Eph/ephrin signaling pathway

RTK class IX Ephrin receptor family

• Ephrin A3 receptor with peptide substrate, nucleotide derivative and Mg+2 ion. Water molecules are shown as red spheres.
• Nucleotide derivative and Mg+2 ion binding site.
• Peptide substrate binding site (3fxx).

Ephrin Type-A Receptor The extracellular part of Eph receptors includes the N-terminal ephrin (Ligand)-binding domain (LBD), a cysteine-rich domain (CRD), and 2 fibronectin Type-III Repeats (FN3). EphA binds ephrins with its LBD. Most ephrins have a similar rigid structure which includes four loops, AB, CD, FG, & GH. The LBD of EphA4 is said to be a “structural chameleon” able bind both A and B class ephrins. This explains why Ephrin Type-A receptors exhibit cross-class reactivity. The overall structure of the EphA4 LBD includes four important loops, the BC, DE, GH, & JK loops. EphA4 binds the GH loop of the ephrin ligand within a deep pocket created by the EphA4 DE and JK loops. It is these loops, DE and JK, which undergo the greatest conformational shifts when binding either EphrinA2 or EphrinB2. When binding EphrinA2, EphA4-Arg 162 forms a hydrogen bond with EphrinA2-Leu 138, while EphA4-Met 164 and EphA4-Leu 166 participate in hydrophobic interactions with EphrinA2-Leu 138 and EphrinA2-PHe 136. Although EphA4 binds EphrinB2 in the same binding pocket, the local interactions are significantly different. Most notably, the α-helix present in the EphA4-EphrinA2 JK loop is disrupted in the EphA4-EphrinB2 structure. This is due to the steric clash that would occur between EphrinB2-Trp 122 and EphA4 Met 164. Instead, EphA4-Arg 162 and EphrinB2-Trp 122 form hydrophobic stacking interactions among other interactions which stabilize the receptor-ligand complex. A morph of the movements EphA4 undergoes to bind EphrinA2 and EphrinB2 can be seen here.

Eph-Ephrin complexes form two unique heterotetrameric assemblies consisting of distinct EphA2-EphA2 interfaces. The 1st tetrameric form is generated by Eph-Eph interactions only within the LBD. The 2nd tetrameric form involves complex interactions in the LBD and in the region near the CRD.^[1] These two heterotetramers generate a continuous Eph-ephrin assembly when combined (Alternative Coloring). The proximity of kinase domains in an eph-ephrin tetramer, favors transphosphorylation of tyrosines in the cytoplasmic domains. Phosphorylation promotes kinase activity by orienting the activation segment of the kinase domain in a way that favors subsrate binding and subsequent signaling.