br The DDR kinase domain
The DDR1 kinase domain The DDR1 intracellular kinase domain shares the typical structure of other kinase domains (Fig. 1). However, how DDR1 kinase is activated upon collagen binding is poorly understood. It is thought that the process is fundamentally different from the accepted paradigm of ligand-induced RTK dimerization. Unlike typical RTKs, DDR1 exists as a preformed dimer and, following collagen binding, undergoes receptor oligomerization and internalization, and is phosphorylated unusually slowly. A recent study showed that collagen binding to DDR1 fails to induce a major conformational change that could explain kinase activation, and instead proposed that collagen-induced receptor oligomerization might be responsible for kinase activation . In support of this hypothesis, events that reduce receptor oligomerization, such as sodium ion channel that bind to DS-like domain or enforced covalent receptor dimerization at residues within the DS-like domain, reduce DDR1 phosphorylation and activation. However, mutation of Asn211, a conserved glycosylation site within the DS-like domain, results in ligand-independent activation of DDR1, enhanced receptor dimerization, and internalization, suggesting that, in addition to receptor clustering, ligand-induced internalization may also contribute to receptor activation . Collagen binding to DDR1 induces a slow receptor tyrosine autophosphorylation of multiple tyrosine residues, including Tyr792, Tyr796, and Tyr797, in the activation loop, which likely causes the kinase domain to switch from the inactive to the active state . The active state satisfies chemical restraints that allow the transfer of the γ-phosphate of ATP to the hydroxyl group of tyrosine on the loop, which enables recruitment of substrate proteins. Here, we refer to the residues of the DDR1 kinase domain [Protein Data Bank (PDB): 3ZOS] in relation to their corresponding residues in protein kinase A (PKA, PDB: 1ATP) and the kinase domain of Abl tyrosine kinase (PDB: 3QRK). Positions indicated in italics and normal in square brackets are PKA and Abl kinase residue numbers, respectively, equivalent to those in DDR1.
Kinase domain structure and important residues The tyrosine kinase domain comprises an N-terminal (N-lobe) and a C-terminal (C-lobe) lobe . Fig. 1a shows the kinase domain of DDR1 (PDB: 3ZOS) . The N-lobe comprises a five-stranded β-sheet and a prominent α-helix, called αC helix, whereas the C-lobe is mostly helical . The ATP binding pocket lies in the cleft between the two lobes and sits beneath a highly conserved glycine-rich loop, which is between the β1 and β2 strands  (Fig. 1a). In the active conformation (Fig. 1b), this loop positions the γ-phosphate of ATP for catalysis and a conserved valine, Val624 [Val57, Val254] makes a hydrophobic contact to the base of ATP. As with other domains, the DDR1 kinase domain contains the highly conserved DFG and HRD (YRD in case of PKA) motifs on the activation and catalytic loops, respectively. Asp784 [Asp184, Asp381] of the Asp-Phe-Gly (DFG) motif forms polar contacts with all three ATP phosphates. The phenylalanine of Asp784-Phe785-Gly786 [Asp184-Phe185-Gly186, Asp381-Phe382-Gly383] makes hydrophobic contacts with the Met676 [Leu95, Met290] of the αC helix and the histidine of the conserved His764-Arg765-Asp766 [Tyr164-Arg165-Asp166, His361-Arg362-Asp363] motif. The His-Arg-Asp (HRD) motif of DDR1 and Abl [Tyr-Arg-Asp (YRD) in PKA] is part of the ‘activation loop’ that provides a platform for peptide substrate binding. Phosphorylation of tyrosine residues within the activation loop is required to support a configuration that enables binding and phosphorylation of substrate protein. A conserved glutamate residue Glu672 [Glu91, Glu286] located on the αC helix forms an ion pair with the Lys655 [Lys72, Lys271] side chain that coordinates the α- and β-phosphates of ATP. In several active kinases, αC makes direct contact with N-terminal region of activation loop, with its conformation often linked to the DFG motif. Although there is no experimental structure of DDR1 in its active conformation, it is expected that this feature is preserved.