Structural and Energetic Evidence Supports the Non-Covalent Phosphate Cyclization by the Class II Phospholipase D from Loxosceles intermedia

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Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorFederal University of Rio Grande do Sul (UFRGS)-
Autor(es): dc.contributorFederal University of Health Sciences of Porto Alegre (UFCSPA)-
Autor(es): dc.contributorUniversidade Federal do Paraná (UFPR)-
Autor(es): dc.creatorGismene, Carolina-
Autor(es): dc.creatorRuggiero Bachega, José Fernando-
Autor(es): dc.creatorDoherty, Daniel Z.-
Autor(es): dc.creatorVeiga, Silvio Sanches-
Autor(es): dc.creatorArni, Raghuvir K.-
Autor(es): dc.creatorHernández González, Jorge Enrique-
Data de aceite: dc.date.accessioned2025-08-21T22:53:24Z-
Data de disponibilização: dc.date.available2025-08-21T22:53:24Z-
Data de envio: dc.date.issued2025-04-29-
Data de envio: dc.date.issued2025-03-01-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.3390/toxins17030111-
Fonte completa do material: dc.identifierhttps://hdl.handle.net/11449/304897-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/304897-
Descrição: dc.descriptionPhospholipase D (PLD) enzymes from Loxosceles spider venom mediate envenomation pathology by cleaving phospholipid headgroups. We revisited the crystal structure of Loxosceles intermedia PLD (PDB: 3RLH) to evaluate two alternative mechanisms—covalent and non-covalent—for headgroup cleavage. The covalent mechanism involves a nucleophilic attack on the substrate’s P atom by catalytic histidine, forming a phosphohistidine intermediate. It was originally suggested that this intermediate hydrolyzes, leading to linear phosphates. The non-covalent mechanism relies on the substrate’s hydroxyl group performing an intramolecular attack on the P atom, thereby generating a cyclic phosphate. Structural refinement of the crystal structure revealed a cyclic phosphate bound at the active site, replacing previously assigned PEG molecules. This cyclic product, stabilized by His12, His47, and Mg2+, provides structural evidence that supports phosphate cyclization. The results of computational analyses, including molecular dynamics and quantum mechanics/molecular mechanics simulations, further support the non-covalent mechanism as the energetically preferred pathway, with a significantly lower activation barrier. Our findings highlight the role of substrate orientation and of the catalytic His residues in transphosphatidylation, advancing our understanding of PLD enzymology and providing insights for the design of inhibitors against Loxosceles envenomation.-
Descrição: dc.descriptionBiological Structures Group Multiuser Center for Biomolecular Innovation (CMIB) São Paulo State University—UNESP, SP-
Descrição: dc.descriptionGraduate Program in Molecular and Cellular Biology Federal University of Rio Grande do Sul (UFRGS), Porto Alegre CEP 90050-170, RS-
Descrição: dc.descriptionDepartament of Farmacosciences Federal University of Health Sciences of Porto Alegre (UFCSPA), Porto Ale-gre, RS-
Descrição: dc.descriptionDepartment of Cell Biology Federal University of Paraná (UFPR), Curitiba CEP, PR-
Descrição: dc.descriptionBiological Structures Group Multiuser Center for Biomolecular Innovation (CMIB) São Paulo State University—UNESP, SP-
Idioma: dc.languageen-
Relação: dc.relationToxins-
???dc.source???: dc.sourceScopus-
Palavras-chave: dc.subjectcatalytic mechanism-
Palavras-chave: dc.subjectcrystal structure-
Palavras-chave: dc.subjectcyclic phosphate-
Palavras-chave: dc.subjectLoxosceles-
Palavras-chave: dc.subjectphospholipase D-
Palavras-chave: dc.subjectspider venom-
Título: dc.titleStructural and Energetic Evidence Supports the Non-Covalent Phosphate Cyclization by the Class II Phospholipase D from Loxosceles intermedia-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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