Ethylene is an endogenous plant hormone that influences many aspects of plant growth and development. Some defense related genes that are induced by ethylene were found to contain a cis-regulatory element known as the Ethylene-Responsive Element (ERE) [1]. Sequence analysis on various ERE regions identified a short motif rich in G/C nucleotides, the GCC-box, essential for the response to ethylene. This short motif is recognized by a family of transcrition factors, the ERE binding factors (ERF) [2,3].

ERF proteins contain an about 60 amino acid region which is also found in the APETALA2 (AP2) protein, the AP2/ERF domain [4]. It has been shown in various proteins that the AP2/ERF domain is necessary and sufficient to bind GCC-box [5].

The structure of the AP2/ERF domain in complex with the target DNA has been solved (see <PDB:1GCC>) [6]. The structure resemble that of bacteriophage integrases and the methyl-CpG-binding domain (MBD) (see <PDOC50982>): a three-stranded β-sheet and an α helice almost parallel to the β-sheet. It contacts DNA via Arg and Trp residues located in the β-sheet.

Some proteins known to contain an AP2/ERF domain are listed below:

• Arabidopsis thaliana ERF1 to 6.
• Tobacco ethylene-responsive element-binding proteins (EREBPs), homologues of ERFs proteins.
• Arabidopsis thaliana AP2 protein. It regulates meristeme identity, floral organ specification and seed coat development.
• Arabidopsis thaliana C-repeat/dehydration-responsive element (DRE) binding factor 1 (CBF1 or DREB1) and DREB2. They bind a GCC-box-like element found in dehydratation responsive element. Binding to this element mediates cold-inducible transcription.
• Arabidopsis thaliana and maize abscisic acid (ABA)-insensitive 4 (ABI4) proteins. They bind to a GCC-box-like element found in ABA-responsive genes.
• Octadecanoid-derivative responsive catharenthus AP2-domain (ORCA2) protein. It binds a GCC-box-like element in the jasmonate responsive element of Str promoter.
• Tomato Pto-interacting proteins 4 to 6 (Pti4 to Pti6). Pti5 and 6 bind a GCC-box-like element in regulatory regions of various pathogenesis-related (PR) genes.
• Trichodesmium erythraeum, Tetrahymena thermophila, Enterobacteria phage RB49 and bacteriophage Felix 01 HNH endonucleases. HNH endonucleases are homing endonucleases that move extensively via lateral gene transfer [7].

The profile we developed covers the whole AP2/ERF domain.