Karakterisasi Enzim Kutinase dan Lipase Brevundimonas sp. Sebagai Pendegradasi Polycaprolactone Secara In Silico

In Silico Characterization of Cutinase and Lipase from Brevundimonas sp. As Polycaprolactone Degraders

Peningkatan pencemaran akibat residu plastik yang tertimbun di dilingkungan dapat diatasi dengan berbagai upaya salah satunya adalah bioremediasi. Bioremediasi dengan mikroorganisme dapat mendegradasi rantai polimer dari plastik. Penelitian oleh Lisdiana et al., (personal communication), menemukan bahwa isolat yang diambil dari plastisfer di estuari Pantai Mangrove Wonorejo adalah bakteri Brevundimonas sp. Brevundimonas sp. telah diteliti kemampuannya dalam mendegradasi rantai polimer polycarpolactone, namun belum dipastikan memiliki enzim kutinase dan lipase. Untuk itu penelitian bertujuan untuk mengidentifikasi adanya enzim kutinase dan lipase pada Brevundimonas sp. serta mengkarakterisasi enzim kutinase dan lipase tersebut berdasarkan analisis in silico. Metode yang digunakan berupa penelitian eksplorasi dengan mengumpulkan data dari databese berupa templat kutinase (PDB: 5ZOA), templat lipase (PDB: 1EX9), dan sekuens genom Brevundimonas vesicularis (GenBank: UAQP01000005.1) yaitu ABH 1 hingga 5. Data dianalisis karakteristik fisikokimia, lokasi subseluler, sinyal peptida, struktur sekunder, struktur tersier, dan motif fungsional, lalu dibandingkan dengan templat kutinase dan lipase. Penelitian menunjukkan ABH 1 dan ABH 4 memiliki instability index (II) diatas 40 sehingga struktur proteinnya tidak stabil dan tidak diuji lebih lanjut. Sampel ABH 2 tergolong hidrofobik, sedangkan ABH 3, ABH 5, dan templat tergolong hidrofilik. Namun ABH 5 merupakan protein membran sehingga tidak diuji lebih lanjut. Selanjutnya pada struktur sekunder diketahui nilai struktur α-helix lebih tinggi dari beta sheet. Setelahnya pada struktur tersier dan hasil refinement kedua didapatkan bahwa REF-2 model 4 ABH 2 dan REF-2 model 4 ABH 3 memiliki model protein paling optimal. Dan didapatkan ABH 2 memiliki struktur protein mirip kutinase serta ABH 3 memiliki struktur mirip lipase.

Environmental pollution caused by plastic waste can be addressed through bioremediation. Microbial bioremediation can degrade the polymer found in plastics. Lisdiana et al., (personal communication), identified an isolate from the plastisphere in Mangrove Wonorejo Beach and classified it as Brevundimonas sp. Although many studies have researched Brevundimonas sp. ability to degrade polycaprolactone polymer, there’s no information about cutinase and lipase found in Brevundimonas sp.. To address this gap, this research will identify and characterize cutinase and lipase in Brevundimonas sp. using in silico analysis. The method involves collecting cutinase (PDB: 5ZOA) and lipase (PDB: 1EX9) templates, as well as the genome sequences of Brevundimonas vesicularis (GenBank: UAQP01000005.1), which identified as ABH 1, ABH 2, ABH 3, ABH 4, and ABH 5. The data was then analyzed for its physicochemical characterization, subcellular localization, peptide signal, secondary structure, tertiary structure, and functional motifs, and then will be compared with cutinase and lipase templates. The research indicated that ABH 1 and ABH 4 had instability index (II) exceeding 40, suggesting their protein structures were unstable and unsuitable for the following research. ABH 2 was identified as hydrophobic, while ABH 3, ABH 5, and the enzyme templates (cutinase and lipase) were identified as hydrophilic. However, since ABH 5 was also identified as a membrane protein, it would not be used in further research. In the following research about secondary structure, it was found that the α-helix structures were more prevalent than beta-sheet structures. Further exa the tertiary structure and secondary refinement found that REF-2 model 4 ABH 2 and REF-2 model 4 ABH 3 had the highest score and identified as the most optimum sample protein. It can also be concluded that ABH 2 exhibited a cutinase-like protein structure while ABH 3 displayed a lipase-like protein structure.