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Open AccessArticle

The Influence of Calcium toward Order/Disorder Conformation of Repeat-in-Toxin (RTX) Structure of Family I.3 Lipase from Pseudomonas fluorescens AMS8

1
Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
2
Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
3
Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
4
Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia
*
Author to whom correspondence should be addressed.
Toxins 2020, 12(9), 579; https://doi.org/10.3390/toxins12090579
Received: 22 July 2020 / Revised: 10 August 2020 / Accepted: 17 August 2020 / Published: 9 September 2020
(This article belongs to the Special Issue Bacterial Toxins: Protein Folding and Membrane Interactions)
Calcium-binding plays a decisive role in the folding and stabilization of many RTX proteins, especially for the RTX domain. Although many studies have been conducted to prove the contribution of Ca2+ ion toward the folding and stabilization of RTX proteins, its functional dynamics and conformational structural changes remain elusive. Here, molecular docking and molecular dynamics (MD) simulations were performed to analyze the contribution of Ca2+ ion toward the folding and stabilization of the RTX lipase (AMS8 lipase) structure. AMS8 lipase contains six Ca2+ ions (Ca1–Ca6). Three Ca2+ ions (Ca3, Ca4, and Ca5) were bound to the RTX parallel β-roll motif repeat structure (RTX domain). The metal ion (Ca2+) docking analysis gives a high binding energy, especially for Ca4 and Ca5 which are tightly bound to the RTX domain. The function of each Ca2+ ion is further analyzed using the MD simulation. The removal of Ca3, Ca4, and Ca5 caused the AMS8 lipase structure to become unstable and unfolded. The results suggested that Ca3, Ca4, and Ca5 stabilized the RTX domain. In conclusion, Ca3, Ca4, and Ca5 play a crucial role in the folding and stabilization of the RTX domain, which sustain the integrity of the overall AMS8 lipase structure. View Full-Text
Keywords: repeat-in-toxin; lipase; metal binding protein; order/disorder; calcium ion; structure; function; folding repeat-in-toxin; lipase; metal binding protein; order/disorder; calcium ion; structure; function; folding
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MDPI and ACS Style

Ali, N.S.M.; Salleh, A.B.; Leow, T.C.; Rahman, R.N.Z.R.A.; Ali, M.S.M. The Influence of Calcium toward Order/Disorder Conformation of Repeat-in-Toxin (RTX) Structure of Family I.3 Lipase from Pseudomonas fluorescens AMS8. Toxins 2020, 12, 579. https://doi.org/10.3390/toxins12090579

AMA Style

Ali NSM, Salleh AB, Leow TC, Rahman RNZRA, Ali MSM. The Influence of Calcium toward Order/Disorder Conformation of Repeat-in-Toxin (RTX) Structure of Family I.3 Lipase from Pseudomonas fluorescens AMS8. Toxins. 2020; 12(9):579. https://doi.org/10.3390/toxins12090579

Chicago/Turabian Style

Ali, Nur S.M.; Salleh, Abu B.; Leow, Thean C.; Rahman, Raja N.Z.R.A.; Ali, Mohd S.M. 2020. "The Influence of Calcium toward Order/Disorder Conformation of Repeat-in-Toxin (RTX) Structure of Family I.3 Lipase from Pseudomonas fluorescens AMS8" Toxins 12, no. 9: 579. https://doi.org/10.3390/toxins12090579

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