Functional implications of the beta-helical protein fold: differences in chemical and thermal stabilities of Erwinia chrysanthemi EC16 pectate lyases B, C, and E

Biological Function(s) and Application (s) of Pectin and Pectin Degrading Enzymes

Pectin is an integral part of plant cell wall and since centuries pectin extracted from plants is widely used in food and fruit juice processing. Moreover, in last half century, the applications have also invaded into many bio-processing applications such as pharmaceutical, bioenergy, textile, paper and tea processing. In these growing industries, the use of pectinases has grown with a significant amount i.e. approximately 10 % of total global enzyme market comes from pectinases. Herein comprehensive analyses of information related to structure and function of pectin in plant cell wall as well as structural classes of pectins have been discussed. The major function of pectin is in cementing the cellulose and hemicelluloses network, cell-cell adhesion and plant defence. Keeping the wide use of pectin in food industry and growing need of environment friendly technology for pectin extraction has accelerated the demand of pectin degrading enzymes (PDEs). PDEs are from three enzyme classes: carbohydrate esterases from CE8 and CE12 family, glycoside hydrolases from GH28 family and lyases from PL1, 2, 3, 9 and 10. We have reviewed the literature related to abundance and structure-function of these abovementioned enzymes from bacteria. From the current available literature, we found very limited information is present about thermostable PDEs. Hence, in future it could be a topic of study to gain the insight about structure-function of enzymes together with the expanded role of thermostable enzymes in development of bioprocesses based on these enzymes.

The contribution of ionic interactions to the conformational stability and function of polygalacturonase from A. niger

Aspergillus niger produces multiple forms of polygalacturonases with molecular masses ranging from 30 to 60 kDa. The high molecular weight polygalacturonase (61+/-2 kDa) from A. niger possesses a pH optimum of 4.3 and a pI of 3.9. The enzyme exhibited high sensitivity, both in terms of activity and structure, in the pH range of 4.3-7.0. The enzyme was irreversibly inactivated at pH 7.0. The enzyme is predominantly rich in parallel beta structure. There is unfolding of the enzyme molecule between 4.3 and 7.0 resulting in irreversible loss of secondary and tertiary structure with the exposure of hydrophobic surfaces. ANS binding measurements, intrinsic fluorescence and acrylamide quenching measurements have confirmed the unfolding and exposure of hydrophobic surfaces. The midpoint of pH transition for both activity and secondary structure is 6.2+/-0.1. The pH-induced changes of polygalacturonase confirm the role of histidine residues in structure and activity of the enzyme. The irreversible nature of inactivation is due to the unfolding induced exposure of hydrophobic surfaces leading to association/aggregation of the molecule. Size exclusion chromatography measurements have established the association of enzyme at higher pH. Urea induced unfolding measurements at pH 4.3 and 7.0 have confirmed the loss in stability as we approach neutral pH.

Differences in the solution structures of the parallel beta-helical pectate lyases as determined by limited proteolysis

The pectate lyase family of proteins has been shown to fold into a novel domain motif, the right-handed parallel beta-helix. As a means of gaining insight to the solution structure of the pectate lyases, the enzymes were subjected to limited proteolytic digestion by the endoproteases AspN, GluC and trypsin. The effects of proteolytic cleavage on enzymatic activity were determined, and the early products of proteolysis were identified by capillary electrophoresis, MALDI-TOF mass spectrometry and HPLC. A single peptide bond between Lys158 and Asp159 in pectate lyase B (PLb) was cleaved by both AspN and trypsin, with no detectable hydrolysis of PLb by GluC. Pectate lyase E (PLe) was hydrolyzed by trypsin between Lys164 and Asp165, a bond on an analogous loop structure found to be susceptible to proteolytic attack in PLb. AspN and GluC preferentially hydrolyzed peptide bonds (at Asp127 and Glu124, respectively) on another loop extending from the central beta-helical core of PLe. A single beta-strand of the central cylinder of the pectate lyase C (PLc) molecule was susceptible to all three proteases used. These data demonstrate that the most susceptible peptide bonds to proteolytic scission within the native enzymes lie on or near one of the three parallel beta-sheets that compose the core domain motif Despite the proximity of the proteolytic cleavages to the catalytic sites of the enzymes, significant retention of lyase activity was observed after partial proteolysis, indicating preservation of functional tertiary structure in the proteolytic products.

Cloning and characterization of an intracellular isoamylase gene from Pectobacterium chrysanthemi PY35

The gene encoding an intracellular isoamylase from the Pectobacterium chrysanthemi PY35 was cloned in Escherichia coli DH5alpha and sequenced. The isoamylase gene (amyX) had an open reading frame of 1974 bp encoding 657 amino acid residues with a calculated molecular weight of 74,151 Da. The molecular weight of the enzyme was also estimated to be 74 kDa by activity staining of a SDS-PA gel. Isoamylase from P. chrysanthemi PY35 had 59% pairwise amino acid identity with glycogen debranching enzyme from E. coli and contained the four regions conserved among all amylolytic enzymes. The isoamylase was optimally active at pH 7 and 40 degrees C. AmyX hydrolyzed alpha-1,6-glycosidic linkages of amylopectin, while did not hydrolyze alpha-1,4-glycosidic linkages of amylose.

Functional characterization of a novel xylanase from a corn strain of Erwinia chrysanthemi

A beta-1,4-xylan hydrolase (xylanase A) produced by Erwinia chrysanthemi D1 isolated from corn was analyzed with respect to its secondary structure and enzymatic function. The pH and temperature optima for the enzyme were found to be pH 6.0 and 35 degrees C, with a secondary structure under those conditions that consists of approximately 10 to 15% alpha-helices. The enzyme was still active at temperatures higher than 40 degrees C and at pHs of up to 9.0. The loss of enzymatic activity at temperatures above 45 degrees C was accompanied by significant loss of secondary structure. The enzyme was most active on xylan substrates with low ratios of xylose to 4-O-methyl-D-glucuronic acid and appears to require two 4-O-methyl-D-glucuronic acid residues for substrate recognition and/or cleavage of a beta-1,4-xylosidic bond. The enzyme hydrolyzed sweetgum xylan, generating products with a 4-O-methyl-glucuronic acid-substituted xylose residue one position from the nonreducing terminus of the oligoxyloside product. No internal cleavages of the xylan backbone between substituted xylose residues were observed, giving the enzyme a unique mode of action in the hydrolysis compared to all other xylanases that have been described. Given the size of the oligoxyloside products generated by the enzyme during depolymerization of xylan substrates, the function of the enzyme may be to render substrate available for other depolymerizing enzymes instead of producing oligoxylosides for cellular metabolism and may serve to produce elicitors during the initiation of the infectious process.