@article { ISI:000339470100014,
	title = {Improved method for specificity annotation shows a distinct evolutionary divergence among the microbial enzymes of the cholylglycine hydrolase family},
	journal = {Microbiology-SGM},
	volume = {160},
	number = {6},
	year = {2014},
	month = {JUN},
	pages = {1162-1174},
	publisher = {SOC GENERAL MICROBIOLOGY},
	address = {MARLBOROUGH HOUSE, BASINGSTOKE RD, SPENCERS WOODS, READING RG7 1AG, BERKS, ENGLAND},
	abstract = {<p>Bile salt hydrolases (BSHs) are gut microbial enzymes that play a significant role in the bile acid modification pathway. Penicillin V acylases (PVAs) are enzymes produced by environmental microbes, having a possible role in pathogenesis or scavenging of phenolic compounds in their microbial habitats. The correct annotation of such physiologically and industrially important enzymes is thus vital. The current methods relying solely on sequence homology do not always provide accurate annotations for these two members of the cholylglycine hydrolase (CGH) family as BSH/PVA enzymes. Here, we present an improved method [binding site similarity (BSS)-based scoring system] for the correct annotation of the CGH family members as BSH/PVA enzymes, which along with the phylogenetic information incorporates the substrate specificity as well as the binding site information. The BSS scoring system was developed through the analysis of the binding sites and binding modes of the available BSH/PVA structures with substrates glycocholic acid and penicillin V. The 198 sequences in the dataset were then annotated accurately using BSS scores as BSH/PVA enzymes. The dataset presented contained sequences from Gram-positive bacteria, Gram-negative bacteria and archaea. The clustering obtained for the dataset using the method described above showed a clear distinction in annotation of Gram-positive bacteria and Gram-negative bacteria Based on this clustering and a detailed analysis of the sequences of the CGH family in the dataset, we could infer that the CGH genes might have evolved in accordance with the hypothesis stating the evolution of diderms and archaea from the monoderms.</p>},
	issn = {1350-0872},
	doi = {10.1099/mic.0.077586-0},
	author = {Panigrahi, Priyabrata and Sule, Manas and Sharma, Ranu and Ramasamy, Sureshkumar and Suresh, C. G.}
}
@article { ISI:000333675600057,
	title = {In-Silico analysis of binding site features and substrate selectivity in plant flavonoid-3-o glycosyltransferases (F3GT) through molecular modeling, docking and dynamics simulation studies},
	journal = {Plos One},
	volume = {9},
	number = {3},
	year = {2014},
	month = {MAR},
	pages = {e92636},
	publisher = {PUBLIC LIBRARY SCIENCE},
	address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
	abstract = {<p>Flavonoids are a class of plant secondary metabolites that act as storage molecules, chemical messengers, as well as participate in homeostasis and defense processes. They possess pharmaceutical properties important for cancer treatment such as antioxidant and anti-tumor activities. The drug-related properties of flavonoids can be improved by glycosylation. The enzymes glycosyltransferases (GTs) glycosylate acceptor molecules in a regiospecific manner with the help of nucleotide sugar donor molecules. Several plant GTs have been characterized and their amino acid sequences determined. However, three-dimensional structures of only a few are reported. Here, phylogenetic analysis using amino acid sequences have identified a group of GTs with the same regiospecific activity. The structures of these closely related GTs were modeled using homologous GT structures. Their substrate binding sites were elaborated by docking flavonoid acceptor and UDP-sugar donor molecules in the modeled structures. Eight regions near the acceptor binding site in the N- and C-terminal domain of GTs have been identified that bind and specifically glycosylate the 3-OH group of acceptor flavonoids. Similarly, a conserved motif in the C-terminal domain is known to bind a sugar donor substrate. In certain GTs, the substitution of a specific glutamine by histidine in this domain changes the preference of sugar from glucose to galactose as a result of changed pattern of interactions. The molecular modeling, docking, and molecular dynamics simulation studies have revealed the chemical and topological features of the binding site and thus provided insights into the basis of acceptor and donor recognition by GTs.</p>},
	issn = {1932-6203},
	doi = {10.1371/journal.pone.0092636},
	author = {Sharma, Ranu and Panigrahi, Priyabrata and Suresh, C. G.}
}
