Isolation of a transcription factor DREB1A gene from Phaseolus vulgaris and computational insights into its characterization: protein modeling, docking and mutagenesis

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dc.contributor.authorVatansever, Recep
dc.contributor.authorUras, Mehmet Emin
dc.contributor.authorŞen, Uğur
dc.contributor.authorÖzyiğit, İbrahim İlker
dc.contributor.authorFiliz, Ertuğrul
dc.date.accessioned2020-04-30T23:18:47Z
dc.date.available2020-04-30T23:18:47Z
dc.date.issued2017
dc.departmentDÜ, Çilimli Meslek Yüksekokulu, Bitkisel ve Hayvansal Üretim Bölümüen_US
dc.descriptionOzyigit, Ibrahim Ilker/0000-0002-0825-5951en_US
dc.descriptionWOS: 000418477200010en_US
dc.descriptionPubMed: 27687894en_US
dc.description.abstractA transcription factor DREB1A (dehydration-responsive element-binding 1A) gene was amplified and sequenced from the common bean (Phaseolus vulgaris). PvDREB1A had a 777 base pairs (bp) open reading frame encoding a protein of 225 residues. The protein sequence contained a conserved DNA-binding AP2 domain of about 60 residues and a nuclear localization signal (NLS) at N-terminus site. PvDREB1A demonstrated high homology with other DREB1 members only in AP2 domain and NLS site. The phylogenetic distribution of different DREB members showed three main groups as DREB1-3 and PvDREB1A was a member of DREB1 group. Homology modeling and secondary structure analyses revealed that PvDREB1A AP2 domain was packed into the three-stranded antiparallel beta sheets (beta 1-3) and an alpha helix (alpha 1) almost parallel to these beta sheets. Moreover, DNA-binding AP2 domain of PvDREB1A and GCC-box containing double helix DNA were docked. The docking analysis showed that PvDREB1A AP2 domain could bind to the major groove of the DNA by three-stranded antiparallel beta sheets, with residues Gly86 or Thr87 in beta 1-sheet and Arg63 or Arg64 in beta 3-sheet. The docked complex also indicated that AP2 domain has a preferential for the binding of GCC stretches in the double helix DNA. A total of 36 reliably estimated hot spots residues were identified with high mutability grade but none of these residues was essential for the protein function since they are located at outside the DNA-binding AP2 domain of PvDREB1A.en_US
dc.identifier.doi10.1080/07391102.2016.1243487en_US
dc.identifier.endpage3118en_US
dc.identifier.issn0739-1102
dc.identifier.issn1538-0254
dc.identifier.issue14en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.startpage3107en_US
dc.identifier.urihttps://doi.org/10.1080/07391102.2016.1243487
dc.identifier.urihttps://hdl.handle.net/20.500.12684/3526
dc.identifier.volume35en_US
dc.identifier.wosWOS:000418477200010en_US
dc.identifier.wosqualityQ2en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakPubMeden_US
dc.indekslendigikaynakScopusen_US
dc.language.isoenen_US
dc.publisherTaylor & Francis Incen_US
dc.relation.ispartofJournal Of Biomolecular Structure & Dynamicsen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjecttranscription factoren_US
dc.subjectDREBen_US
dc.subjectAP2 domainen_US
dc.subjecthomology modelingen_US
dc.subjectdockingen_US
dc.titleIsolation of a transcription factor DREB1A gene from Phaseolus vulgaris and computational insights into its characterization: protein modeling, docking and mutagenesisen_US
dc.typeArticleen_US

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