title: In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour.
abstract: BACKGROUND
  DNA double-strand breaks (DSBs) are highly cytotoxic and mutagenic. MRE11 plays an essential role in repairing DNA by cleaving broken ends through its 3' to 5' exonuclease and single-stranded DNA endonuclease activities.
  
  
  METHODS
  The present study aimed to in silico characterization and molecular modeling of MRE11 from Phoenix dactylifera L cv deglet nour (DnMRE11) by various bioinformatic approaches. To identify DnMRE11 cDNA, assembled contigs from our cDNA libraries were analysed using the Blast2GO2.8 program.
  
  
  RESULTS
  The DnMRE11 protein length was 726 amino acids. The results of HUMMER show that DnMRE11 is formed by three domains: the N-terminal core domain containing the nuclease and capping domains, the C-terminal half containing the DNA binding and coiled coil region. The structure of DnMRE11 is predicted using the Swiss-Model server, which contains the nuclease and capping domains. The obtained model was verified with the structure validation programs such as ProSA and QMEAN servers for reliability. Ligand binding studies using COACH indicated the interaction of DnMRE11 protein with two Mn(2+) ions and dAMP. The ConSurf server predicted that residues of the active site and Nbs binding site have high conservation scores between plant species.
  
  
  CONCLUSIONS
  A model structure of DnMRE11 was constructed and validated with various bioinformatics programs which suggested the predicted model to be satisfactory. Further validation studies were conducted by COACH analysis for active site ligand prediction, and revealed the presence of six ligands binding sites and two ligands (2 Mn(2+) and dAMP).
authors.affiliation: Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax, Tunisia. imenbmc@yahoo.fr.
authors.forename: Imen
authors.initials: I
authors.lastname: Rekik
authors.affiliation: Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax, Tunisia.
authors.forename: Zayneb
authors.initials: Z
authors.lastname: Chaabene
authors.affiliation: Leibniz Institute of Plant Biochemistry, Halle, Germany.
authors.forename: C Douglas
authors.initials: CD
authors.lastname: Grubb
authors.affiliation: Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax, Tunisia.
authors.forename: Noureddine
authors.initials: N
authors.lastname: Drira
authors.affiliation: High Institute of Applied Biology of Medenine, Medenine, Tunisia.
authors.forename: Foued
authors.initials: F
authors.lastname: Cheour
authors.affiliation: Laboratory of plant biotechnology, Faculty of sciences of Sfax, University of Sfax, Sfax, Tunisia.
authors.forename: Amine
authors.initials: A
authors.lastname: Elleuch
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair; D008958:Models, Molecular; D005810:Multigene Family; D065749:Phoeniceae / Q000737:chemistry*; D010940:Plant Proteins / Q000737:chemistry* / Q000235:genetics; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D010940:Plant Proteins