Biochemical characterization and molecular docking analysis of novel esterases from Sphingobium chungbukense DJ77

We identified three novel microbial esterase (Est1, Est2, and Est3) from Sphingobium chungbukense DJ77. Multiple sequence alignment showed the Est1 and Est3 have distinct motifs, such as tetrapeptide motif HGGG, a pentapeptide sequence motif GXSXG, and catalytic triad residues Ser-Asp-His, indicatin...

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Bibliographic Details
Published in:International journal of biological macromolecules 2021-01, Vol.168, p.403-411
Main Authors: Shin, Woo-Ri, Um, Hyun-Ju, Kim, Young-Chang, Kim, Sun Chang, Cho, Byung-Kwan, Ahn, Ji-Young, Min, Jiho, Kim, Yang-Hoon
Format: Article
Language:English
Subjects:
Amino Acid Motifs
Amino Acid Sequence
Bacterial Proteins - chemistry
Bacterial Proteins - genetics
Bacterial Proteins - metabolism
Biocatalysis
Biochemical characterization
Catalytic Domain
Cloning, Molecular - methods
Esterase
Esterases - chemistry
Esterases - genetics
Esterases - metabolism
Hydrogen-Ion Concentration
Hydrolysis
Molecular docking analysis
Molecular Docking Simulation
Polyesters - chemistry
Sequence Alignment
Sphingobium chungbukense DJ77
Sphingomonadaceae - chemistry
Sphingomonadaceae - enzymology
Sphingomonadaceae - genetics
Substrate Specificity
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Summary:We identified three novel microbial esterase (Est1, Est2, and Est3) from Sphingobium chungbukense DJ77. Multiple sequence alignment showed the Est1 and Est3 have distinct motifs, such as tetrapeptide motif HGGG, a pentapeptide sequence motif GXSXG, and catalytic triad residues Ser-Asp-His, indicating that the identified enzymes belong to family IV esterases. Interestingly, Est1 exhibited strong activity toward classical esterase substrates, p-nitrophenyl ester of short-chain fatty acids and long-chain. However, Est3 did not exhibit any activity despite having high sequence similarity and sharing the identical catalytic active residues with Est1. Est3 only showed hydrolytic degradation activity to polycaprolactone (PCL). MOE-docking prediction also provided the parameters consisting of binding energy, molecular docking score, and molecular distance between substrate and catalytic nucleophilic residue, serine. The engineered mutEst3 has hydrolytic activity for a variety of esters ranging from p-nitrophenyl esters to PCL. In the present study, we demonstrated that MOE-docking simulation provides a valuable insight for facilitating biocatalytic performance.
ISSN:0141-8130
1879-0003
DOI:10.1016/j.ijbiomac.2020.12.077