Ponnandy Prabhu

Probing the Molecular Determinant for the Catalytic Efficiency of l-Arabinose Isomerase from Bacillus licheniformis

ABSTRACT Bacillus licheniformis l-arabinose isomerase (l-AI) is distinguished from other l-AIs by its high degree of substrate specificity for l-arabinose and its high turnover rate. A systematic strategy that included a sequence alignment-based first screening of residues and a homology model-based second screening, followed by site-directed mutagenesis to alter individual screened residues, was used to study the molecular determinants for the catalytic efficiency of B. licheniformisl-AI. One conserved amino acid, Y333, in the substrate binding pocket of the wild-type B. licheniformisl-AI was identified as an important residue affecting the catalytic efficiency of B. licheniformisl-AI. Further insights into the function of residue Y333 were obtained by replacing it with other aromatic, nonpolar hydrophobic amino acids or polar amino acids. Replacing Y333 with the aromatic amino acid Phe did not alter catalytic efficiency toward l-arabinose. In contrast, the activities of mutants containing a hydrophobic amino acid (Ala, Val, or Leu) at position 333 decreased as the size of the hydrophobic side chain of the amino acid decreased. However, mutants containing hydrophilic and charged amino acids, such as Asp, Glu, and Lys, showed almost no activity with l-arabinose. These data and a molecular dynamics simulation suggest that Y333 is involved in the catalytic efficiency of B. licheniformisl-AI.

Immobilization of Bacillus licheniformis L-arabinose isomerase for semi-continuous L-ribulose production.

Bacillus licheniformis L-arabinose isomerase (BLAI) with a broad pH range, high substrate specificity, and high catalytic efficiency for L-arabinose was immobilized on various supports. Eupergit C, activated-carboxymethylcellulose, CNBr-activated agarose, chitosan, and alginate were tested as supports, and Eupergit C was selected as the most effective. After determination of the optimum enzyme concentration, the effects of pH and temperature were investigated using a response surface methodology. The immobilized BLAI enzyme retained 86.4% of the activity of the free enzyme. The optimal pH for the immobilized BLAI was 8.0, and immobilization improved the optimal temperature from 50 °C (free enzyme) to a range between 55 and 65 °C. The half life improved from 2 at 50 °C to 212 h at 55 °C following immobilization. The immobilized BLAI was used for semi-continuous production of L-ribulose. After 8 batch cycles, 95.1% of the BLAI activity was retained. This simple immobilization procedure and the high stability of the final immobilized BLAI on Eupergit C provide a promising solution for large-scale production of L-ribulose from an inexpensive L-arabinose precursor.

Structure-based studies on the metal binding of two-metal-dependent sugar isomerases

Two‐metal‐dependent sugar isomerases are important in the synthesis of rare sugars. Many of their properties, specifically their metal dependency, have not been sufficiently explored. Here we used X‐ray crystallography, site‐directed mutagenesis, isothermal titration calorimetry and electron paramagnetic resonance spectroscopy to investigate the molecular determinants of the metal‐binding affinity of l‐rhamnose isomerase, a two‐Mn2+‐dependent isomerase from Bacillus halodurans (BHRI). The crystal structure of BHRI confirmed the presence of two metal ion‐binding sites: a structural metal ion‐binding site for substrate binding, and a catalytic metal ion‐binding site that catalyzes a hydride shift. One conserved amino acid, W38, in wild‐type BHRI was identified as a critical residue for structural Mn2+ binding and thus the catalytic efficiency of BHRI. This function of W38 was explored by replacing it with other amino acids. Substitution by Phe, His, Lys, Ile or Ala caused complete loss of catalytic activity. The role of W38 was further examined by analyzing the crystal structure of wild‐type BHRI and two inactive mutants of BHRI (W38F and W38A) in complex with Mn2+. A structural comparison of the mutants and the wild‐type revealed differences in their coordination of Mn2+, including changes in metal–ligand bond length and affinity for Mn2+. The role of W38 was further confirmed in another two‐metal‐dependent enzyme: xylose isomerase from Bacillus licheniformis. These data suggest that W38 stabilizes protein–metal complexes and in turn assists ligand binding during catalysis in two‐metal‐dependent isomerases.

Crystallization and preliminary X-ray crystallographic analysis of L-rhamnose isomerase with a novel high thermostability from Bacillus halodurans.

L-Rhamnose isomerases catalyze isomerization between L-rhamnose (6-deoxy-L-mannose) and L-rhamnulose (6-deoxy-L-fructose), which is the first step in rhamnose catabolism. L-Rhamnose isomerase from Bacillus halodurans ATCC BAA-125 (BHRI) exhibits interesting characteristics such as high thermostability and selective substrate specificity. BHRI fused with an HHHHHH sequence was purified and crystallized in order to elucidate the molecular basis of its unique enzymatic properties. The crystals were grown by the hanging-drop vapour-diffusion method and belonged to the monoclinic space group P2(1), with unit-cell parameters a = 83.2, b = 164.9, c = 92.0 A, beta = 116.0 degrees . Diffraction data were collected to 2.5 A resolution. According to a Matthews coefficient calculation, there are four monomers in the asymmetric unit with a V(M) of 3.0 A(3) Da(-1) and a solvent content of 59.3%. The initial structure of BHRI has been determined by the molecular-replacement method.

In silico studies on the substrate specificity of an l-arabinose isomerase from Bacillus licheniformis

l-Arabinose isomerase (BLAI) from Bacillus licheniformis was found to be active only with l-arabinose, unlike other l-arabinose isomerases (l-AIs) active with a variety of aldoses. Therefore, the differences in molecular interactions and substrate orientation in the active site of l-AIs have been examined and the residue at position 346 is proposed to be responsible for the unique substrate specificity of BLAI.

ENHANCED STABILITY OF BACILLUS LICHENIFORMIS L-ARABINOSE ISOMERASE BY IMMOBILIZATION WITH ALGINATE

Recombinant Escherichia coli whole cells harboring Bacillus licheniformis L-arabinose isomerase (BLAI) were harvested to prepare alginate-immobilized biocatalysts. The operational conditions for immobilization were optimized according to relative activity and the cell leakage of the immobilized cell. The optimal conditions are as follows: alginate concentration, Ca2+ concentration, cell mass loading, and curing time were 2% (w/v), 0.1 M, 50 g l−1, and 4 hours, respectively. After immobilization, cross-linking with 0.1% glutaraldehyde significantly reduced cell leakage. The immobilized whole cells harboring BLAI were very stable with 89% residual activity remaining after 33 days of incubation at 50°C and were much more stable than the free enzyme and cells. The results showed that immobilizing whole cells harboring BLAI is suitable for use as a biocatalyst in the production of L-ribulose, largely due to its high stability and low cost.