Dataset Information

Enantioselectivity and Enzyme-Substrate Docking Studies of a Ketoreductase from Sporobolomyces salmonicolor (SSCR) and Saccharomyces cerevisiae (YOL151w).

ABSTRACT: Models for two ketoreductases were created and used to predict the stereoselectivity of the enzymes. One was based on the crystal structure of Sporobolomyces salmonicolor. This model was used to predict the stereoselectivity for 46 ketone reductions using this enzyme; only 6 were incorrectly predicted. The stereochemistries of the products were compared to the experimental values found in the literature. The Prelog rules were also used to predict the stereoselectivity for this enzyme; however the Prelog rules seem to be highly substrate dependent. As a result, predicting stereoselectivity of KREDs is more complicated than is allowed for with just substrate size and geometry. This enzyme showed Prelog docking geometry for 13 substrates if the enzyme is assumed to prefer an anti-Prelog docking geometry. For SSCR the molecular modeling proved to be a better method for predicting stereoselectivity of the enzymes. The second model was a homology model for YOL151w based on the enzyme crystal structure of Sporobolomyces salmonicolor carbonyl reductase, SSCR. In this homology model, 14 compounds were docked and the predicted stereochemistry was compared to the literature values. Of these, 5 were incorrectly predicted.

SUBMITTER: Nguyen PH

PROVIDER: S-EPMC4897451 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Enantioselectivity and Enzyme-Substrate Docking Studies of a Ketoreductase from Sporobolomyces salmonicolor (SSCR) and Saccharomyces cerevisiae (YOL151w).

Nguyen Phung-Hoang PH West Maya M Feske Brent D BD Padgett Clifford W CW

International scholarly research notices 20140817

Models for two ketoreductases were created and used to predict the stereoselectivity of the enzymes. One was based on the crystal structure of Sporobolomyces salmonicolor. This model was used to predict the stereoselectivity for 46 ketone reductions using this enzyme; only 6 were incorrectly predicted. The stereochemistries of the products were compared to the experimental values found in the literature. The Prelog rules were also used to predict the stereoselectivity for this enzyme; however th ...[more]

PMID: 27350963

Similar Datasets

Project description:Cellulose, a linear polymer of ? 1-4, linked glucose, is the most abundant renewable fraction of plant biomass (lignocellulose). It is synergistically converted to glucose by endoglucanase (EG) cellobiohydrolase (CBH) and ?-glucosidase (BGL) of the cellulase complex. BGL plays a major role in the conversion of randomly cleaved cellooligosaccharides into glucose. As it is well known, Saccharomyces cerevisiae can efficiently convert glucose into ethanol under anaerobic conditions. Therefore, S.cerevisiae was genetically modified with the objective of heterologous extracellular expression of the BGLI gene of Trichoderma virens making it capable of utilizing cellobiose to produce ethanol.The cDNA and a genomic sequence of the BGLI gene of Trichoderma virens was cloned in the yeast expression vector pGAPZ? and separately transformed to Saccharomyces cerevisiae. The size of the BGLI cDNA clone was 1363 bp and the genomic DNA clone contained an additional 76 bp single intron following the first exon. The gene was 90% similar to the DNA sequence and 99% similar to the deduced amino acid sequence of 1,4-?-D-glucosidase of T. atroviride (AC237343.1). The BGLI activity expressed by the recombinant genomic clone was 3.4 times greater (1.7 x 10-3 IU ml-1) than that observed for the cDNA clone (5 x 10-4 IU ml-1). Furthermore, the activity was similar to the activity of locally isolated Trichoderma virens (1.5 x 10-3 IU ml-1). The estimated size of the protein was 52 kDA. In fermentation studies, the maximum ethanol production by the genomic and the cDNA clones were 0.36 g and 0.06 g /g of cellobiose respectively. Molecular docking results indicated that the bare protein and cellobiose-protein complex behave in a similar manner with considerable stability in aqueous medium. The deduced binding site and the binding affinity of the constructed homology model appeared to be reasonable. Moreover, it was identified that the five hydrogen bonds formed between the amino acid residues of BGLI and cellobiose are mainly involved in the integrity of enzyme-substrate association.The BGLI activity was remarkably higher in the genomic DNA clone compared to the cDNA clone. Cellobiose was successfully fermented into ethanol by the recombinant S.cerevisiae genomic DNA clone. It has the potential to be used in the industrial production of ethanol as it is capable of simultaneous saccharification and fermentation of cellobiose. Homology modeling, docking studies and molecular dynamics simulation studies will provide a realistic model for further studies in the modification of active site residues which could be followed by mutation studies to improve the catalytic action of BGLI.

Dataset Information

Enantioselectivity and Enzyme-Substrate Docking Studies of a Ketoreductase from Sporobolomyces salmonicolor (SSCR) and Saccharomyces cerevisiae (YOL151w).

Publications

Enantioselectivity and Enzyme-Substrate Docking Studies of a Ketoreductase from Sporobolomyces salmonicolor (SSCR) and Saccharomyces cerevisiae (YOL151w).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets