Crystal structure of beta-amylase from Bacillus cereus var. mycoides at 2.2 A resolution.
(1/94)
The crystal structure of beta-amylase from Bacillus cereus var. mycoides was determined by the multiple isomorphous replacement method. The structure was refined to a final R-factor of 0.186 for 102,807 independent reflections with F/sigma(F) > or = 2.0 at 2.2 A resolution with root-mean-square deviations from ideality in bond lengths, and bond angles of 0.014 A and 3.00 degrees, respectively. The asymmetric unit comprises four molecules exhibiting a dimer-of-dimers structure. The enzyme, however, acts as a monomer in solution. The beta-amylase molecule folds into three domains; the first one is the N-terminal catalytic domain with a (beta/alpha)8 barrel, the second one is the excursion part from the first one, and the third one is the C-terminal domain with two almost anti-parallel beta-sheets. The active site cleft, including two putative catalytic residues (Glu172 and Glu367), is located on the carboxyl side of the central beta-sheet in the (beta/alpha)8 barrel, as in most amylases. The active site structure of the enzyme resembles that of soybean beta-amylase with slight differences. One calcium ion is bound per molecule far from the active site. The C-terminal domain has a fold similar to the raw starch binding domains of cyclodextrin glycosyltransferase and glucoamylase. (+info)
The evolution of starch-binding domain.
(2/94)
Amylolytic enzymes belonging to three distinct families of glycosidases (13, 14, 15) contain the starch-binding domain (SBD) positioned almost exclusively at the C-terminus. Detailed analysis of all available SBD sequences from 43 different amylases revealed its independent evolutionary behaviour with regard to the catalytic domains. In the evolutionary tree based on sequence alignment of the SBDs, taxonomy is respected so that fungi and actinomycetes form their own separate parts surrounded by bacteria that are also clustered according to taxonomy. The only known N-terminal SBD from Rhizopus oryzae glucoamylase is on the longest branch separated from all C-terminal SBDs. The 3-dimensional (3-D) structures of fungal glucoamylase and bacterial CGTase SBDs are compared and used to discuss the interesting SBD evolution. (+info)
Prediction of protein cleavage sites by the barley cysteine endoproteases EP-A and EP-B based on the kinetics of synthetic peptide hydrolysis.
(3/94)
Hordeins, the natural substrates of barley (Hordeum vulgare) cysteine endoproteases (EPs), were isolated as protein bodies and degraded by purified EP-B from green barley malt. Cleavage specificity was determined by synthesizing internally quenched, fluorogenic tetrapeptide substrates of the general formula 2-aminobenzoyl-P(2)-P(1)-P(1)'-P(2)' 1-tyrosine(NO(2))-aspartate. The barley EPs preferred neutral amino acids with large aliphatic and nonpolar (leucine, valine, isoleucine, and methionine) or aromatic (phenylalanine, tyrosine, and tryptophan) side chains at P(2), and showed less specificity at P(1), although asparagine, aspartate, valine, and isoleucine were particularly unfavorable. Peptides with proline at P(1) or P(1)' were extremely poor substrates. Cleavage sites with EP-A and EP-B preferred substrate sequences are found in hordeins, their natural substrates. The substrate specificity of EP-B with synthetic peptides was used successfully to predict the cleavage sites in the C-terminal extension of barley beta-amylase. When all of the primary cleavage sites in C hordein, which occur mainly in the N- and C-terminal domains, were removed by site-directed mutagenesis, the resulting protein was degraded 112 times more slowly than wild-type C hordein. We suggest that removal of the C hordein terminal domains is necessary for unfolding of the beta-reverse turn helix of the central repeat domain, which then becomes more susceptible to proteolytic attack by EP-B. (+info)
Water stress enhances beta-amylase activity in cucumber cotyledons.
(4/94)
Cotyledons detached from 4-d-old cucumber (Cucumis sativus L.) seedlings were subjected to water stress (air-drying or PEG-treatment) to examine the effects of the stress on carbohydrate metabolism. Amylolytic activity in the cotyledon was increased about 6-fold by water stress within 1 d. The substrate specificity and the action pattern indicated that beta-amylase is responsible for the activity. Activities of azocaseinase, malate dehydrogenase and triose-phosphate isomerase were not affected by water stress, indicating that the effect of the stress on beta-amylase is rather specific. Cycloheximide-treatment strongly reduced the enhancement of beta-amylase activity. The hypocotyl of cucumber seedlings also exhibited an increase in the enzyme activity when subjected to water stress. The major free sugars in cucumber cotyledons were glucose, fructose, maltose, and sucrose; sucrose being the most abundant. Sucrose content in excised, unstressed cotyledons increased markedly during the incubation. Changes in other free sugars were small compared with that of sucrose. Starch also accumulated in unstressed cotyledons. In stressed cotyledons more sucrose and less starch accumulated than in unstressed ones. Such results were discussed in relation to the enhancement of beta-amylase activity. (+info)
Polymorphism in rice amylases at an early stage of seed germination.
(5/94)
A polymorphism in rice amylases at an early stage of seed germination is analyzed by zymogram. In non-glutinous cultivars of rice, alpha-amylase isozymes are mainly confirmed in germinating seeds. However, in glutinous cultivars, beta-amylase isozymes, which are not confirmed in nonglutinous cultivars, make up the major part of the total amylase activity and the expression of alpha-amylases are repressed. (+info)
Molecular mimicry of substrate oxygen atoms by water molecules in the beta-amylase active site.
(6/94)
Soybean beta-amylase (EC 3.2.1.2) has been crystallized both free and complexed with a variety of ligands. Four water molecules in the free-enzyme catalytic cleft form a multihydrogen-bond network with eight strategic residues involved in enzyme-ligand hydrogen bonds. We show here that the positions of these four water molecules are coincident with the positions of four potential oxygen atoms of the ligands within the complex. Some of these waters are displaced from the active site when the ligands bind to the enzyme. How many are displaced depends on the shape of the ligand. This means that when one of the four positions is not occupied by a ligand oxygen atom, the corresponding water remains. We studied the functional/structural role of these four waters and conclude that their presence means that the conformation of the eight side chains is fixed in all situations (free or complexed enzyme) and preserved from unwanted or forbidden conformational changes that could hamper the catalytic mechanism. The water structure at the active pocket of beta-amylase is therefore essential for providing the ligand recognition process with plasticity. It does not affect the protein active-site geometry and preserves the overall hydrogen-bonding network, irrespective of which ligand is bound to the enzyme. We also investigated whether other enzymes showed a similar role for water. Finally, we discuss the potential use of these results for predicting whether water molecules can mimic ligand atoms in the active center. (+info)
Activities of starch hydrolytic enzymes and sucrose-phosphate synthase in the stems of rice subjected to water stress during grain filling.
(7/94)
To understand the effect of water stress on the remobilization of prestored carbon reserves, the changes in the activities of starch hydrolytic enzymes and sucrose-phosphate synthase (SPS) in the stems of rice (Oryza sativa L.) during grain filling were investigated. Two rice cultivars, showing high lodging-resistance and slow remobilization, were grown in the field and subjected to well-watered (WW, psi(soil)=0) and water-stressed (WS, psi(soil)=-0.05 MPa) treatments 9 d after anthesis (DAA) till maturity. Leaf water potentials of both cultivars markedly decreased during the day as a result of WS treatment, but completely recovered by early morning. WS treatment accelerated the reduction of starch in the stems, promoted the reallocation of prefixed (14)C from the stems to grains, shortened the grain filling period, and increased the grain filling rate. More soluble sugars including sucrose were accumulated in the stems under WS than under WW treatments. Both alpha- and beta-amylase activities were enhanced by the WS, with the former enhanced more than the latter, and were significantly correlated with the concentrations of soluble sugars in the stems. The other two possible starch-breaking enzymes, alpha-glucosidase and starch phosphorylase, showed no significant differences in the activities between the WW and WS treatments. Water stress also increased the SPS activity that is responsible for sucrose production. Both V(limit) and V(max), the activities of the enzyme at limiting and saturating substrate concentrations, were enhanced and the activation state (V(limit)/V(max)) was also increased as a result of the more significant enhancement of V(limit). The enhanced SPS activity was closely correlated with an increase of sucrose accumulation in the stems. The results suggest that the fast hydrolysis of starch and increased carbon remobilization were attributed to the enhanced alpha-amylase activity and the high activation state of SPS when the rice was subjected to water stress. (+info)
Purification, characterization, immunolocalization and structural analysis of the abundant cytoplasmic beta-amylase from Calystegia sepium (hedge bindweed) rhizomes.
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An abundant catalytically active beta-amylase (EC 3.2.1.2) was isolated from resting rhizomes of hedge bindweed (Calystegia sepium). Biochemical analysis of the purified protein, molecular modeling, and cloning of the corresponding gene indicated that this enzyme resembles previously characterized plant beta-amylases with regard to its amino-acid sequence, molecular structure and catalytic activities. Immunolocalization demonstrated that the beta-amylase is exclusively located in the cytoplasm. It is suggested that the hedge bindweed rhizome beta-amylase is a cytoplasmic vegetative storage protein. (+info)