Shamkant Anant Patkar

Structure of a feruloyl esterase from Aspergillus niger

The crystallographic structure of feruloyl esterase from Aspergillus niger has been determined to a resolution of 1.5 A by molecular replacement. The protein has an alpha/beta-hydrolase structure with a Ser-His-Asp catalytic triad; the overall fold of the protein is very similar to that of the fungal lipases. The structure of the enzyme-product complex was determined to a resolution of 1.08 A and reveals dual conformations for the serine and histidine residues at the active site.

Purification, crystallization and preliminary X-ray crystallographic studies on acetolactate decarboxylase.

Acetolactate decarboxylase has the unique ability to decarboxylate both enantiomers of acetolactate to give a single enantiomer of the decarboxylation product, (R)-acetoin. A gene coding for alpha-acetolactate decarboxylase from Bacillus brevis (ATCC 11031) was cloned and overexpressed in B. subtilis. The enzyme was purified in two steps to homogeneity prior to crystallization. Three different diffraction-quality crystal forms were obtained by the hanging-drop vapour-diffusion method using a number of screening conditions. The best crystal form is suitable for structural studies and was grown from solutions containing 20% PEG 2000 MME, 10 mM cadmium chloride and 0.1 M Tris-HCl pH 7.0. They grew to a maximum dimension of approximately 0.4 mm and belong to the trigonal space group P3(1,2)21, with unit-cell parameters a = 47.0, c = 198.9 A. A complete data set was collected to 2 A from a single native crystal using synchrotron radiation.

A comparative study of activity and apparent inhibition of fungal β-glucosidases

β‐Glucosidases (BGs) from Aspergillus fumigates, Aspergillus niger, Aspergillus oryzae, Chaetomium globosum, Emericella nidulans, Magnaporthe grisea, Neurospora crassa, and Penicillium brasilianum were purified to homogeneity, and analyzed by isothermal titration calorimetry with respect to their hydrolytic activity and its sensitivity to glucose (product) using cellobiose as substrate. Global non‐linear regression of several reactions, with or without added glucose, to a product inhibition equation enabled the concurrent derivation of the kinetic parameters kcat, Km, and the apparent product inhibition constant appKi for each of the enzymes. A more simple fit is not advisable to use as the determined appKi are in the same range as their Km for some of the tested BGs and produced glucose would in these cases interfere. The highest value for kcat was determined for A. fumigatus (768 s−1) and the lowest was a factor 9 less. Km varied by a factor of 3 with the lowest value determined for C. globosum (0.95 mM). The measured appKi varied a factor of 15; the hydrolytic activity of N. crassa being the most resistant to glucose with an apparent product inhibition constant of 10.1 mM. Determination of appKi using cellobiose as substrate is important as it reflects to what extent the different BGs are hydrolytically active under industrial conditions where natural substrates are hydrolyzed and the final glucose concentrations are high. Biotechnol. Bioeng. 2010;107: 943–952.

Characterization of protein transacetylase from human placenta as a signaling molecule calreticulin using polyphenolic peracetates as the acetyl group donors

We have earlier shown that a unique membrane-bound enzyme mediates the transfer of acetyl group(s) from polyphenolic peracetates (PA) to functional proteins, which was termed acetoxy drug: protein transacetylase (TAase) because it acted upon several classes of PA. Here, we report the purification of TAase from human placentral microsomes to homogeneity with molecular mass of 60 kDa, exhibiting varying degrees of specificity to several classes of PA confirming the structure-activity relationship for the microsome-bound TAase. The TAase catalyzed protein acetylation by a model acetoxy drug, 7,8-diacetoxy-4-methyl coumarin (DAMC) was established by the demonstration of immunoreactivity of the acetylated target protein with anti-acetyl lysine antibody. TAase activity was severely inhibited in calcium-aggregated microsomes as well as when Ca2+ was added to purified TAase, suggesting that TAase could be a calcium binding protein. Furthermore, the N-terminal sequence analysis of purified TAase (EPAVYFKEQFLD) using Swiss Prot Database perfectly matched with calreticulin (CRT), a major microsomal calcium binding protein of the endoplasmic reticulum (ER). The identity of TAase with CRT was substantiated by the observation that the purified TAase avidly reacted with commercially available antibody raised against the C-terminus of human CRT (13 residues peptide, DEEDATGQAKDEL). Purified TAase also showed Ca2+ binding and acted as a substrate for phosphorylation catalyzed by protein kinase C (PKC), which are hallmark characteristics of CRT. Further, purified placental CRT as well as the commercially procured pure CRT yielded significant TAase catalytic activity and were also found effective in mediating the acetylation of the target protein NADPH cytochrome P-450 reductase by DAMC as detected by Western blot using anti-acetyl lysine antibody. These observations for the first time convincingly attribute the transacetylase function to CRT. Hence, this transacetylase function of CRT is designated calreticulin transacetylase (CRTAase). We envisage that CRTAase plays an important role in protein modification by way of acetylation independent of Acetyl CoA.

Novel function of calreticulin: Characterization of calreticulin as a transacetylase-mediating protein acetylator independent of acetyl CoA using polyphenolic acetates

Our earlier investigations culminated in the discovery of a unique membrane-bound enzyme in mammalian cells catalyzing the transfer of acetyl group from polyphenolic acetates (PAs) to certain functional proteins, resulting in the modulation of their activities. This enzyme was termed acetoxy drug:protein transacetylase (TAase) since it acted upon several classes of PAs. TAase was purified from rat liver microsomes to homogeneity and exhibited the molecular weight of 55 KDa. TAase-catalyzed protein acetylation by PAs was evidenced by the demonstration of immunoreactivity of the acetylated target protein such as nitric oxide synthase (NOS) with anti-acetyl lysine. The possible acetylation of human platelet NOS by PA as described above resulted in the enhancement of intracellular levels of nitric oxide (NO). PAs unlike the parent polyphenols were found to exhibit NO-related physiological effects. The N-terminal sequence was found to show 100 % homology with N-terminal sequence of mature calreticulin (CRT). The identity of TAase with CRT, an endoplasmic reticulum (ER) protein, was evidenced by the demonstration of the properties of CRT such as immunoreactivity with anti-calreticulin, binding to Ca2+ ions and being substrate for phosphorylation by protein kinase c (PKC), which are the hallmark characteristics of CRT. These observations for the first time convincingly attribute the transacetylase function to CRT, which possibly plays an important role in protein modification by way of carrying out acetylation of various enzymes through a biochemical mechanism independent of acetyl CoA.

Lipase action on a monoolein/sodium oleate aqueous cubic liquid crystalline phase - a NMR and X-ray diffraction study

The effect of adding Thermomyces (formerly Humicola) lanuginosa lipase (TLL) to a monoolein (MO)/sodium oleate (NaO) aqueous cubic liquid crystalline phase has been studied. H-1-NMR, C-13-NMR, H-1-PGSE (Pulsed-magnetic field Gradient Spin-Echo) self-diffusion measurements, and Small Angle X-ray Diffraction were used to follow the degradation of the cubic phase. The reaction sequence in terms of phase transitions follows the order bicontinuous cubic --> reverse hexagonal --> micellar cubic --> micellar phase and corresponds to the previously determined phase diagrams. These changes correlate with changes in the lipid composition observed by C-13-NMR and confirmed by HPLC analysis. The initial decrease of the diffusion coefficients of water and lipid can be related to the transformation of the bicontinuous cubic phase to a reverse hexagonal structure

Studies on ferulic acid esterase activity in fungal lipases and cutinases

In this study we have tested a number of lipases, lipase variants and cutinases for ferulic acid esterase activity, using ferulic acid ethyl ester as substrate. It was shown that Thermomyces lanuginosa lipase (TLL), Candida antartica lipase A, Candida antartica lipase B, Rhizomucor miehei lipase and Fusarium oxysporum lipase have no significant ferulic acid esterase activity. Thirteen variants of TLL were constructed based on a model of Aspergillus niger ferulic acid esterase A (FAE-A). Activity assay using ferulic acid ethyl ester as substrate gave, for FAE-A, 112 U/mg=112 μmol ferulic acid released per min per mg enzyme. Two of the variants of TLL had significant ferulic acid esterase activity, TLLv1 (7 U/mg) and TLLv10 (20 U/mg). Both these variants contain the mutation F113Y that seems to be essential for ferulic acid esterase activity. In addition to lipase activity, three cutinases showed ferulic acid esterase activity, Aspergillus oryzae cutinase (5 U/mg), Fusarium solani pisi cutinase (13 U/mg), Humicola insolence cutinase (20 U/mg).

Selective biocatalytic deacylation studies on furanose triesters: a novel and efficient approach towards bicyclonucleosides

Lipozyme TL IM catalyses the deacylation of 4-C-acyloxymethyl-3,5-di-O-acyl-1,2-O-(1-methylethylidene)-beta-L-threo-pentofuranose to form 3,5-di-O-acyl-4-C-hydroxymethyl-1,2-O-(1-methylethylidene)-alpha-D-xylo-pentofuranose in a highly selective and efficient manner. The rate of lipase-catalyzed deacylation of tributanoyl furanose is 2.3 times faster than the rate of deacylation of the triacetyl furanose derivative. In order to confirm the structure of the lipase-catalyzed deacylated product, it was converted to a bicyclic sugar derivative, which can be used for the synthesis of bicyclic nucleosides of importance in the development of novel antisense and antigene oligonucleotides. Further, it has been established that the monohydroxy product of the lipase-catalyzed reaction is the result of selective deacylation of the 4-C-acyloxymethyl function in the substrate and not of any acyl migration process.

Moonlighting protein in Starkeyomyces koorchalomoides: characterization of dihydrolipoamide dehydrogenase as a protein acetyltransferase utilizing acetoxycoumarin as the acetyl group donor.

In this report we have identified for the first time a transacetylase (TAase) in a mesophilic fungi Starkeyomyces koorchalomoides catalyzing the transfer of acetyl group from polyphenolic acetate (PA) to a receptor protein glutathione S-transferase (GST). An elegant assay procedure was established for TAase based on its ability to mediate inhibition of GST by 7,8-diacetoxy-4-methylcoumarin (DAMC), a model PA. Utilizing this assay procedure, S. koorchalomoides TAase was purified to homogeneity. TAase was found to have MW of 50 kDa. The purified enzyme exhibited maximum activity at 45 degrees C at pH 6.8. The N-terminal sequence of purified fungal TAase (ANDASTVED) showed identity with corresponding N-terminal sequence of dihydrolipoamide dehydrogenase (LADH), a mitochondrial matrix enzyme and an E3 component of pyruvate dehydrogenase complex (PDHC). TAase was found to have all the properties of LADH and avidly interacted with the anti-LADH antibody. TAase catalyzed acetylation of GST by DAMC was identified by LC-MS/MS and a single lysine residue (Lys-113) was found to be acetylated. Further, recombinant LADH from Streptococcus pneumoniae lacking lipoyl domain was found to exhibit little TAase activity, suggesting the role of lipoyl domain in the TAase activity of LADH. These observations bear evidence for the protein acetyltransferase activity of LADH. Such an activity of LADH can be attributed as a moonlighting function of the enzyme.

Glycosylation of Thermomyces lanuginosa lipase enhances surface binding towards phospholipids, but does not significantly influence the catalytic activity

Abstract Binding properties of the native Thermomyces lanuginosa lipase (Tll), the inactive mutant of Tll (S146A; active Ser146 mutated to Ala), and the non-glycosylated mutant of Tll (N33Q) were determined using fluorescence spectroscopy. Tll, S146A mutant and N33Q mutant show significant different binding behavior to phosphatidylcholine (PC) and phosphatidylglycerol (PG) liposomes. Generally, weaker association of lipase molecules is observed to PC liposomes than to PG liposomes. Strong lipase–lipid interactions are observed for the S146A mutant, which is less pronounced for Tll and the N33Q variant. Addition of fatty acid to PG liposomes reduces significantly the binding affinity of the lipases. This effect is less pronounced in fatty acid/PC liposomes. Although the catalytic activity of the N33Q mutant is comparable to Tll, the non-glycosylated variant shows generally lower binding affinity to PC or PG matrix than Tll. Addition of the substrate analog benzene boronic acid (BBA) increases the binding affinity of the S146A and N33Q mutants, while only small changes are observed for Tll suggesting that the dynamics of the active site lid influences the binding affinity and that the flexibility of the loop region 33–48 might contribute to the activation of the lipase.