Biochemical characterization and molecular insights into substrate recognition of pectin methylesterase from Phytophthora infestans
Pectin methylesterases (PMEs) are a class of carbohydrate-active enzymes that act on the O6-methyl ester groups of the homogalacturonan component of pectins, resulting in de-esterification of the substrate polymers and formation of pectate and methanol. PMEs occur in higher plants and microorganisms...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-01-01
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| Series: | Computational and Structural Biotechnology Journal |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022004974 |
| _version_ | 1797978160890904576 |
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| author | Rajender Kumar Sanjiv Kumar Vincent Bulone Vaibhav Srivastava |
| author_facet | Rajender Kumar Sanjiv Kumar Vincent Bulone Vaibhav Srivastava |
| author_sort | Rajender Kumar |
| collection | DOAJ |
| description | Pectin methylesterases (PMEs) are a class of carbohydrate-active enzymes that act on the O6-methyl ester groups of the homogalacturonan component of pectins, resulting in de-esterification of the substrate polymers and formation of pectate and methanol. PMEs occur in higher plants and microorganisms, including fungi, oomycetes, bacteria, and archaea. Microbial PMEs play a crucial role in pathogens’ invasion of plant tissues. Here, we have determined the structural and functional properties of Pi-PME, a PME from the oomycete plant pathogen Phytophthora infestans. This enzyme exhibits maximum activity at alkaline pH (8.5) and is active over a wide temperature range (25–50 °C). In silico determination of the structure of Pi-PME reveals that the protein consists essentially of three parallel β-sheets interconnected by loops that adopt an overall β-helix organization. The loop regions in the vicinity of the active site are extended compared to plant and fungal PMEs, but they are shorter than the corresponding bacterial and insect regions. Molecular dynamic simulations revealed that Pi-PME interacts most strongly with partially de-methylated homogalacturonans, suggesting that it preferentially uses this type of substrates. The results are compared and discussed with other known PMEs from different organisms, highlighting the specific features of Pi-PME. |
| first_indexed | 2024-04-11T05:18:31Z |
| format | Article |
| id | doaj.art-880269920ff44ce0b1fe6f1bc3c22d12 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:18:31Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-880269920ff44ce0b1fe6f1bc3c22d122022-12-24T04:55:03ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012060236032Biochemical characterization and molecular insights into substrate recognition of pectin methylesterase from Phytophthora infestansRajender Kumar0Sanjiv Kumar1Vincent Bulone2Vaibhav Srivastava3Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm, SwedenDivision of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm, SwedenDivision of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm, Sweden; College of Medicine and Public Health, Flinders University, Bedford Park Campus, Sturt Road, South Australia 5042, AustraliaDivision of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, 106 91 Stockholm, Sweden; Corresponding author.Pectin methylesterases (PMEs) are a class of carbohydrate-active enzymes that act on the O6-methyl ester groups of the homogalacturonan component of pectins, resulting in de-esterification of the substrate polymers and formation of pectate and methanol. PMEs occur in higher plants and microorganisms, including fungi, oomycetes, bacteria, and archaea. Microbial PMEs play a crucial role in pathogens’ invasion of plant tissues. Here, we have determined the structural and functional properties of Pi-PME, a PME from the oomycete plant pathogen Phytophthora infestans. This enzyme exhibits maximum activity at alkaline pH (8.5) and is active over a wide temperature range (25–50 °C). In silico determination of the structure of Pi-PME reveals that the protein consists essentially of three parallel β-sheets interconnected by loops that adopt an overall β-helix organization. The loop regions in the vicinity of the active site are extended compared to plant and fungal PMEs, but they are shorter than the corresponding bacterial and insect regions. Molecular dynamic simulations revealed that Pi-PME interacts most strongly with partially de-methylated homogalacturonans, suggesting that it preferentially uses this type of substrates. The results are compared and discussed with other known PMEs from different organisms, highlighting the specific features of Pi-PME.http://www.sciencedirect.com/science/article/pii/S2001037022004974Pectin methylesterasesPhytophthora infestansOomycetePotato late blightMolecular simulation |
| spellingShingle | Rajender Kumar Sanjiv Kumar Vincent Bulone Vaibhav Srivastava Biochemical characterization and molecular insights into substrate recognition of pectin methylesterase from Phytophthora infestans Computational and Structural Biotechnology Journal Pectin methylesterases Phytophthora infestans Oomycete Potato late blight Molecular simulation |
| title | Biochemical characterization and molecular insights into substrate recognition of pectin methylesterase from Phytophthora infestans |
| title_full | Biochemical characterization and molecular insights into substrate recognition of pectin methylesterase from Phytophthora infestans |
| title_fullStr | Biochemical characterization and molecular insights into substrate recognition of pectin methylesterase from Phytophthora infestans |
| title_full_unstemmed | Biochemical characterization and molecular insights into substrate recognition of pectin methylesterase from Phytophthora infestans |
| title_short | Biochemical characterization and molecular insights into substrate recognition of pectin methylesterase from Phytophthora infestans |
| title_sort | biochemical characterization and molecular insights into substrate recognition of pectin methylesterase from phytophthora infestans |
| topic | Pectin methylesterases Phytophthora infestans Oomycete Potato late blight Molecular simulation |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022004974 |
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