Crystallization and preliminary crystallographic analysis of an amylopullulanase from the hyperthermophilic archaeon Pyrococcus woesei

Overexpression, purification and preliminary X-ray analysis of pullulanase from Bacillus subtilis strain 168

The AmyX gene encoding pullulanase from the common spore-forming bacterium Bacillus subtilis strain 168 was cloned, overexpressed in Escherichia coli, purified and crystallized. The recombinant pullulanase was purified to homogeneity using ammonium sulfate precipitation, hydrophobic chromatography and anion-exchange chromatography, resulting in a specific activity of 24.10 U per milligram of protein. SDS-PAGE analysis showed that the molecular weight of the protein is approximately 81.0 kDa, which is similar to the calculated molecular weight, 81.1 kDa, from its translated cDNA sequence. The k(cat) and K(m) of the purified enzyme with pullulan as substrate were approximately 79 s(-1) and 1.284 mg ml(-1), respectively. X-ray crystallographic analysis of the pullulanase crystal showed that the crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 70.568, b = 127.68, c = 189.25 angstroms. The crystal contains two molecules of pullulanase in the asymmetric unit, with a solvent content of 53.15%. The crystal diffracted to 2.1 angstroms resolution at a synchrotron and is suitable for structure determination.

Extreme environments as a resource for microorganisms and novel biocatalysts

The steady increase in the number of newly isolated extremophilic microorganisms and the discovery of their enzymes by academic and industrial institutions underlines the enormous potential of extremophiles for application in future biotechnological processes. Enzymes from extremophilic microorganisms offer versatile tools for sustainable developments in a variety of industrial application as they show important environmental benefits due to their biodegradability, specific stability under extreme conditions, improved use of raw materials and decreased amount of waste products. Although major advances have been made in the last decade, our knowledge of the physiology, metabolism, enzymology and genetics of this fascinating group of extremophilic microorganisms and their related enzymes is still limited. In-depth information on the molecular properties of the enzymes and their genes, however, has to be obtained to analyze the structure and function of proteins that are catalytically active around the boiling and freezing points of water and extremes of pH. New techniques, such as genomics, metanogenomics, DNA evolution and gene shuffling, will lead to the production of enzymes that are highly specific for countless industrial applications. Due to the unusual properties of enzymes from extremophiles, they are expected to optimize already existing processes or even develop new sustainable technologies.

Proteins from hyperthermophiles: stability and enzymatic catalysis close to the boiling point of water

It has become clear since about a decade ago, that the biosphere contains a variety of microorganisms that can live and grow in extreme environments. Hyperthermophilic microorganisms, present among Archaea and Bacteria, proliferate at temperatures of around 80-100 degrees C. The majority of the genera known to date are of marine origin, however, some of them have been found in continental hot springs and solfataric fields. Metabolic processes and specific biological functions of these organisms are mediated by enzymes and proteins that function optimally under these extreme conditions. We are now only starting to understand the structural, thermodynamic and kinetic basis for function and stability under conditions of high temperature, salt and extremes of pH. Insights gained from the study of such macromolecules help to extend our understanding of protein biochemistry and -biophysics and are becoming increasingly important for the investigation of fundamental problems in structure biology such as protein stability and protein folding. Extreme conditions in the biosphere require either the adaptation of the amino acid sequence of a protein by mutations, the optimization of weak interactions within the protein and at the protein-solvent boundary, the influence of extrinsic factors such as metabolites, cofactors, compatible solutes. Furthermore folding catalysts, known as chaperones, that assist the folding of proteins may be involved or increased protein protein synthesis in order to compensate for destruction by extreme conditions. The comparison of structure and stability of homologous proteins from mesophiles and hyperthermophiles has revealed important determinants of thermal stability of proteins. Rather than being the consequence of one dominant type of interactions or of a general stabilization strategy, it appears that the adaptation to high temperatures reflects a number of subtle interactions, often characteristic for each protein species, that minimize the surface energy and the hydration of apolar surface groups while burying hydrophobic residues and maximizing packing of the core as well as the energy due to charge-charge interactions and hydrogen bonds. In this article, mechanisms of intrinsic stabilization of proteins are reviewed. These mechanisms are found on different levels of structural organization. Among the extrinsic stabilization factors, emphasis is put on archaea chaperonins and their still strongly debated function. It will be shown, that optimization of weak protein-protein and protein-solvent interactions plays a key role in gaining thermostability. The difficulties in correlating suitable optimization criteria with real thermodynamic stability measures are due to experimental difficulties in measuring stabilization energies in large proteins or protein oligomers and will be discussed. Thus small single domain proteins or isolated domains of larger proteins may serve as model systems for large or multidomain proteins which due to the complexity of their thermal unfolding transitions cannot be analyzed by equilibrium thermodynamics. The analysis of the energetics of the thermal unfolding of a small, hyperthermostable DNA binding protein from Sulfolobus has revealed that a high melting temperature is not synonymous with a larger maximum thermodynamic stability. Finally, it is now well documented, that many thermophilic and hyperthermophilic proteins show a statistically increased number of salt bridges and salt bridge networks. However their contribution to thermodynamic and functional stability is still obscure.

Sequence of archaeal Methanococcus jannaschii alpha-amylase contains features of families 13 and 57 of glycosyl hydrolases: a trace of their common ancestor?

Two sequentially different, seemingly unrelated alpha-amylase families exist, known as family-13 and family-57 glycosyl hydrolases. Despite the common enzyme activity, it has as yet been impossible to detect any sequence similarity between the two families. The detailed analysis of the recently determined sequence of the alpha-amylase from methanogenic archaeon Methanococcus jannaschii using the sensitive Hydrophobic Cluster Analysis method revealed that this alpha-amylase contains features of both families of alpha-amylases. Thus the M. jannaschii alpha-amylase is similar to the Pyrococcus furiosus alpha-amylase from family 57 while it obviously contains most of the sequence fingerprints characteristic for alpha-amylase family 13. Importantly, a glutamic acid residue equivalent with the family-13 catalytic glutamate positioned in the beta 5-strand segment was identified in members of family 57. The results presented in this report indicate that the two families, 13 and 57, are either the products of a very distant common ancestor or have evolved from each other, although at present they can represent two different alpha-amylase families with evolved different catalytic mechanisms, catalytic machinery and folds.