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The ''LFY'' gene encodes a 424 amino acids protein that containing two domains. The N-terminal domain of LFY has been proved mediating homodimerization (ref) and it is also thought to be responsible for  transcriptional activation <ref name="Weigel1992" /><ref name="Coen1990" />. The C-terminal consensus is highly conserved among land species and functioning as DNA-binding domain. Two DNA-protein binding structure for LEAFY were first published by Hame et al.  2008. These two structures include a recombinant C-terminal domain of LEAFY expressed by ''Escherichia coli'' strain RosettaBlue (DE3) and a short nucleotide structure from AP1 or AG promoter region. Final models of LFY-pAP1 and LFY-pAG were solved at 2.1 Å and 2.3 Å by X-ray diffraction and deposited as PDB entry <scene name='57/579703/2vy1/1'>2VY1</scene>/<scene name='57/579703/2vy2/1'>2VY2</scene>.  

=== Site specific DNA recognition is conducted by a HTH-like motif ===

The general structure of LEAFY DNA binding domain consists 2 <scene name='57/579703/Beta-strand/1'>β strands</scene> at the beginning followed by 7 <scene name='57/579703/Alpha-helices_color/2'> α helices</scene>. A <scene name='57/579703/Alpha-helices_color/3'>helix-turn-helix</scene> (HTH) motif can be found between α2 and  α3 helices, which is recruited to the <scene name='57/579703/Major_groove/2'>major groove </scene>of the binding DNA. There are two amino acid at this motif, <scene name='57/579703/Major_groove_asn291/1'>Asn 291</scene> on α2 and <scene name='57/579703/Major_groove_asn291/2'>Lys 307</scene> on α3 directly mediate site specific recognition with <scene name='57/579703/Major_groove_detail/1'>two guanines</scene> at the DNA strand. These two recognition sites were further validated by electrophoresis mobility shift assay (EMSA): mutation at either Asn 291 or Lys 307 dramatically decrease binding affinity to pAP1. In the minor groove, site specific recognition is conducted by <scene name='57/579703/Arg_237/1'>Arg 237</scene>, which is at the beginning of this structure. ''Arabidopsis'' intermediate mutant ''lfy-4'' (P240L) and ''lfy-5'' (T244M) were located near this site and validate the function ''in planta''<ref name="Weigel1992" />. The super position of specific recognition sites is summaries at figure 2.   

=== DNA binding required cooperative dimerization ===

Transcription factors tent to form homodimer or heterodimer to increase the binding specificity and affinity. Experimental evidence indicates a potential LFY dimer on the binding site. Crystal structure proved that LFY can form dimers at both <scene name='57/579703/Ap1-dimer/2'>pAP1</scene> and <scene name='57/579703/2vy2_assembly/2'>pAG</scene> sites. The binding affinity of LFY protein dimer binds increased by 90-fold compared to the first LFY monomer in EMSA assay. Detailed structure revealed that the contact of two dimerized protein is mediated by <scene name='57/579703/Ap1-dimer/8'>three residues</scene> located at on helix (<scene name='57/579703/Ap1-dimer/3'>α7</scene>) and one loop (<scene name='57/579703/Ap1-dimer/4'>loop12</scene>) at the other protein. Hydrogen bonds can be formed between <scene name='57/579703/Ap1-dimer/7'>Asp 280</scene> and <scene name='57/579703/Ap1-dimer/5'>His 387</scene>/<scene name='57/579703/Ap1-dimer/6'>Arg 390</scene> are essential for this dimeriation. The detailed interaction is shown in figure 3 produced by Pymol. Mutation in any of these three amino acids abolished the binding in EMSA assay. Recently, another experiment showing that besides these three residues, the entire N-terminal consensus is critical important for stabilizing the homodimerization, where strong physical interaction can be found by GST-pull down, Y2H and BiFC experiment at ''in vitro'', ''in vivo'' and ''in planta'' level <ref name= ''Siriwardana2012'' > Siriwardana, N. S. & Lamb, R. S. 2012. A conserved domain in the N-terminus is important for LEAFY dimerization and function in Arabidopsis thaliana. The Plant Journal 71: 736–749. http://dx.doi.org/10.1111/j.1365-313X.2012.05026.x8</ref> .