Non-Receptor Tyrosine Kinases: Their Structure and Mechanistic Role in Tumor Progression and Resistance

Abstract

Protein tyrosine kinases (PTKs) function as key molecules in the signaling pathways in addition to their impact as a therapeutic target for the treatment of many human diseases, including cancer. PTKs are characterized by their ability to phosphorylate serine, threonine, or tyrosine residues and can thereby rapidly and reversibly alter the function of their protein substrates in the form of significant changes in protein confirmation and affinity for their interaction with protein partners to drive cellular functions under normal and pathological conditions. PTKs are classified into two groups: one of which represents tyrosine kinases, while the other one includes the members of the serine/threonine kinases. The group of tyrosine kinases is subdivided into subgroups: one of them includes the member of receptor tyrosine kinases (RTKs), while the other subgroup includes the member of non-receptor tyrosine kinases (NRTKs). Both these kinase groups function as an "on" or "off" switch in many cellular functions. NRTKs are enzymes which are overexpressed and activated in many cancer types and regulate variable cellular functions in response to extracellular signaling-dependent mechanisms. NRTK-mediated different cellular functions are regulated by kinase-dependent and kinase-independent mechanisms either in the cytoplasm or in the nucleus. Thus, targeting NRTKs is of great interest to improve the treatment strategy of different tumor types. This review deals with the structure and mechanistic role of NRTKs in tumor progression and resistance and their importance as therapeutic targets in tumor therapy.

Keywords: Abl; Ack; Csk; Fak; Fes; Jak; NRTKs; PTK; Src; Syk kinases; Tec.

Figure 1

Structure of non-receptor tyrosine kinase families and their functional domains. Non-receptor tyrosine kinases (NRTKs) including Ack, Jak, Fes, Fak, Tec, Src, Csk, Abl, and Syk kinases. NRTKs consist of a single protein with N- and C-terminal regions. The N-terminus contains a kinase domain, which extends over approximately 300 residues, while the N-terminus of NRTKs is larger than the N-terminus. The structure and the functional domains and regions of different members of NRTKs include the following: Src homology (SH) domains that are referred to as SH4, SH3, SH2, and catalytic SH1 domains, the Pleckstrin homology (PH), four-point-one, ezrin, radixin, moesin (FERM), the Janus homology 2 (JH2) domain, and the Fes/Fer/Cdc-42-interacting protein homology (FCH) domains, Bruton’s tyrosine kinase (Btk)-like zinc finger, the coiled-coil motifs (CC), and proline-rich region (pr). The Cdc42/Rac-interactive (CRIB) domains, DNA-binding domains (DNA), action-binding domain, and a focal adhesion targeting domain (FAT).

Figure 2

An overview of the domain organization of Ack1. The different structural domains of Ack1 are shown. These domains include the sterile alpha motif (SAM); the nuclear transport signal (NES); catalytic kinase domain (Cat. K. domain); Src homology domain 3 (SH3); Cdc42; Rac-interactive binding domain (CRIB); Cdc42 binding domain (CB); CL, clathrin-binding domain (CB), proline-rich region, Mig6 homology region (MHR); UBA, ubiquitin association domain (UBA).

Figure 3

Structure and functional domains of JAKs. Each member of the JAKs (JAK1, JAK2, JAK3, and TYK2) consists of seven homology domains (JH) organized into four different domains, including the kinase domain that constitutes the JH1, the pseudo domain that constitutes JH2, the Src homology2 (SH2) that constitutes both JH3 and JH4, and the four-point-one, ezrin, radixin, and moesin (FERM) domain that constitutes JH5, JH5, JH6, and JH7. The phosphorylation of JAK1 occurs at Tyr¹⁰³⁸/Tyr¹⁰³⁹ residues; the phosphorylation of JAK2 occurs at -Tyr¹⁰⁰⁷/Tyr¹⁰⁰⁸; the phosphorylation of JAK3 occurs at Tyr⁹⁸⁰/Tyr⁹⁸¹ residues; and the phosphorylation of Tyk2 occurs at Tyr1054/Tyr1055 residues.

Figure 4

Structure and functional domains of FES/FER kinases. FES and FER share a similar domain organization, including F-Bin–Amphiphysin–Rvs (F-BAR), F-BAR extension (FX), Src homology2 (SH2), and protein tyrosine kinase (PTK) domains. Fes is structured as a dimer mediated by its F-BAR domain that can exist in higher-order oligomers. The N-terminal domain of Fes is to repress its kinase activity, which can be attenuated by proline insertion mutations, leading to the destruction of oligomerization. As a consequence, the repressed Fes oligomer undergoes significant conformation via the interaction of the F-BAR domain with the phosphatidylinositol 4,5-bisphosphate or FX domain binding to phosphatidic acid, which can be produced by phospholipase D. Accordingly, Fes more readily interacts with SH2 ligands, which leads to kinase activation via the SH2–PTK interface.

Figure 5

(A) Structure of focal adhesion kinase (FAK) and its homologous FAK-related proline-rich tyrosine kinase 2 (Pyk2). Both FAK and PyK2 kinases consists of three domains, including the four-point-one, ezrin, radixin, and moesin (FERM) that is divided into three subdomains, referred to as F1, F2, and F3, central kinase domain, and focal adhesion targeting (FAT) domain. Both FAK and Pyk2 kinases contain a nuclear localization sequence (NLS) and a nuclear export sequence (NES) in addition to several shared conserved phosphorylation sites of tyrosine (Tyr) residues that are in the FAK protein sequence at Tyr³⁹⁷, Tyr⁵⁷⁶, and Tyr⁵⁷⁷ residues, while in PyK2, the phosphorylation sites of tyrosine are located at Tyr⁴⁰², Tyr⁵⁷⁹, and Tyr⁵⁸⁰ residues. Both FAK and PyK2 kinases possess a lysine (Lys) mutation in the kinase domain of FAK at Lys⁴⁵⁴ residue and in the kinase domain of Pyk2 at Lys⁴⁵⁷ residue. (B) Src/FAK-mediated transduction pathways contribute to cancer progression. FAK is activated by integrins to enhance the activity of phosphoinositide 3-kinase (PI3K). The activation of FAK-dependent pathways is associated with the stimulation of cell proliferation, angiogenesis, and survival. Upon the phosphorylation of FAK, we are able to recruit Grb2 and the p85 regulatory subunit of PI3K to enhance the activation of both the Grb2/Ras/MAPK and PI3K/Akt pathways, respectively, to promote tumor angiogenesis, survival, and proliferation.

Figure 6

Structure of TEC family kinases. The five kinases of the TEC family are represented by a diagram showing their structural domains. PH: Pleckstrin homology domain; TH: Tec homology domain; BH: Btk homology motif PR: proline-rich region; Cys: cysteine-rich sequence; N-Myr: N-terminal myristylation signal; SH: Src homology domain (SH3, SH2, and kinase) domains.

Figure 7

Structure of SRC family kinases, including their functional domains and dependent signals. Activation of Src family kinases is a membrane-dependent mechanism and is regulated by lipid/myristate modification within the SH4 domain and membrane binding. The modification of SH4 by myristylation and/or palmytoilation is to facilitate the localization of Src family kinases to the cell membrane, and the phosphorylation of tyrosine residues within the kinase domain to enhance Src activity. The inhibition of Src family kinases is mediated via ubiquitination sites, lysine 429 (Lys⁴²⁹) residue, and/or by the phosphorylation of tyrosine (Tyr) residues located in C-regulatory tail. Domain/regulatory regions are shown as boxes: Src homology 1 (SH1); tyrosine kinase/catalytic domain; Src homology 2 (SH2); Src homology 3 (SH3); Src homology 4 (SH4); and unstructured unique domain (UD).

Figure 8

Structure and domains of human SRMS, BRK, FRK, c-Src, Csk, IYK/BSK, and chicken v-Src. These kinases constitute SH3, SH2, and the kinase domain on their N-terminal region. Key residues, which are essential for the regulation of the enzymatic activity of these kinases, are highlighted. These include SRMS Tyr³⁸⁰ of the SRMS, Tyr³⁴² of BRK, Tyr³⁸⁷ of FRK, Tyr⁴¹⁹ of c-Src, Tyr⁴⁹⁷ of IYK/BSK, and Tyr⁴¹⁶ of v-Src. The C-terminal regulatory tyrosine residues include Tyr⁴⁴⁷ of BRK, Tyr⁴⁹⁷ of FRK, Tyr⁵³⁰ of c-Src, and Tyr⁵⁰⁴ of IYK/BSK. The ATP-contacting lysine residues include Lys²⁵⁸ of SRMS, Lys²¹⁹ of BRK, Lys²⁶² of FRK, Lys²⁹⁸ of c-Src, Lys²²² of Csk, Lys²⁶⁹ of IYK/BSK, and Lys²⁹⁵ of v-Src Lys²⁹⁵. All numbering is for human proteins, and v-Src is from a retroviral source with its own numbering.

Figure 9

(A) Structural and functional domains of the Abl kinases. Alternative splicing of both Abl1 and Abl2 results in the production of protein variants/isoforms. The isoforms of Abl1 and Abl2, namely Abl1a and Abl2b, are characterized by their myristylation at the N-termini. Abl1 possesses two splice variants, Abl1a and Abl1b, and Abl2 also possesses two splice variants, Abl2a and Abl2b. The N-terminal region of Abl constitutes SH3, SH2, and SH1/kinase domains. The C- terminus of Abl constitutes conserved filamentous (F)-actin-binding (BD), globular (G)-actin-binding, and DNA-binding domains, and three nuclear localization signal (NLS) motifs and one nuclear export signal (NES). Both Abl1 and Abl2 kinases share the same domains in their N-terminus and are different in terms of their C-terminus. The C-terminus of Abl2 constitutes two BD domains and a microtubule (MT)-binding domain. Both Abl1 and Abl2 have conserved PXXP motifs to facilitate protein–protein interactions and tyrosine phosphorylation sites as indicated. (B) Three-dimensional conformation of Abl kinase protein. The different domains of the ABL kinase including SH3 (Green), SH2 (red), and SH1/kinase (yellow) domains, and the catalytic pocket, allosteric pocket, activation loop, and the carboxy-terminal helix are demonstrated.

Figure 10

Structure of spleen tyrosine kinase (Syk)/Syk-B and ZAP-70 family protein tyrosine kinases. Syk kinases is organized in three functional domains, including two Src-homology 2 (SH2) domains and kinase domains. The three functional domains of the Syk kinase are connected via two A and B intermediate domains. Tyrosine residues of Syk that undergo phosphorylation are indicated. These tyrosine residues are essential for the regulation of enzymatic activity and to recruit other signaling proteins. The phosphorylation of Tyr³⁴² and Tyr³⁴⁶ is dependent on the Src family kinases (SFK); phosphorylation of Tyr¹³⁰, Tyr³¹⁷, Tyr⁵¹⁹, and Tyr⁵²⁰ is dependent on Syk itself and is target for autophosphorylation.