Structural Modeling and Functional Evaluation of Pectate Lyase Protein from Prunus armeniaca

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dc.contributor.authorAkbulut, Gulcin Beker
dc.date.accessioned2026-06-19T06:41:12Z
dc.date.available2026-06-19T06:41:12Z
dc.date.issued2023
dc.departmentMalatya Turgut Özal Üniversitesi
dc.description.abstractPrunus armeniaca (P. armeniaca) is a stone fruit that is widely consumed around the world with its appealing and delicious taste. Pectate lyases (Pels) cleave the alpha-1,4-glycosidic bond of polygalacturonic acid. Pels have a role in the development, ripening, and in providing intracellular entry by disrupting the integrity of the cell wall of pathogenic microorganisms. The three-dimensional structures of proteins and enzymes provide important data on their functional properties and catalytic roles. The protein structure of any Prunus is unknown. In this study, P. armeniaca protein homology models were modeled using ProMod3 and trRosetta deep learning algorithms in order to elucidate the molecular mechanism of ripening and cell wall degradation processes in which pectate lyase (Pel) plays a role. Substrate binding patterns were demonstrated by molecular docking. The (Pel) homology models from P. armeniaca were within x-ray quality limits. The three-dimensional structure of P. armeniaca pectate lyase (PaPel) has been shown to have an unusual beta-folding formation that we have encountered in other Pels. We determined that (RXPXXR302)-R-297 and (WIDH233)-W-230 residues preserved in known Pels were preserved in Pel from P. armeniaca. The (NVHI171)-N-168 and (NVHI192)-N-189 repeat sites in the vicinity of the catalytic site may be responsible for substrate stability. The lowest binding energy for the substrate was -4.18 kcal.mol(-1). The data presented in this study may provide an important model for elucidating the catalytic mechanism of development, ripening, and cell wall destruction processes of Prunus Pel.
dc.identifier.doi10.1007/s10341-023-00854-3
dc.identifier.endpage477
dc.identifier.issn0014-0309
dc.identifier.issn1439-0302
dc.identifier.issue3
dc.identifier.scopus2-s2.0-85149968102
dc.identifier.scopusqualityQ2
dc.identifier.startpage469
dc.identifier.urihttps://doi.org/10.1007/s10341-023-00854-3
dc.identifier.urihttps://hdl.handle.net/20.500.12899/6123
dc.identifier.volume65
dc.identifier.wosWOS:000948746700002
dc.identifier.wosqualityQ3
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.institutionauthorAkbulut, Gulcin Beker
dc.language.isoen
dc.publisherSpringer
dc.relation.ispartofErwerbs-Obstbau
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanı
dc.rightsinfo:eu-repo/semantics/closedAccess
dc.snmzKA_WOS_20260612
dc.subjectPrunus
dc.subjectHomology Model
dc.subjectApricot
dc.subjectTertiary Structure
dc.subjectPhylogenomics
dc.titleStructural Modeling and Functional Evaluation of Pectate Lyase Protein from Prunus armeniaca
dc.typeArticle

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