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RESEARCH PAPER
Bioinformatics study of biotin carboxylase B-subdomain isolated from Lactococcus lactis subsp. lactis (Lac3)
1
Program of Biotechnology, IPB University, Bogor, Indonesia
2
Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, Indonesia
3
Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia
4
Department of Physics, IPB University, Bogor, Indonesia
5
Tropical Biopharmaca Research Center, IPB University, Bogor, Indonesia
Submission date: 2024-02-15
Final revision date: 2025-05-23
Acceptance date: 2025-06-30
Corresponding author
Apon Zaenal Mustopa
Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
KEYWORDS
whole genome sequencing (WGS)molecular dockingmolecular dynamicsLactococcus lactis subsp. lactis (Lac3)biotin carboxylase B-subdomainATP-grasp superfamily
TOPICS
Protein sequence and structure analysis and modelingNucleic acids and protein complexesNucleic acids sequencing and assemblyStructure prediction
ABSTRACT
Background:
The increasing threat of antibiotic-resistant bacteria is a significant global health concern, with millions of people worldwide infected with these resistant strains each year. This study aims to conduct a bioinformatics analysis to investigate the biotin carboxylase (BC) B-subdomain from Lactococcus lactis subsp. lactis (Lac3) (accession number NZ_JAGRPZ010000035.1) as a potential target for the identification and development of novel antibiotics. Lac3 was isolated from one of the Indonesian traditional probiotics called dadih, and its whole-genome sequence analysis was revealed in a previous study.
Material and methods:
Whole-genome sequencing data of Lac3, generated using the Illumina MiSeq sequencer (Novogene Co., Ltd.), were used to analyze gene clusters with AntiSMASH. Molecular docking (PyRx Virtual Screening Tool; AutoDock Vina) and molecular dynamics simulations (CPPTRAJ software) were performed to elucidate the potential binding sites of the BC B-subdomain and compare them with the BC domain from a L. lactis reference strain (accession number KLK97304). The 3D structure of the BC B-subdomain was predicted using AlphaFold2. Visualization of the simulated protein–ligand complex conformations was conducted using PyMOL v2.3 software.
Results:
Bioinformatics analysis showed that the BC B-subdomain gene was located in the b-lactone gene cluster on contig 7.1 and consisted of 32.1% a-helix, 37.6% b-strand, and 24.8% random coil. Physicochemical analysis indicated that the BC B-subdomain protein exhibited a high degree of solubility. The BC B-subdomain shared similarities with the ATP-grasp domain of the BC domain from the reference strain, particularly in amino acid residues involved in ATP binding (His207, Gln231, Asn234, and Glu274). Molecular docking analysis demonstrated that the BC B-subdomain–ATP complex (–6.1 kcal/mol) was comparable to the BC domain–ATP complex (–8.8 kcal/mol). This was supported by molecular dynamics simulations, which indicated that the complex models remained stable throughout the simulations, based on several validation parameters, including RMSD, RMSF, Rg, and SASA. Furthermore, ionic interactions with the phosphate group’s amino acid residues – critical for ATP binding and function within ATP-grasp enzymes – were observed in both the BC B-subdomain (His207 and Lys236) and the BC domain (Lys236 and Arg290).
Conclusions:
These findings suggest that the BC B-subdomain could serve as a potential target for fragment-based drug discovery and may provide a reference for developing novel BC inhibitors with potent antibacterial activity by targeting ATP binding, possibly through its phosphate group binding sites. However, further analysis is needed to support the development of innovative antibacterial treatments in the future.
The increasing threat of antibiotic-resistant bacteria is a significant global health concern, with millions of people worldwide infected with these resistant strains each year. This study aims to conduct a bioinformatics analysis to investigate the biotin carboxylase (BC) B-subdomain from Lactococcus lactis subsp. lactis (Lac3) (accession number NZ_JAGRPZ010000035.1) as a potential target for the identification and development of novel antibiotics. Lac3 was isolated from one of the Indonesian traditional probiotics called dadih, and its whole-genome sequence analysis was revealed in a previous study.
Material and methods:
Whole-genome sequencing data of Lac3, generated using the Illumina MiSeq sequencer (Novogene Co., Ltd.), were used to analyze gene clusters with AntiSMASH. Molecular docking (PyRx Virtual Screening Tool; AutoDock Vina) and molecular dynamics simulations (CPPTRAJ software) were performed to elucidate the potential binding sites of the BC B-subdomain and compare them with the BC domain from a L. lactis reference strain (accession number KLK97304). The 3D structure of the BC B-subdomain was predicted using AlphaFold2. Visualization of the simulated protein–ligand complex conformations was conducted using PyMOL v2.3 software.
Results:
Bioinformatics analysis showed that the BC B-subdomain gene was located in the b-lactone gene cluster on contig 7.1 and consisted of 32.1% a-helix, 37.6% b-strand, and 24.8% random coil. Physicochemical analysis indicated that the BC B-subdomain protein exhibited a high degree of solubility. The BC B-subdomain shared similarities with the ATP-grasp domain of the BC domain from the reference strain, particularly in amino acid residues involved in ATP binding (His207, Gln231, Asn234, and Glu274). Molecular docking analysis demonstrated that the BC B-subdomain–ATP complex (–6.1 kcal/mol) was comparable to the BC domain–ATP complex (–8.8 kcal/mol). This was supported by molecular dynamics simulations, which indicated that the complex models remained stable throughout the simulations, based on several validation parameters, including RMSD, RMSF, Rg, and SASA. Furthermore, ionic interactions with the phosphate group’s amino acid residues – critical for ATP binding and function within ATP-grasp enzymes – were observed in both the BC B-subdomain (His207 and Lys236) and the BC domain (Lys236 and Arg290).
Conclusions:
These findings suggest that the BC B-subdomain could serve as a potential target for fragment-based drug discovery and may provide a reference for developing novel BC inhibitors with potent antibacterial activity by targeting ATP binding, possibly through its phosphate group binding sites. However, further analysis is needed to support the development of innovative antibacterial treatments in the future.
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