3D STRUCTURE AND FUNCTION ANALYSIS OF RECOMBINANT ALDII PROTEIN FROM Uncultured Acidilobus sp. USING I-TASSER
Downloads
The AldII protein is a new recombinant protein produced from a novel gene obtained via a metagenome approach. Previous studies showed that this protein is strong and has the same metal binding aspect as the class II Aldolase enzyme. Aldolase is a valuable enzyme used in pharmaceuticals, food processing, and biochemistry. Further investigation is required to comprehend the structure and function of the AldII protein due to its potential. Researchers will conduct sophisticated bioinformatic analysis on the 3D shape and function prediction of AldII using the I-TASSER webserver from Zhanglab.
The AldII protein is a new recombinant protein produced from a novel gene obtained via a metagenome approach. Previous studies showed that this protein is strong and has the same metal binding aspect as the class II Aldolase enzyme. Aldolase is a valuable enzyme used in pharmaceuticals, food processing, and biochemistry. Further investigation is required to comprehend the structure and function of the AldII protein due to its potential. Researchers will conduct sophisticated bioinformatic analysis on the 3D shape and function prediction of AldII using the I-TASSER webserver from Zhanglab. The I-TASSER server is an online tool for the automated prediction of protein structure and annotation of functions based on structure. Analysis of the AldII protein using the I-TASSER webserver shows that this protein has a stable structure with the closest structural homology to deoxyribose-phosphate aldolase from Bacillus thuringiensis with PDB code 6btdA. Additionally, the biological structure analysis shows that this protein shares the biological function of the enzyme L-fuculose-1-phosphate aldolase, which is part of the class II Aldolase enzyme that plays a role in the catabolism of arabinose, L-Fuculose, and Rhamnose. The results align with prior research that states the AldII protein is a stable protein with a catalytic side that is homologous to the class II Aldolase enzyme.
Higgins, M. A., Suits, M. D., Marsters, C., and Boraston, A. B., 2014. Structural and Functional Analysis of Fucose-Processing Enzymes from Streptococcus pneumoniae. Journal of Molecular Biology, 426(7), 1469–1482.
Luo, Y., Samuel, J., Mosimann, S. C., Lee, J. E., Tanner, M. E., and Strynadka, N. C. J., 2001. The Structure L-Ribulose-5-Phosphate 4-Epimerase: An Aldolase-like Platform for Epimerization . Biochemistry, 40(49), 14763–14771.
Meray, N. W., Suharti, S., and Akhmaloka, A., 2021. Studi Bioinformasi Urutan Asam Amino dan Struktur 3D Protein Aldolase Kelas II (AldII) dari Uncultured Acidilobus sp. Jurnal Kimia Riset, 6(2), 117.
Rocha, J. F., Sousa, S. F., and Cerqueira, N. M. F. S. A., 2022. Computational Studies Devoted to the Catalytic Mechanism of Threonine Aldolase, a Critical Enzyme in the Pharmaceutical Industry to Synthesize β-Hydroxy-α-amino Acids. ACS Catalysis, 12(9), 4990–4999.
Roy, A., Kucukural, A., and Zhang, Y., 2010. I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols, 5(4), 725–738.
Suharti, Meray, N. W., Nurbaiti, S., and Akhmaloka., 2015. Cloning and expression of a novel gene encoded thermostable archaeal aldolase class II from natural Sample. Biosciences Biotechnology Research Asia, 12(2), 1023–1029.
Windle, C. L., Müller, M., Nelson, A., and Berry, A., 2014. Engineering aldolases as biocatalysts. Current Opinion in Chemical Biology, 19, 25–33.
Yang, J., Wang, Y., and Zhang, Y., 2016. ResQ: An Approach to Unified Estimation of B -Factor and Residue-Specific Error in Protein Structure Prediction. Journal of Molecular Biology, 428(4), 693–701.
Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., and Zhang, Y., 2014. The I-TASSER suite: Protein structure and function prediction. In Nature Methods (Vol. 12, Issue 1, pp. 7–8). Nature Publishing Group.
Yang, J., and Zhang, Y., 2015. I-TASSER server: New development for protein structure and function predictions. Nucleic Acids Research, 43(W1), W174–W181.
Zhang, C., Freddolino, P. L., and Zhang, Y., 2017. COFACTOR: improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Research, 45(W1), W291–W299.
Zhang, Y., 2008. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9.
Zheng, W., Zhang, C., Li, Y., Pearce, R., Bell, E. W., and Zhang, Y., 2021. Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods, 1(3), 100014.
Copyright (c) 2024 Jurnal Kimia Riset
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
COPYRIGHT NOTICE
1. By submitting the article to Jurnal Kimia Riset (JKR), the author has agreed to transfer some of the copyrights to the publisher of the research chemistry journal, Universitas Airlangga, indicated in the Copyright Transfer Agreement.
2. Authors still retain significant rights to use and share their own published articles for non-commercial purposes subject to Creative Commons Attribution-NonComercial 4.0 International License
3. All publications (printed/electronic) are open access for educational purposes, research, library, and other non-commercial purposes. Besides the purposes mentioned above, the editorial board is not responsible for copyright violations.
