Preliminary structure analysis of canavalin from jack bean.

The plant seed protein canavalin has been crystallized alter trypsinization by using vapor diffusion to effect isoelectric precipitation. The space groups and cell dimensions are R3 with $\text{a}\text{?}\text{= 81.3}\text{A}\text{?}\text{, γ = 111 °}$ and having extremely high R32 pseudo symmetry, P6³ with $\text{a}\text{?}\text{= 126}\text{A}\text{?}\text{and}\text{c}\text{?}\text{= 51}\text{A}\text{?}\text{, C222}{}_1\text{,}\text{with}\text{a}\text{?}\text{= 136}\text{A}\text{?}\text{,}\text{b}\text{?}\text{= 152}\text{A}\text{?}\text{, and}\text{c}\text{?}\text{= 131}\text{A}\text{?}$. X-ray data combined with electron microscopy suggests the molecule to be composed of six identical subunits. each of 18,500 daltons, arranged in a staggered hexameric ring and related by perfect or near perfect 3 2 point group symmetry. The outside diameter of the molecule is approximately 65 Å and there appears to be a large solvent channel coincident with the molecular triad.     

The three-dimensional structure of canavalin from jack bean (Canavalia ensiformis).

The three-dimensional structure of the vicilin storage protein canavalin, from Canavalia ensiformis, has been determined in a hexagonal crystal by x-ray diffraction methods. The model has been refined at 2.6 A resolution to an R factor of 0.197 with acceptable geometry. Because of proteolysis, 58 of 419 amino acids of the canavalin polypeptide are not visible in the electron density map. The canavalin subunit is composed of two extremely similar structural domains that reflect the tandem duplication observed in the cDNA and in the amino acid sequence. Each domain consists of two elements, a compact, eight-stranded beta-barrel having the "Swiss roll" topology and an extended loop containing several short alpha-helices. The root mean square deviation between 84 pairs of corresponding C alpha atoms making up the strands of the two beta-barrels in a subunit is 0.78 A, and for 112 pairs of structurally equivalent C alpha atoms of the two domains the deviation is 1.37 A. The interface between domains arises from the apposition of broad hydrophobic surfaces formed by side chains originating from one side of the beta-barrels, supplemented by at least four salt bridges. The interfaces between subunits in the trimer are supplied by the extended loop elements. These interfaces are also composed primarily of hydrophobic residues supplemented by six salt bridges. The canavalin subunits have dimensions about 40 x 40 x 86 A, and the oligomer is a disk-shaped molecule about 88 A in diameter with a thickness of about 40 A. The distribution of domains lends a high degree of pseudo-32-point group symmetry to the molecule. There is a large channel of 18 A diameter, lined predominantly by hydrophilic and charged amino acids, running through the molecule along the 3-fold axis. The majority of residues conserved between domains and among vicilins occur at the interface between subunits but appear otherwise arbitrarily distributed within the subunit, although predominantly on its exterior.     

Isolation and characterization of jack bean beta-galactosidase.

A simple procedure has been devised to isolate beta-galactosidase from jack bean meal. The final preparation gives one major protein banc in disc gel electrophoresis. The substrate specificity of this enzyme toward some natural oligosaccharides, glycoproteins, and sphingoglycolipids has been examined in detail. Among three isomers of N-acetyllactosamine, Galbeta1leads to4GlcNAc; while Galbeta1leads to3GlcNAc was hydrolyzed very slowly. This property can be used to distinguish the galactose linkage in asialo-GM1 (Galbeta1leads to3GalNAcbeta1leads to4Galbeta1leads to4Glcleads toCer) and that in lacto-N-neotetraosylceramide (Galbeta1leads to4GlcNAcbeta1leads to 3Galbeta1leads to4Glcleads toCer). For hydrolyzing glycolipids, the effect of sodium taurodeoxycholate and sodium taurochenodeoxycholate on the rate of hydrolysis was carefully examined. This enzyme hydrolyzes lactosylceramide and asialo-GM1 faster than GM1. These results suggest that in addition to the type and linkage of the penultimate sugar unit, the sugar unit at the distal position of the saccharide chain also affects the hydrolysis rate. It also readily liberates 80% D-galactosyl units from asialo alpha1-acid glycoprotein. Escherichia coli beta-galactosidase on the other hand cannot hydrolyze asialo-alpha1-acid glycoprotein, lactosylceramide, GM1, asialo-GM1, and lacto-N-neotetraosylceramide. The molecular weight of this enzyme is about 75,000 and the isoelectric point is pH 8.0. With p-nitrophenyl beta-D-galactopyranoside as substrate, optimal activity occurs at pH 2.8 with glycine-HCl buffer and at pH 3.5 with citrate-phosphate buffer. With lactose as substrate, the pH optimum in these two buffers are 2.8 and 4.0, respectively. Km values for p-nitrophenyl beta-D-galactopyranoside, o-nitrophenyl beta-D-galactopyranoside and lactose are 0.51 mM, 0.63 mM, and 12.23 mM, respectively. Many inhibitors for this enzyme including inorganic ions, monosaccharides, and glycosides are investigated. In contrast to E. coli beta-galactosidase, jack bean beta-galactosidase is not inhibited by p-aminophenyl thio-beta-D-galactopyranoside.     

Biochemical characterization of the major sorghum grain peroxidase

The major cationic peroxidase in sorghum grain (SPC4) , which is ubiquitously present in all sorghum varieties was purified to apparent homogeneity, and found to be a highly basic protein (pI approximately 11). MS analysis showed that SPC4 consists of two glycoforms with molecular masses of 34,227 and 35,629 Da and it contains a type-b heme. Chemical deglycosylation allowed to estimate sugar contents of 3.0% and 6.7% (w/w) in glycoform I and II, respectively, and a mass of the apoprotein of 33,246 Da. High performance anion exchange chromatography allowed to determine the carbohydrate constituents of the polysaccharide chains. The N-terminal sequence of SPC4 is not blocked by pyroglutamate. MS analysis showed that six peptides, including the N-terminal sequence of SPC4 matched with the predicted tryptic peptides of gene indice TC102191 of sorghum chromosome 1, indicating that TC102191 codes for the N-terminal part of the sequence of SPC4, including a signal peptide of 31 amino acids. The N-terminal fragment of SPC4 (213 amino acids) has a high sequence identity with barley BP1 (85%), rice Prx23 (90%), wheat WSP1 (82%) and maize peroxidase (58%), indicative for a common ancestor. SPC4 is activated by calcium ions. Ca2+ binding increased the protein conformational stability by raising the melting temperature (Tm) from 67 to 82 degrees C. SPC4 catalyzed the oxidation of a wide range of aromatic substrates, being catalytically more efficient with hydroxycinnamates than with tyrosine derivatives. In spite of the conserved active sites, SPC4 differs from BP1 in being active with aromatic compounds above pH 5.     

Synthesis of the major storage protein,hordein, in barley

A liquid culture system for culturing detached spikes of barley (Hordeum vulgare L.) at different nutritional levels was established. The synthesis of hordein polypeptides was studied by pulse-labeling with [¹⁴C]sucrose at different stages of development and nitrogen (N) nutrition. All polypeptides were synthesised at 10 d after anthesis and hercafter an increase was observed for all polypeptides. A fivefold increase in total hordein was observed within the N range tested. Hordein-1 increased considerably more than hordein-2 with increased N nutrition, and hordein-1 synthesis exceeded that of hordein-2 at the highest N level 20 and 25 d after anthesis. Hordein-1 thus appears to act as the main N sink at high N levels. The synthesis of the major groups of hordein-2 polypeptides responded differently to increasing N in that the slower-migrating polypeptides increased more with increasing N than the faster-migrating polypeptides.     

A 28-kilodalton pod storage protein of French bean plants. Purification, characterization, and primary structure.

When French bean (Phaseolus vulgaris) plants were depodded in the early stages of fruit development, relative levels of a specific protein with a relative molecular weight of 28,000 were enhanced in the young pods that formed later. The protein, designated pod storage protein (PSP), was purified from extracts of newly formed pods from plants that had been previously depodded four times at intervals of 2 weeks. Two-dimensional polyacrylamide gel electrophoresis showed the presence of three forms (designated A, B, and C) of PSP with identical electrophoretic mobilities but different charges. The molecular mass of native PSP was estimated by gel filtration to be 67 kD; therefore, the protein was most likely present as a dimer. The antisera raised against forms A and C were crossreactive with each other. Form B lacked the N-terminal alanine of forms A and C. An expression library from French bean pods was screened using the antiserum against form A, and a full-length cDNA clone was isolated. The cDNA insert included 765 bp potentially encoding a polypeptide with 255 amino acid residues (and a calculated molecular mass of 28,854 D). The amino acid sequence deduced from the PSP cDNA had 65 to 71% identity with soybean (Glycine max) vegetative storage protein sequences (P.E. Staswick [1988] Plant Physiol 87: 250-254; and Correction [1989] Plant Physiol 89: 717). Genomic Southern blot analysis suggested that PSP is derived from a single-copy gene.     

Inactivation of jack bean urease by allicin

Allicin--diallyl thiosulfinate--is the main biologically active component of freshly crushed garlic. Allicin was synthesized as described elsewhere and was tested for its inhibitory ability against jack bean urease in 20 mM phosphate buffer, pH 7.0 at 22 degrees C. The results indicate that allicin is an enzymatic inactivator. The loss of urease activity was irreversible, time- and concentration dependent and the kinetics of the inactivation was biphasic; each phase, obeyed pseudo-first-order kinetics. The rate constants for inactivation were measured for the fast and slow phases and for several concentrations of allicin. Thiol reagents, and competitive inhibitor (boric acid) protected the enzyme from loss of enzymatic activity. The studies demonstrate that urease inactivation results from the reaction between allicin and the SH-group, situated in the urease active site (Cys592).     

Evidence for phosphorylation of the major seed storage protein of the common bean and its phosphorylation-dependent degradation during germination

Phaseolin is the major seed storage protein of common bean, Phaseolus vulgaris L., accounting for up to 50 % of the total seed proteome. The regulatory mechanisms responsible for the synthesis, accumulation and degradation of phaseolin in the common bean seed are not yet sufficiently known. Here, we report on a systematic study in dormant and 4-day germinating bean seeds from cultivars Sanilac (S) and Tendergreen (T) to explore the presence and dynamics of phosphorylated phaseolin isoforms. High-resolution two-dimensional electrophoresis in combination with the phosphoprotein-specific Pro-Q Diamond phosphoprotein fluorescent stain and chemical dephosphorylation by hydrogen fluoride–pyridine enabled us to identify differentially phosphorylated phaseolin polypeptides in dormant and germinating seeds from cultivars S and T. Phosphorylated forms of the two subunits of type α and β that compose the phaseolin were identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and MALDI-TOF/TOF tandem MS. In addition, we found that the levels of phosphorylation of the phaseolin changed remarkably in the seed transition from dormancy to early germination stage. Temporal changes in the extent of phosphorylation in response to physiological and metabolic variations suggest that phosphorylated phaseolin isoforms have functional significance. In particular, this prospective study supports the hypothesis that mobilization of the phaseolin in germinating seeds occurs through the degradation of highly phosphorylated isoforms. Taken together, our results indicate that post-translational phaseolin modifications through phosphorylations need to be taken into consideration for a better understanding of the molecular mechanisms underlying its regulation.     

An EXAFS study of jack bean urease,a nickel metalloenzyme

EXAFS and XANES spectra have been recorded above the nickel K edge of urease and three model compounds. Preliminary results indicate that the local environment of the nickel ions in urease resemble most closely that of the nickel ions in the model compound [Ni(L)₂(L)₁] (ClO₄)₁, where L is 1-n-propyl-2-α-hydroxybenzyl benzimidazole and L is the deprotonated form.     

Purification of the major UsnRNPs from broad bean nuclear extracts and characterization of their protein constituents.

Small nuclear ribonucleoprotein particles containing the five major nucleoplasmic snRNAs U1, U2, U4, U5 and U6 as well as two smaller sized snRNAs were purified from broad bean nuclear extracts by anti-m3G, monoclonal antibody, immunoaffinity chromatography. We have so far defined 13 polypeptides of approximate mol. wts. of 11 kd, 11.5 kd, 12.5 kd, 16 kd, 17 kd, 17.5 kd, 18.5 kd, 25 kd (double band), 30 kd, 31 kd, 35 kd, 36 kd and 54 kd. Upon fractionation of the UsnRNPs by anion exchange chromatography, essentially pure U5 snRNPs were obtained, containing the 11 kd, 11.5 kd, 12.5 kd, 16 kd, 17 kd, 17.5 kd, 35 kd and 36 kd polypeptides. These may therefore represent the common snRNP polypeptides and which may also be present in the other snRNPs. By immunoblotting studies, using anti-Sm sera and mouse monoclonal antibodies we show that the 35 kd and 36 kd proteins are immunologically related to the mammalian common B/B' proteins. The broad bean 16 kd and 17 kd proteins appear to share structural elements with the mammalian D protein. The three proteins of mol. wts. 11 kd, 11.5 kd and 12.5 kd probably represent the broad bean polypeptides E, F, and G. Cross-reactivity of proteins of mol. wts of 30 kd and 31 kd with Anti-(U1/U2)RNP antibodies suggests that they may represent the broad bean A and B" polypeptides. The 54 kd protein and the 18.5 kd protein could be candidates for the U1 specific 70 k and C polypeptides. Our results demonstrate a strong similarity between the overall structure of broad bean and mammalian snRNPs.     

Albumin storage proteins in the protein bodies of castor bean

Of the total protein in the protein bodies of castor bean (Ricinus communis L.), approximately 40% is represented by a group of closely related albumins localized in the matrix of the organelle. This group of albumins has a sedimentation value of 2S and is resolved into several proteins of molecular weight around 12,000 daltons by sodium dodecyl sulfate-acrylamide gel electrophoresis. It has a high content of glutamate/glutamine and undergoes rapid degradation during the early stage of germination. In view of the abundance and ubiquitous occurrence of albumins in various seeds, we suggest that albumins, in addition to globulins, glutelins, and prolamines, are important storage proteins in seeds.     

Identification of canavalin as a proteolytically modified form of Jack bean α-d-mannosidase

The structure to 3.0 Å resolution of the protein canavalin from Jack beans has been determined by conventional X-ray crystallographic techniques. We present evidence that canavalin is a proteolytically modified form of the enzyme α-d-mannosidase. This is based on the facts that the purified precursor protein possesses substantial α-d-mannosidase activity; it comigrates on SDS-PAGE with Jack bean α-d-mannosidase prepared by other means; and its oligomer molecular weight and Zn²⁺ content are the same as those of Jack bean α-d-mannosidase.     

Inhibition of jack bean urease by organobismuth compounds

Inhibitory activity of organobismuth compounds, triarylbismuthanes 1 and their dihalides 2 and 3, was examined against jack bean urease. Besides triarylbismuth dichlorides 2, triarylbismuth difluorides 3 and bismuthanes 1 exhibited the activity. Of all these compounds, triphenylbismuth difluoride 3a and tris(4-fluorophenyl)bismuth dichloride 2b showed the highest activity. These results indicate that generation of the inhibitory effect is not always governed by the Lewis acidity at the bismuth center. Such a tendency of inhibition by the organobismuth compounds is in good accord with that observed in the antibacterial activity against Helicobacter pylori, suggesting that H. pylori-produced urease may be a therapeutic target by bismuth-based drugs.     

Irreversible inhibition of jack bean urease by pyrocatechol

Pyrocatechol was studied as an inhibitor of jack bean urease in 20 mM phosphate buffer, pH 7.0, 25 degrees C. The inhibition was monitored by an incubation procedure in the absence of substrate and reaction progress studies in the presence of substrate. It was found that pyrocatechol acted as a time- and concentration dependent irreversible inactivator of urease. The dependence of the residual activity of urease on the incubation time showed that the rate of inhibition increased with time until there was total loss of enzyme activity. The inactivation process followed a non-pseudo-first order reaction. The obtained reaction progress curves were found to be time-dependent. The plots showed that the rate of the enzyme reaction in the final stages reached zero. From protection experiments it appeared that thiol-compounds such as L-cysteine, 2-mercaptoethanol and dithiothreitol prevented urease from pyrocatechol inactivation as well as the substrate, urea, and the competitive inhibitor boric acid. These results proved that the urease active site was involved in the pyrocatechol inactivation.     

The degradation of canavanine by jack bean cotyledons

Summary Germinating jack bean cotyledons liberated ¹⁴CO₂ when fed ¹⁴C-guanidoxy-canavanine but did not accumulate any ¹⁴C-compounds other than the applied canavanine. This suggested that the canavanine was being degraded by the action of canavanase to canaline and urea, the urea then being converted to ammonia and carbon dioxide by the action of urease. Hydroxyurea and acetohydroxamic acid (both inhibitors of urease activity) strongly inhibited the liberation of ¹⁴CO₂ from ¹⁴C-guanidoxy-canavanine by the cotyledons but neither compound induced the accumulation of ¹⁴C-urea within the tissues. This inhibitory action of hydroxyurea on ¹⁴CO₂ output was thought to be due at least in part, to this inhibition of canavanase activity.