Structure guided mutagenesis reveals the substrate determinants of guanine deaminase

Guanine deaminases (GDs) are essential enzymes that regulate the overall nucleobase pool. Since the deamination of guanine to xanthine results in the production of a mutagenic base, these enzymes have evolved to be very specific in nature. Surprisingly, they accept structurally distinct triazine ammeline, an intermediate in the melamine pathway, as one of the moonlighting substrates. Here, by employing NE0047 (a GD from Nitrosomonas europaea), we delineate the nuance in the catalytic mechanism that allows these two distinct substrates to be catalyzed. A combination of enzyme kinetics, X-ray crystallographic, and calorimetric studies reveal that GDs operate via a dual proton shuttle mechanism with two glutamates, E79 and E143, crucial for deamination. Additionally, N66 appears to be central for substrate anchoring and participates in catalysis. The study highlights the importance of closure of the catalytic loop and of maintenance of the hydrophobic core by capping residues like F141 and F48 for the creation of an apt environment for activation of the zinc-assisted catalysis. This study also analyzes evolutionarily distinct GDs and asserts that GDs incorporate subtle variations in the active site architectures while keeping the most critical active site determinants conserved.     

Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking

Background  

The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research. Beginning with a browser capable of rendering views of XML-based genomic information and providing scalable vector graphics output, we have now completed version 1.0 of the system with many additional features. Our development efforts were guided by our observation that biologists who use both gene expression profiling and comparative genomics gain functional insights above and beyond those provided by traditional per-gene analyses.     

In vitro propagation of Coleus forskohlii Briq. for forskolin synthesis

Shoot multiplication was obtained in vitro within 20–25 d from shoot tip expiants of 30 d old aseptically germinated seedlings of Coleus forskohlii Briq., using 2 mg/1 of 6 benzylaminopurine (BA). Shoot multiplication was further enhanced with the gradual decrease in the level of BA, and its final omission after 4 months. Different auxins supplemented at the level of 0.05 mg/1 with BA did not yield better results. Seven regenerated plants showed only diploid cells in their root tips, while three plants did not. Of these, two were diploid with occasional aneuploid cells. In one plant 32 chromosomes were observed. The potential of shoot culture in vitro and use of micropropagated plants for the production of forskolin has been demonstrated.     

Hydrophobic residues of melittin mediate its binding to αA−crystallin

The molecular chaperone αA‐crystallin, mainly localized in the human ocular lens, is believed to protect the lens from opacification and cataract, by suppressing the aggregation of the other lens proteins. The present study provides structural and thermodynamic insights into the ability of human αA‐crystallin (HAA) to bind to its partially unfolded clients in the lens, using a small peptide, melittin from bee venom, as a model client. We characterized the thermodynamic parameters of the binding process between melittin and HAA through isothermal titration calorimetry (ITC), and found the binding to be endothermic and entropy‐driven. We identified the amino acids in melittin important for binding to HAA by saturation‐transfer difference (STD) nuclear magnetic resonance (NMR) experiments, and analysis of NMR line broadening upon titration of melittin with HAA. Our results suggest that hydrophobic residues Ile17 and Ile20 on the C‐terminal region of melittin are in close contact with HAA in the melittin‐HAA complex. Information obtained from NMR experiments was used to generate structural models of the melittin‐HAA complex by molecular docking with high‐ambiguity driven docking (HADDOCK). Structural models of the melittin‐HAA complex reveal important principles underlying the interaction of HAA with its clients.