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<p>Pectin lyase (PNL), a key member of the pectinases, employs a distinct β-elimination mechanism to break down pectin polymer into 4,5-unsaturated oligogalacturonides. PNLs have several industrial applications, though predominately preferred in fruit juice processing industries mainly because of their ability to preserve the natural flavour of juice and to avoid the production of highly hazardous methanol as a byproduct. The gene coding for PNL represents multigene families, and several PNL genes have been reported. In the present study, four PNL genes were PCR amplified using genomic DNA of <i>Fusarium proliferatum</i> strain MTCC 9375 and <i>Fusarium fujikuroi</i> strain MTCC 9930 as templates. Further, these were cloned, sequenced, and assigned GenBank accession numbers. Several physico-chemical and structural attributes were assessed using bioinformatics tools. Further, the suitability of the substrate for efficient catalysis, structural rigidity, and stability of the docked complexes was investigated using homology modelling, molecular docking, and molecular dynamics (MD) simulations. The docking results revealed that the WRQ97881.1 showed best binding energy with Kdo (3-Deoxy-D-Manno-Oct-2-ulosonic Acid) (-5.1&#xa0;kcal/mol), WRQ97882.1 with D-glucuronic Acid (-5.5&#xa0;kcal/mol), WUR05396.1 with D-galacturonic Acid (-5.9&#xa0;kcal/mol) and WUR05397.1 with D-galacturonic Acid (-5.8) respectively.&#xa0;</p>

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Molecular modelling and docking of cloned pectin lyases from Fusarium species

  • 期刊论文

  • 发表日期：

    2025年3月11日

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  • Kanchan Yadav,
  • Kavita Patel,
  • Mohan Varghese,
  • Ashutosh Mani,
  • Sangeeta Yadav,
  • Dinesh Yadav

摘要

Pectin lyase (PNL), a key member of the pectinases, employs a distinct β-elimination mechanism to break down pectin polymer into 4,5-unsaturated oligogalacturonides. PNLs have several industrial applications, though predominately preferred in fruit juice processing industries mainly because of their ability to preserve the natural flavour of juice and to avoid the production of highly hazardous methanol as a byproduct. The gene coding for PNL represents multigene families, and several PNL genes have been reported. In the present study, four PNL genes were PCR amplified using genomic DNA of Fusarium proliferatum strain MTCC 9375 and Fusarium fujikuroi strain MTCC 9930 as templates. Further, these were cloned, sequenced, and assigned GenBank accession numbers. Several physico-chemical and structural attributes were assessed using bioinformatics tools. Further, the suitability of the substrate for efficient catalysis, structural rigidity, and stability of the docked complexes was investigated using homology modelling, molecular docking, and molecular dynamics (MD) simulations. The docking results revealed that the WRQ97881.1 showed best binding energy with Kdo (3-Deoxy-D-Manno-Oct-2-ulosonic Acid) (-5.1 kcal/mol), WRQ97882.1 with D-glucuronic Acid (-5.5 kcal/mol), WUR05396.1 with D-galacturonic Acid (-5.9 kcal/mol) and WUR05397.1 with D-galacturonic Acid (-5.8) respectively.