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Molecular dynamics simulations reveal the disparity in specific recognition of GCC‐box by AtERFs transcription factors super family in Arabidopsis

Arabidopsis ethylene responsive element binding factors (AtERFs) form a transcription factor super family. While the functions of most AtERFs are unknown, a number of AtERFs appear to be involved in regulation of stress‐related genes through their DNA binding domains (DBD), namely ERF domains, which recognize a consensus motif GCC‐box at the regulatory region. In this study, molecular dynamics simulations were performed on the four ERF domain‐GCC‐box complexes, AtERF1, AtERF4, AtEBP and CFBF1, to determine disparity in specific binding to the GCC‐box by the AtERFs. Our results suggested that three amino acid residues Arg29, Glu39 and Arg41, played a vital role in direct readout of DNA. The position of the consensus sequence GCCGCC has an intrinsic disparity on binding with ERF domains. The third C, fourth G and the last C in the GCC motif was compulsory for recognition by ERF domains. Our results provide structural evidence for a sequence‐dependent recognition mechanism for AtERFs. Copyright © 2009 John Wiley & Sons, Ltd.