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Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis

Efficient degradation of alkanes in crude oil by the isolated Aspergillus flavus MM1 alluded to the presence of highly active alkane-degrading enzymes in this fungus. A long-chain alkane-degrading, LadA-like enzyme family in A. flavus was identified, and possible substrate-binding modes were analyze...

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Autores principales: Perera, Madushika, Wijesundera, Sulochana, Wijayarathna, C. Dilrukshi, Seneviratne, Gamini, Jayasena, Sharmila
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
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Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9468676/
https://www.ncbi.nlm.nih.gov/pubmed/36110294
http://dx.doi.org/10.3389/fmicb.2022.898456
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author Perera, Madushika
Wijesundera, Sulochana
Wijayarathna, C. Dilrukshi
Seneviratne, Gamini
Jayasena, Sharmila
author_facet Perera, Madushika
Wijesundera, Sulochana
Wijayarathna, C. Dilrukshi
Seneviratne, Gamini
Jayasena, Sharmila
author_sort Perera, Madushika
collection PubMed
description Efficient degradation of alkanes in crude oil by the isolated Aspergillus flavus MM1 alluded to the presence of highly active alkane-degrading enzymes in this fungus. A long-chain alkane-degrading, LadA-like enzyme family in A. flavus was identified, and possible substrate-binding modes were analyzed using a computational approach. By analyzing publicly available protein databases, we identified six uncharacterized proteins in A. flavus NRRL 3357, of which five were identified as class LadAα and one as class LadAβ, which are eukaryotic homologs of bacterial long-chain alkane monooxygenase (LadA). Computational models of A. flavus LadAα homologs (Af1-Af5) showed overall structural similarity to the bacterial LadA and the unique sequence and structural elements that bind the cofactor Flavin mononucleotide (FMN). A receptor-cofactor-substrate docking protocol was established and validated to demonstrate the substrate binding in the A. flavus LadAα homologs. The modeled Af1, Af3, Af4, and Af5 captured long-chain n-alkanes inside the active pocket, above the bound FMN. Isoalloxazine ring of reduced FMN formed a π–alkyl interaction with the terminal carbon atom of captured alkanes, C(16)–C(30), in Af3–Af5 and C(16)–C(24) in Af1. Our results confirmed the ability of identified A. flavus LadAα monooxygenases to bind long-chain alkanes inside the active pocket. Hence A. flavus LadAα monooxygenases potentially initiate the degradation of long-chain alkanes by oxidizing bound long-chain alkanes into their corresponding alcohol.
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spelling pubmed-94686762022-09-14 Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis Perera, Madushika Wijesundera, Sulochana Wijayarathna, C. Dilrukshi Seneviratne, Gamini Jayasena, Sharmila Front Microbiol Microbiology Efficient degradation of alkanes in crude oil by the isolated Aspergillus flavus MM1 alluded to the presence of highly active alkane-degrading enzymes in this fungus. A long-chain alkane-degrading, LadA-like enzyme family in A. flavus was identified, and possible substrate-binding modes were analyzed using a computational approach. By analyzing publicly available protein databases, we identified six uncharacterized proteins in A. flavus NRRL 3357, of which five were identified as class LadAα and one as class LadAβ, which are eukaryotic homologs of bacterial long-chain alkane monooxygenase (LadA). Computational models of A. flavus LadAα homologs (Af1-Af5) showed overall structural similarity to the bacterial LadA and the unique sequence and structural elements that bind the cofactor Flavin mononucleotide (FMN). A receptor-cofactor-substrate docking protocol was established and validated to demonstrate the substrate binding in the A. flavus LadAα homologs. The modeled Af1, Af3, Af4, and Af5 captured long-chain n-alkanes inside the active pocket, above the bound FMN. Isoalloxazine ring of reduced FMN formed a π–alkyl interaction with the terminal carbon atom of captured alkanes, C(16)–C(30), in Af3–Af5 and C(16)–C(24) in Af1. Our results confirmed the ability of identified A. flavus LadAα monooxygenases to bind long-chain alkanes inside the active pocket. Hence A. flavus LadAα monooxygenases potentially initiate the degradation of long-chain alkanes by oxidizing bound long-chain alkanes into their corresponding alcohol. Frontiers Media S.A. 2022-08-30 /pmc/articles/PMC9468676/ /pubmed/36110294 http://dx.doi.org/10.3389/fmicb.2022.898456 Text en Copyright © 2022 Perera, Wijesundera, Wijayarathna, Seneviratne and Jayasena. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Perera, Madushika
Wijesundera, Sulochana
Wijayarathna, C. Dilrukshi
Seneviratne, Gamini
Jayasena, Sharmila
Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis
title Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis
title_full Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis
title_fullStr Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis
title_full_unstemmed Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis
title_short Identification of long-chain alkane-degrading (LadA) monooxygenases in Aspergillus flavus via in silico analysis
title_sort identification of long-chain alkane-degrading (lada) monooxygenases in aspergillus flavus via in silico analysis
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9468676/
https://www.ncbi.nlm.nih.gov/pubmed/36110294
http://dx.doi.org/10.3389/fmicb.2022.898456
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