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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).    Electronic supplementary material  The online version of this article (doi:10.1186/s12976-015-0013-2) contains supplementary material, which is available to authorized users.

In silico characterization and Molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour