Title

Characterization of a hypothetical protein YVRE from Bacillus subtilis indicates its key role as
glucono-lactonase in pentose phosphate pathway and glucose metabolism

Authors

S.V. Reshma¹, Nitish Sathyanarayanan^{2, 3}, H.G. Nagendra^2*

Affiliation

¹Department of Biotechnology, PES University, Bangalore;

²Department of Biotechnology, Sir M Visvesvaraya Institute of Technology, Hunasemaranahalli, Bangalore 562157;

³Present Address: National Centre for Biological Sciences, Tata Institute for Fundamental Research, GKVK Campus, Bellary Road, Bangalore 65;

Email

nagshaila@gmail.com

Article Type

Hypothesis

Date

Received November 26, 2017; Revised December 5, 2017; Accepted December 5, 2017; Published December 31, 2017

Hypothetical proteins are functionally uncharacterized proteins with assigned function using sequence annotation tools. Almost half of the coding regions of several genomes are hypothetical proteins. Therefore, it is of our interest to characterize a hypothetical protein YVRE from the model system Bacillus subtilis using known data. YVRE is assigned the function as a glucono-lactonase using prediction and phylogenetic analysis. A molecular dynamics simulated homology model of YVRE (with calcium) using human senescence marker protein 30 /SMP30 (PDB ID: 3G4E) as template is reported for functional inference. It is observed that the protein possesses bivalent metal binding domain. Molecular docking studies with the substrate glucono-δ-lactone show YVRE binding with the substrate. This data was further validated using cloning and sub-cloning in pUC57 and pET22b+ respectively, followed by expression and purification using nickel affinity chromatography. The enzymatic activity of YVRE using glucono-δ-lactone was used as substrate was calculated. The results show the function of YVRE as a gluconolactonase, with higher preference to zinc than calcium or magnesium. Thus, YVRE is shown to play key role in three metabolic pathways namely, pentose phosphate pathway, ascorbate and aldarate metabolism, and caprolactam degradation.

Keywords

Hypothetical protein, Bacillus subtilis, SMP-30/Gluconolactonase/Regucalcin, Gluconolactonase, pentose phosphate pathway, glucose metabolism.

Citation

Reshma et al. Bioinformation 13(12): 430-438 (2017)

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.