Molecular structure of nicotinamide adenine dinucleotide

Nicotinamide adenine dinucleotide (NAD) has a fundamental role in metabolic processes as an electron transport molecule. Although its chemical structure was elucidated in 1934, its detailed conformation remains still to be established in spite of numerous physicochemical applications. NAD analogues with a variety of substitutions on the bases are known to retain considerable activity of the natural coenzyme as long as the pyrophosphate diester group has been retained. The geometry of this backbone moiety is therefore indispensable to our understanding of the conformation and function of the coenzyme. We have so far no experimental evidence on this in NAD or any other nucleotide coenzyme molecule. X-ray studies have been possible only on those analogues where the nicotinamide and adenine rings are linked by a trimethylene bridge. The results are conflicting and it is difficult to use them to provide a structural basis for the NAD molecule itself, particularly as the phosphate backbone is absent from these analogues

Crystallization and preliminary X-ray crystallographic studies of thermostable xylanase crystals isolated from Paecilomyces varioti

A highly thermostable xylanase isolated from the thermophilic fungus Paecilomyces varioti has been crystallized by the vapour diffusion method. The isolation of this enzyme by crystallization directly from the culture filtrate projects this fungus as an important source for large-scale production of pure xylanase. The crystals belong to orthorhombic space group P212121 with the unit cell dimensions a=38.48 Å, b=53.87 Å and c=90.23 Å. Four molecules occupy a volume of 187,039.4 Å 3 along with 34% of solvent. The data collected with an area detector to the resolution of 2.7 Å were used to calculate the unit cell parameters and Matthews constant. The optical behaviour of the crystals was studied at different temperatures to understand its thermal stability

Crystal structure at 1.8 Å resolution and proposed amino acid sequence of a thermostable xylanase from Thermoascus aurantiacus

Thermoascus aurantiacus xylanase is a thermostable enzyme which hydrolyses xylan, a major hemicellulose component in the biosphere. Crystals belonging to P21 space group with a = 41.7 Å, b = 68.1 Å, c = 51.4 Å and β = 113.6 °, Z = 2 were grown that could diffract to better than 1.8 Å resolution. The structure was solved by molecular replacement method using the Streptomyces lividans xylanase model. The amino acid sequence was determined from the electron density map aided by multiple alignment of related xylanase sequences. The sequence thus obtained provides a correction to the sequence reported earlier based on biochemical methods. The final refined protein model at 1.8 Å resolution with 301 amino acid residues and 266 water molecules has an R-factor of 16.0 % and free R of 21.1 % with good stereochemistry. The single polypeptide chain assumes (α/β)8TIM-barrel fold and belongs to F/10 family of glycoside hydrolases. The active site consists of two glutamate residues located at the C terminus end of the β-barrel, conforming to the double displacement mechanism for the enzyme action. A disulphide bond and more than ten salt bridges have been identified. In particular, the salt bridge Arg124-Glu232 which is almost buried, bridges the β-strands β4 and β7 where the catalytic glutamate residues reside, and it may play a key role in the stability and activity at elevated temperature. To our knowledge, for the first time in the F/10 family xylanases, we observe a proline residue in the middle of the α-helix α6 which may be contributing to better packing. Earlier studies show that the enzyme retains its activity even at 70 °C. The refined protein model has allowed a detailed comparison with the other known structures in the F/10 family of enzymes. The possible causative factors for thermostability are discussed

Conformation of cyclolinopeptide dihydrate: An antamanide analogue

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