹³C isotopes and application of triple-resonance, backbone-directed strategies for the sequential assignments. Elements of regular secondary structure have been identified by characteristic patterns of NOE cross peaks and values of vicinal ³J_H n _H coupling constants. Amide protons that exchange slowly (rates less than 1.0×10^-4 per min) are concentrated in the central -sheet and the second and third -helices, suggesting that these elements of secondary structure form very stable hydrogen bonds. Assignments for the amide nitrogens and protons have been examined as a function of pH and calcium concentration. Based on the conservation of chemical shifts in the core of the domain, villin 14T maintains the same overall fold in the pH range from 4.15 to 6.91 and the calcium range from 0 to 50 mM. The calcium data indicate the presence of two calcium-binding sites and suggest their locations.     

D-Aminoacylase from a novel producer: Stenotrophomonas maltophilia ITV-0595

A novel bacterial strain producing D-aminoacylase was isolated from organic waste and identified as Stenotrophomonas maltophilia ITV-0595. The isolation was performed using N-acetyl-D-phenylglycine (NAcDPG) as the sole source of C and N. The optimum pH for enzyme expression was 8 at 37°C. Using N-Ac-DPG concentrations from 0.5 up to 3% w/v, it was observed that at the 1% level, the microorganism showed acceptable responses in both enzyme activities and cell growth. From the different tested compounds N-acetyl-D-methionine (1%) was the best enzyme inducer (Sp. act. = 4.14 U mg⁻¹ protein, Vol. act. = 0.17 U ml⁻¹) and the only one that increased cell growth. Received 13 June 1997/ Accepted in revised form 29 October 1998