The Janus Kinase (JAK) FERM and SH2 Domains: Bringing Specificity to JAK-Receptor Interactions

Abstract

The Janus kinases (JAKs) are non-receptor tyrosine kinases essential for signaling in response to cytokines and interferons and thereby control many essential functions in growth, development, and immune regulation. JAKs are unique among tyrosine kinases for their constitutive yet non-covalent association with class I and II cytokine receptors, which upon cytokine binding bring together two JAKs to create an active signaling complex. JAK association with cytokine receptors is facilitated by N-terminal FERM and SH2 domains, both of which are classical mediators of peptide interactions. Together, the JAK FERM and SH2 domains mediate a bipartite interaction with two distinct receptor peptide motifs, the proline-rich "Box1" and hydrophobic "Box2," which are present in the intracellular domain of cytokine receptors. While the general sidechain chemistry of Box1 and Box2 peptides is conserved between receptors, they share very weak primary sequence homology, making it impossible to posit why certain JAKs preferentially interact with and signal through specific subsets of cytokine receptors. Here, we review the structure and function of the JAK FERM and SH2 domains in light of several recent studies that reveal their atomic structure and elucidate interaction mechanisms with both the Box1 and Box2 receptor motifs. These crystal structures demonstrate how evolution has repurposed the JAK FERM and SH2 domains into a receptor-binding module that facilitates interactions with multiple receptors possessing diverse primary sequences.

Keywords: FERM; Interferon; JAK1; JAK2; JAK3; Janus kinase; SH2; TYK2.

Figure 1

Comparison of Janus kinase (JAK) FERM/SH2 domains. (A) Cartoon depiction of a JAK FERM and SH2 module bound to a receptor, illustrating receptor recognition principles discovered in recent crystal structures, followed by representations of crystal structures solved for (B) TYK2 (PDB ID 4PO6), (C) JAK1 (PDB ID 5L04), and (D) JAK2 (PDB ID 4Z32). The F1, F2, and F3 FERM subdomains are colored in various shades of orange, green, and blue, respectively. SH2 domains are colored in various shades of pink. Linkers L1, L2, and L3 are colored in various shades of gray. The IFNAR1 receptor peptide is colored blue, and the IFNLR1 is in yellow.

Figure 2

Comparison of Janus kinase (JAK) and ERM family FERM domains. (A) Comparison of the FERM F2 subdomains of TYK2 (orange) and radixin (blue, PDB ID 1GC7). TYK2 and radixin F2 domains were superposed in PyMol with a root-mean-square deviation of 2.98 Å over 545 atoms. (B) Comparison of the F3 subdomains of JAK2 (top left, teal), JAK1 (top right, green), TYK2 (bottom left, orange), and radixin (bottom right, blue, PDB ID 1GC7).

Figure 3

Detailed views of the interactions between TYK2–IFNAR1 Box2 and JAK1 IFNLR1 Box1. (A) Overview of the interaction between TYK2 FERM and SH2 (colored as in Figures 1A,B) domains in complex with the IFNAR1 Box2 region (left, PDB ID 4PO6). Detailed interactions are shown for three regions of the TYK2–IFNAR1 complex (right panels). In the N-terminal tri-leucine region, Leu490, Leu491, and Leu492 of IFNAR1 pack against a hydrophobic groove between the TYK2 F1 (tan), L1 (gray), and F2 (orange) domains (top panel). In the center of the interaction, Glu497 of IFNAR1 forms hydrogen bonds with Ser476 and Thr477 (middle panel). At the C-terminus of IFNAR1, Cys502 and Ile504 insert into a groove between the β-G1/2 hairpin and EF loop of the TYK2 SH2 domain (bottom panel). (B) Overview of the bipartite interaction between JAK1 FERM and SH2 (colored as in Figure 1C) domains in complex with the IFNLR1 Box1 region (left, 5IXD). Detailed interactions are shown for two regions of the JAK1–IFNLR1 complex (right panels). At the first site, IFNLR1 residue Trp257 inserts itself into a groove between JAK1 F2-α2 and F2-α3 (top panel). At the second site, hydrophobic residues Pro264, Leu267, and Phe269 of IFNLR1 pack into a groove formed by JAK1 F2-α2, F2-α3, and F2-α4 (bottom panel).

Figure 4

Alignment of Box1 and Box2 motifs from Janus kinase (JAK)-interacting cytokine receptors. The juxtamembrane intracellular sequences from all known signaling receptors that interact with JAKs were aligned by their Box1 proline motifs. Receptors are grouped by class I and class II, followed by subgroupings by either the JAK they interact with (class II) or by subfamily (class I). Due to the low sequence homology between receptors, the alignments were produced by hand, and the residues colored in order to highlight some of the shared features of the receptors. Hydrophobic residues within the Box1 region are colored in blue and prolines in yellow. For the Box2 region, putative four-residue hydrophobic motifs (aliphatic-X-aliphatic-X) are colored in blue, with glutamate residues three to seven residues N-terminal to these motifs are colored in purple. Receptors with known structures (IFNAR1, IFNLR1, and IL10RA) are marked with a star.

Figure 5

JAK1 and TYK2 recognize the Box2 motif via a conserved mechanism. (A) Cartoon representation of JAK1 (colored as in Figure 1C) bound to IFNLR1 receptor peptide (yellow) containing both the Box1 and Box2 motifs (PDB ID 5L04). For comparison, the IFNLR1 Box1 motif (orange) and the IFNAR1 Box2 (blue) are shown after superposition of JAK1 and TYK2, respectively. (B) Detailed comparison of the pTyr/Glu binding pocket of the TYK2 (PDB ID 4PO6), JAK1, and SHP-2 (PDB ID 1AYA) SH2 domains. TYK2 (left) contains a histidine residue (H474) at the base of the pocket, while JAK1 and SHP-2 have an arginine at this position that forms a salt bridge with either the glutamate in IFNLR1 or phosphate group in the PDGF receptor peptide. (C) Detailed comparison of the Box2 binding groove of TYK2, JAK1, and JAK2. IFNAR1 residues Cys502 and Ile504 pack into a groove in the TYK2 SH2 domain between the β-G1/2 hairpin and EF loop (left). In the JAK1/IFNLR1 structure, Leu290 and Leu292 pack into this groove (center). The SH2 domain of JAK2 (PDB ID 4Z32) maintains this conformation in the absence of receptor (right).

Figure 6

Janus kinases (JAKs) use conserved surfaces to mediate receptor interactions. (A) CONSURF analysis (55) of a ClustalO alignment of 245 JAK homologs projected onto the surface of JAK1 (PDB ID 5L04). Less conserved residues are colored in green, highly conserved residues are colored purple. IFNLR1 (yellow) shown to illustrate highly conserved residues at receptor-binding surface. (B) Superposition of JAK1 (green, PDB ID 5IXD) and JAK2 (cyan, PDB ID 4Z32) with a root-mean-square deviation of 1.17 Å over 1,119 atoms to illustrate shift in position of the F2-α3 and F2-α2″ helices in JAK2.