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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences Agrotekno METAMORFOSA Journal of Biological Sciences Buletin Udayana Mengabdi JURNAL REKAYASA DAN MANAJEMEN AGROINDUSTRI Itepa : Jurnal Ilmu dan Teknologi Pangan Jurnal Veteriner Jurnal Biologi Udayana SIMBIOSIS Media Ilmiah Teknologi Pangan (Scientific Journal of Food Technology) Indonesian Journal of Biotechnology Jurnal Ilmiah Teknologi Pertanian Agrotechno Jurnal Teknologi & Industri Hasil Pertanian Jurnal Pascapanen dan Bioteknologi Kelautan dan Perikanan Teknologi Indonesia Canrea Journal: Food Technology, Nutritions, and Culinary Journal Jurnal Gastronomi Indonesia AJARCDE (Asian Journal of Applied Research for Community Development and Empowerment) SEAS (Sustainable Environment Agricultural Science) Seminar Ilmiah Nasional Teknologi, Sains, dan Sosial Humaniora (SINTESA)
Ida Bagus Wayan Gunam
Program Studi Teknologi Industri Pertanian, Fakultas Teknologi Pertanian, Universitas Udayana, Badung, Bali, Indonesia.
Agriculture, Biological Sciences & Forestry Biochemistry, Genetics & Molecular Biology Computer Science & IT Earth & Planetary Sciences Education Energy Environmental Science Health Professions Immunology & microbiology Industrial & Manufacturing Engineering Materials Science & Nanotechnology Social Sciences Veterinary

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In silico Characterization of Poly (ethylene) Terephthalate (PET): Degrading Enzymes from Rhizobacter sp. for Enzymatic Degradation Mechanisms: Characterization of Rhizobacter sp. PET Hydrolases Damuri, Nur Wahida; Mohd Rozdhi, Amira Azawani; Tirmizhi Abubakar, Munkaila; Wayan Gunam, Ida Bagus; Huyop, Fahrul; Oyewusi, Habeebat Adekilekun
Journal of Tropical Life Science Vol. 15 No. 1 (2025)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/

Abstract

Dienelactone hydrolase (DHL) from Rhizobacter sp. is an enzyme from the β‐ketoadipate pathway that belongs to the α/β hydrolase family. It involves the conversion of chloroaromatics, such as nitrophenols and hydrocarbons, into harmless metabolites. The sequence-based analysis of Dienelactone hydrolase from Rhizobacter sp. shows significant homology to the extensively studied polyethylene terephthalate hydrolase of Ideonella sakaiensis (IsPETase). IsPETase can degrade the polymer, polyethylene terephthalate (PET), at room temperature. It was chosen as a template for dienelactone hydrolase from Rhizobacter sp. that was studied as a putative PET hydrolase. This study employs bioinformatics tools such as Expasy Protparam, Clustal Omega, SWISS-MODEL, GROMACS and Autodock vina to analyse the amino acid sequence of this enzyme, predict its three-dimensional structure and study its binding interaction. The structure of the putative PET hydrolase has been determined with 0.9 GMQE value and an overall quality factor of 96%. The residues responsible in substrate binding interactions are Leu88, Ser160 and Trp185. Thus, this in silico analysis depicts the ability of the putative PET hydrolase to bind to the polymer polyethylene terephthalate.
Structural Comparison of α-agarase (α-AgaD) from Thalassomonas sp. LD5: An in-silico study: Structural Comparison of α-agarase (α-AgaD) from Thalassomonas sp. LD5 Oyewusi, Habeebat Adekilekun; Oladipo, Oluwatosin; Abdul Wahab, Roswanira; Adekilekun , Habeebulahi Ajibola; Wayan Gunam, Ida Bagus; Huyop, Fahrul
Journal of Tropical Life Science Vol. 15 No. 2 (2025): In Press
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/

Abstract

The significance of agarase enzymes spans various high-value industries, including food, cosmetics, and medicine. These enzymes play a crucial role in the hydrolysis of agar to produce bioactive oligosaccharides, enabling wide-ranging applications across multiple fields. Among them, α-AgaD is a novel α-agarase enzyme produced by the Thalassomonas sp. LD5 strain. However, the structural and functional characteristics of α-AgaD within biological systems remain largely unexplored. This study therefore aims to provide a comprehensive in silico analysis of α-AgaD, focusing on its physicochemical properties, phylogenetic relationships, secondary structure composition, and 3D homology modelling. A range of computational tools was employed to validate the findings and enhance the structural understanding of this newly identified α-AgaD enzyme. The α-AgaD protein consists of 1,466 amino acids with a molecular weight of 158,787.82 Da. It has a theoretical isoelectric point (pI) of 4.14, indicating an overall acidic nature. Structural analysis revealed that alpha helices and random coils are the predominant secondary structures. Hydrophobic amino acids were more abundant than hydrophilic ones, with glycine accounting for approximately 10.4% of the total residues. The protein's aliphatic index was 72.05, and the instability index was 28.28, suggesting that α-AgaD is stable and likely to maintain its structure across a wide temperature range. Three-dimensional models of α-AgaD were constructed using I-TASSER, NCBI-PDB, SWISS-MODEL, and AlphaFold2, and subsequently validated using ERRAT, Verify3D, and PROCHECK. Among the models generated, AlphaFold2 produced the most accurate prediction, with nearly all amino acid residues located in the preferred regions of the Ramachandran plot. This further confirmed the reliability and quality of the refined models. The in silico structural analysis of α-AgaD offers valuable insights into the enzyme’s primary sequence, functional domains, and overall structural architecture, enhancing our understanding of α-agarase from Thalassomonas sp. LD5.
Co-Authors A.A.S. A. Sukmaningsih Ab Wahabb, Roswanira Abdul Wahab, Roswanira Adekilekun , Habeebulahi Ajibola Adekilekun Oyewusi, Habeebat Ambar Kusumaningrum Amna Hartiati Anak Agung Made Dewi Anggreni Azis Akbar Hakim Bambang Admadi Harsojuwono Bimby Issassam Damuri, Nur Wahida Deddy Setiadi Kadir Madjid Dwi Ayu Kirani Paramita Dylla Hanggaeni Dyah Puspaningrum Ella Dewi Yusnia ENIEK KRISWIYANTI Fitra Ayu Sitanggang G.P. Ganda Putra Gde Agung Bagus Surya Adnyana Gede Bagus Suwarrizki G. P Hamonangan Sipayung Huda , Nurul Huyop, Fahrul I B. K. Widnyana Yoga I Dewa Gde Mayun Permana I Dewa Putu Rega Elyana I Gede Arya Sujana I Gede Krisna Putra Pratama I Gusti Ayu Lani Triani I Gusti Bagus Ananta Wijaya Putra I Gusti Ngurah Agung Paranatha I Kadek Adi Wijaya Putra I Komang Trikuti I M. Mahaputra Wijaya I Made Mahaputra Wijaya I Made Mahaputra Wijaya I Made Sugitha I MADE SUPARTHA UTAMA I Made Supartha Utama I Made Yoga Saputra I MADE YOGA SEMARA GUNA I Putu Hendra Prasetya I W W Aryanika I W. Wisma P. Putra I W.G. SEDANA YOGA I Wayan Arnata I Wayan Kasa I Wayan Suarta I Wayan Widia I Wayan Wisma Pradnyana Putra I.M.S. Wijaya IDA AYU ASTARINI Ida Bagus Gede Brahmantara IDA BAGUS N. SURYA DARMA Ida Bagus Wisnu Matra Atmaja Izzah Ismail, Norjihada Janurianti , Ni Made Defy Janurianti, Ni Made Defy Ketut Agus Ary Subakti KETUT BUDA KOMANG AYU NOCIANITRI Kozo Asano Luh Putu Wrasiati Lutfi Suhendra Made Ria Defiani Mahaputra Wijaya Michael Jordi Theofanny Mohd Rozdhi, Amira Azawani Mohd Shariff , Amir Husni Monalisa Nababan Monikasari, Ni Nyoman Trisa Muhammad Iqbal N.P.I. Widyantari Nebay Cronika Simbolon Ni Kadek Eni Juniantari Ni Made Defy Janurianti Ni Made Ratih Despianti Ni Made Wartini Ni Putu Puspadi Aristyanti Ni Putu Suwariani Ni Wayan Wisaniyasa Noval Wahyu Adi Nursatria Purba Nurul Octavia Wasis NYOMAN SEMADI ANTARA Odilia Keron Oladipo, Oluwatosin Oyewusi, Habeebat Adekilekun Pande Ketut Diah Kencana Pande Komang Suparyana Putu Agus Nadiarta Putu Setia Budi Rajindran, Nanthini Rendy Sinaga Rike Pratiwi Sadyasmara, Cokorda Anom Bayu Sandhi Wipradnyadewi, Putu Ari Sayi Hatiningsih Shenni Maulina Teguh Pribadi Girsang Teruo Sone Thobie E. B Kaban Tirmizhi Abubakar, Munkaila WAYAN REDI ARYANTA Wito Setioko Yohanes Setiyo Yohannes Eko Putra Simanullang Yudisthira Dharma Bhusana Dasa Zainul Arifin