Structural studies have shown that NFAT5 binds DNA as a homodimer. Each monomer has two IG-like domains and resembles structurally a Rel Homology Region (RHR), so it is called Rel-like. Obviously, it also shares the most characteristic feature of the Rel way to bind DNA. their loop-DNA interactions.
For a wider explanation of this domains, go to Rel homology domains.
Rel domains are found in NFATs and also in NFkB, but structural comparison by backbone superposition indicates that NFAT5 is more close to NFAT family, which is consistent with identity in the aminoacids sequence: 43% id between NFAT5 and the other NFATs, 25% with p52, the most related NFkB member.
However, there are relevant differences between this protein and the other members of the family: the relative orientation between the N-terminal (N-RHR) and C-terminal (C-RHR) Ig domains in NFAT5 differs drastically from that in NFAT1. While in the NFAT1-Fos-Jun-AP1 complex the C-RHR of NFAT1 is close is adjacent to its N-RHR and makes a small contact to Fos-Jun, the C-RHR of NFAT5 extends away from its N-RHR and makes a large dimer interface with the RHR-C of the other monomer, much like the NFkB dimer-DNA complex.
On the other hand, NFAT5 also differs form NFkB because it has a second dimer interface mediated by the N-RHR domains of the two monomers. This N-terminal dimer interface is on the opposite side of the DNA with respect to the dimer interface of the C-RHR domains. As a result, the NFAT5 dimer forms a complete circle around the DNA.
This relevant features can be observed in the following images, where we show NFAT1-AP1 complex, NFAT5 and, finally, NFkB
The encircled DNA is bound by the TonEBP dimer where the surface potential is relatively positive, as we can see in the next figure, where blue color denotes positive charge.
The inner diameter of the protein ring is larger than the outer diameter of DNA, so the surface of the DNA is not fully contacted by protein around the circle. Instead the DNA is bound to one side of the circle through specific interactions between the N-RHR of the monomer and the TGGAAA half of the NFAT5 site. Nevertheless, the other monomer does not have the consensus sequences in its DNA site and, as a result, the RHR-N binds the non-consensus sequence mostly through contacts to the DNA backbone.
As we have said before, loops are the most important elements in DNA binding, concretely the AB-loop in its N-RHR. The residues Arg217, Arg226, Glu223 and Tyr220 from the AB loop and Gln 364 from the linker between N-RHR and C-RHR interact extensively with DNA in the major groove to specify the base sequence GGAAA. NFAT5 share a conserved Arg (Arg219) with the NFkB proteins (Arg 54 in NF-??B p52). In p53 this residue binds directly DNA, but here it reminds us of the function of His423 in NFAT1-AP1 complex. Thus, the DNA binding mode is closer to NFATs. Moreoever, there is an alpha-helix in the linker connecting C-RHR and N-RHR, short and extended in NFAT5, and contacting the major groove and aling the backbone in NFAT1.