Molecular Modelling of Oryza sativa Starch-branching Enzyme 1

Authors

  • Sulaiman Mohammed Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru. Orcid: 0000 0003 3094 4769.
  • Mohammed Jibrin Ndejiko Department of Microbiology, Faculty of Natural Sciences, Ibrahim Badamasi Babangida University Lapai, Nigeria. Orcid: 0000-0003-0790-833X.
  • Mohammed Maikudi Usman Department of Biotechnology, School of Life Sciences, Modibbo Adama University of Technology Yola, Nigeria. Orcid: 0000-0002-5699-2673.
  • Yilmaz Kaya Department of Plant Biotechnology, Faculty of Agriculture, Ondokuz Mayis University, Samsun, Turkey
  • Fahrul Zaman Huyop Department of Bioscience, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru. Orcid:0000-0003-3979-4087.

DOI:

https://doi.org/10.54987/jobimb.v8i1.501

Keywords:

rice SBE1, secondary structure, domains interaction, 3D model, C-score

Abstract

Starch-branching enzymes (SBE) serves as the only enzyme generating glucan branches in green plants and consequently plays a significant role on the resulting starch final structure. Research on rice (Oryza sativa) SBE1 (OsSBE1) structural biology remain untapped. Therefore, there is a necessity for research on the enzyme molecular structure which could lead to the protein function annotation, starch production and energy booster drug design. Analysis of OsSBE1 secondary structure, domains and their interactions, enzyme 3D structure prediction and validation based on C-score were carried out. The OsSBE1 primary sequence was retrieved from GenBank and its secondary structure was predicted to be; α-helix (27.68%), extended strand (22.78%) and higher random coil (949.54%). Enzyme domains were found to be carbohydrate-binding module (CBM) 48 (isoamylase N-terminal domain), α-amylase catalytic domain and α-amylase C-terminal all-beta domain with active sites important amino acids asparagine and glutamic acid. From the five 3D models generated, model 3 displayed best prediction. The Ramachandran refinement has 97.3 amino acids residues in favoured region and 0.4 C-score. This bioinformatics study has elucidated on the OsSBE1 molecular model and first to report on its domain interaction.

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Published

31.07.2020

How to Cite

Mohammed, S., Ndejiko, M. J., Usman, M. M., Kaya, Y., & Huyop, F. Z. (2020). Molecular Modelling of Oryza sativa Starch-branching Enzyme 1. Journal of Biochemistry, Microbiology and Biotechnology, 8(1), 7–10. https://doi.org/10.54987/jobimb.v8i1.501

Issue

Vol. 8 No. 1 (2020)

Section

Articles

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