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Homology Modeling and Analysis of Vacuolar Aspartyl Protease from a Novel Yeast Expression Host Meyerozyma guilliermondii Strain SO

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Abstract

In eukaryotes, aspartyl protease (PEP4) is a localized hydrolase. PEP4 was recently identified from Meyerozyma guilliermondii strain SO (MgPEP4), a novel yeast expression host. But little is known about the structural properties and its catalytic mechanism. Multiple sequence alignment with other yeast aspartyl proteases revealed the conserved regions of MgPEP4 which belongs to the pepsin/proteinase_A_fungi superfamily. Two catalytic aspartic acid residues (Asp112 and Asp297) existed as a single copy at the DTG motif, a pattern of short conserved amino acids sequence. Homology modeling of MgPEP4 was done using Saccharomyces cerevisiae PEP4 (PDB ID: 1DPJ) as template. Using in silico analysis, we aim to reveal its stability by way of disulfide bridge formation and the catalytic mechanism of MgPEP4 with a universal protease inhibitor (pepstatin A). Structurally, only two out of the four conserved cysteine residues of the polypeptide were involved in intramolecular disulfide bridges in the validated structure as opposed to two disulfide bridges present in the template which conferred a critical stabilizing role in the protein structures. Pepstatin A (pepA) was docked at the substrate-binding site and showed hydrophilic interactions with the essential catalytic aspartic residues, which preliminarily proved the catalytic mechanism of MgPEP4. In conclusion, understanding of the structure and catalytic mechanism of MgPEP4 at the molecular level have given an insight about its role in the degradation of recombinant proteins in M. guilliermondii strain SO as an expression host as well as its potential applications in food, beverages, baking, leather and pharmaceutical industries. Further development of a new yeast strain could be done using MgPEP4 as the target protein.

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Acknowledgements

We would like to thank all the principle investigators in Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia for providing constructive comments and advice for this project. The first author, OEL would like to thank the Ministry of Education, Nigeria for the opportunity to further her study.

Funding

This research work was funded by the Fundamental Research Grant Scheme Projects, (Code: FRGS/1/2019/STG05/UPM/02/1) from the Ministry of Higher Education Malaysia which was awarded to SNO, the corresponding author.

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  1. Enzyme and Microbial Technology Research Centre, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia

    Okojie Eseoghene Lorrine, Raja Noor Zaliha Raja Abd. Rahman, Abu Bakar Salleh & Siti Nurbaya Oslan

  2. School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia

    Joo Shun Tan

  3. Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia

    Okojie Eseoghene Lorrine & Siti Nurbaya Oslan

  4. Enzyme Technology and X-Ray Crystallography Laboratory, VacBio 5, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia

    Raja Noor Zaliha Raja Abd. Rahman & Siti Nurbaya Oslan

  5. Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia

    Raja Noor Zaliha Raja Abd. Rahman

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  1. Okojie Eseoghene Lorrine
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Lorrine, O.E., Rahman, R.N.Z.R.A., Tan, J.S. et al. Homology Modeling and Analysis of Vacuolar Aspartyl Protease from a Novel Yeast Expression Host Meyerozyma guilliermondii Strain SO. Arab J Sci Eng 48, 81–91 (2023). https://doi.org/10.1007/s13369-022-07153-1

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