Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2018 Oct;53(5):535-563.
doi: 10.1080/10409238.2018.1495173. Epub 2018 Sep 5.

The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases

Neel H Shah  1   2   3   4 , Jeanine F Amacher  1   2   3   4 , Laura M Nocka  1   2   3   4 , John Kuriyan  1   2   3   4   5
Affiliations
Review

The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases

Neel H Shah et al. Crit Rev Biochem Mol Biol. 2018 Oct.

Abstract

Tyrosine kinases were first discovered as the protein products of viral oncogenes. We now know that this large family of metazoan enzymes includes nearly one hundred structurally diverse members. Tyrosine kinases are broadly classified into two groups: the transmembrane receptor tyrosine kinases, which sense extracellular stimuli, and the cytoplasmic tyrosine kinases, which contain modular ligand-binding domains and propagate intracellular signals. Several families of cytoplasmic tyrosine kinases have in common a core architecture, the "Src module," composed of a Src-homology 3 (SH3) domain, a Src-homology 2 (SH2) domain, and a kinase domain. Each of these families is defined by additional elaborations on this core architecture. Structural, functional, and evolutionary studies have revealed a unifying set of principles underlying the activity and regulation of tyrosine kinases built on the Src module. The discovery of these conserved properties has shaped our knowledge of the workings of protein kinases in general, and it has had important implications for our understanding of kinase dysregulation in disease and the development of effective kinase-targeted therapies.

Keywords: SH2 domain; SH3 domain; Tyrosine kinase; allostery; autoinhibition; kinase inhibitor; kinase regulation; oncogene.

PubMed Disclaimer

Conflict of interest statement

Disclosure statement

No potential conflict of interest was reported by the authors.

Figures

Figure 1.
Figure 1.
Architectures of eukaryotic protein tyrosine kinases. A. Activation of receptor tyrosine kinases through ligand-induced dimerization. B. Activation of cytoplasmic tyrosine kinases through phosphorylation or the engagement of modular ligand-binding domains. C. Domain architectures of the major families of metazoan cytoplasmic tyrosine kinases. Members of each family, found in humans, are listed. An asterisk for Srm and Txk denotes that these proteins differ slightly from other family members in their regulatory phosphosites or domain architecture. Numbering in panel C and throughout the text corresponds to the following sequences for representative members of each family: chicken c-Src and the human proteins Frk, c-Abl isoform 1b, Btk, Csk, Fes, Syk, Fak1, Jak1, and Ack. D. Schematic diagram of the key structural features of tyrosine kinase domains. Sidechains are numbered according to their position in chicken c-Src (see colour version of this figure at www.tandfonline.com/ibmg).
Figure 2.
Figure 2.
Activation of the Src module. A. Crystal structure of an active conformation of the c-Src kinase domain, bearing the activating T341I mutation and bound to the nonhydrolyzable ATP analog ATPcS (PDB code 3DQW). B. Crystal structure of c-Src in its auto-inhibited Cdk/Src inactive conformation, highlighting only the kinase domain, bound to the nonhydrolyzable ATP analog AMPPNP (PDB code 2SRC). In panels A and B, the conserved catalytic and regulatory spines are highlighted in transparent surface representation. C. Crystal structure of the Src module of the Src-family kinase Hck in the assembled auto-inhibited conformation, bound to the ATP-competitive inhibitor PP1 (PDB code 1QCF). D. Geometry of the activation loop and active site residues in activated c-Src, highlighting the role of activation loop phosphorylation (PDB code 3DQW). E. Geometry of the activation loop and active site residues in auto-inhibited c-Src (PDB code 2SRC). F. Geometry of the activation loop and active site residues in auto-inhibited c-Abl, highlighting a flip of the “DFG” motif aspartate relative to its orientation in c-Src (PDB code 1OPL). G. A model for activation loop trans-autophosphorylation of Src-family kinases in which the activation loop of one Lck molecule is presented into the active site of another Lck molecule (Shah et al. 2016) (see colour version of this figure at www.tandfonline.com/ibmg).
Figure 3.
Figure 3.
Diverse mechanisms of regulation in Src-module-containing kinases. A. Inhibitory tail phosphorylation of Src-family kinases by Csk. Phosphorylation of the conserved C-terminal tail tyrosine in Src-family kinases occurs through specific recognition of Src-family kinase domains by Csk. This docking of tertiary structures positions the tail into the Csk active site for phosphorylation. B. A myristoyl/phosphotyrosine switch in c-Abl. Isoform 1b of c-Abl is auto-inhibited by docking of an N-terminal myristoyl moiety into the C-lobe of the kinase domain. Disruption of this interaction and phosphorylation of a tyrosine residue in the SH2-kinase linker activates the kinase. C. Regulation of Tec-family kinases by the PH-TH module. In Btk, the PH-TH module stabilizes the auto-inhibited configuration of the Src module by binding to the N-lobe of the kinase domain, however, the precise geometry of this binding is not yet known. Engagement of the PH-TH module by binding to soluble inositol phosphates or PIP lipids results in release of auto-inhibitory contacts and facilitates full activation by trans-autophosphorylation of the activation loop (see colour version of this figure at www.tandfonline.com/ibmg).
Figure 4.
Figure 4.
Mechanisms of substrate selection in tyrosine kinases. A. Localization-mediated specificity. Src-module-containing tyro-sine kinases typically colocalize with their substrates through interactions mediated by their noncatalytic domains, and this localization is often coupled to activation of the kinase. Once localized, the kinase will phosphorylate proximal tyrosine residues. B. Structural features of tyrosine kinase-substrate interactions that impact sequence specificity. far-left: Schematic depiction of a substrate docked in the active site of a tyrosine kinase. middle-left: Structure of the insulin receptor kinase bound to a substrate, highlighting typical backbone hydrogen bonds between the kinase activation loop and residues downstream of the target tyrosine (PDB code 1IR3). middle-right: Preferred recognition of a substrate peptide bearing a phosphotyrosine residue at the +1 position by the EGFR kinase domain (PDB code 5CZH). far-right: Model based on molecular dynamics simulations of the extensive electrostatic interactions between ZAP-70 and a preferred substrate derived from the protein LAT (Shah et al. 2016) (see colour version of this figure at www.tandfonline.com/ibmg).
Figure 5.
Figure 5.
Evolution of cytoplasmic tyrosine kinases. A. Presence of cytoplasmic tyrosine kinase families across the metazoan lineage and in closely related nonmetazoan eukaryotes. left: A phylogenetic tree of eukaryotes highlighting specific metazoan species and several nonmetazoan clades. right: Incidence of tyrosine kinase genes across the represented eukaryotic phyla that are likely orthologs of tyrosine kinase genes from the indicated human families. A red circle indicates that a kinase from that family is present in that specific organism/clade, and a white circle indicates that no kinase from that family has been reported on that branch of the evolutionary tree. The yellow circle represents a kinase with domain architecture similar to a Jak-family kinase, but with a kinase domain sequence more homologous to a Syk-family kinase. The blue circles represent the presence of Syk-like tyrosine kinases known as SHARK tyrosine kinases, in which the two SH2 domains are separated by ankyrin repeats. Data for this figure were compiled from Bradham et al. 2006; Manning et al. 2002a; Srivastava et al. 2010; and Suga et al. 2014. B. Evolution of interdomain allostery in the Src module (conceptually adapted from Kuriyan and Eisenberg 2007). In an ancient organism, SH3, SH2, and tyrosine kinase domains likely existed as separte genes, which had no appreciable affinity for one another. It is possible that these individual domains retained some capacity for allosteric modulation, dictated by their intrinsic conformational dynamics. Multiple steps of gene fusion led to the assembly of a gene and its protein product with a domain architecture resembling the Src module. In the earliest iterations of this architecture, the domains interacted weakly and there was no allosteric modulation of kinase activity. Over time, through mutations, noncovent interactions between the domains strengthened, allowing for allosteric regulation of kinase activity through interdomain contacts (see colour version of this figure at www.tandfonline.com/ibmg).
Figure 6.
Figure 6.
Disease-related and drug resistance mutations in in the Src module. A. Oncogenic mutations in c-Src, mapped onto a crystal structure of the auto-inhibited form of c-Src (PDB code 2SRC). Most of the mutation sites indicated by a black sphere are reported activating mutations in the v-Src gene of the Rous sarcoma virus, given in chicken c-Src numbering with the human c-Src numbering in parentheses: R95(98)W, T96(99)I, D117(120)N, R318(321)Q, T338(341)I. The sites at which the C-terminal tail of c-Src starts to differ from v-Src, and where a C-terminal truncation is observed a small subset of human colon cancers, are also marked with a black sphere. Note that the T338(341)I mutation is at the canonical ‘gatekeeper’ residue and also causes resistance to the drug dasatinib. Orange spheres mark the point mutations E378(381)G and I441(444)F, which were identified by passaging a virus encoding c-Src in fibroblast cells and selecting for cell transformation. These mutations are independently sufficient to hyperactivate c-Src (Kato et al. 1986; Levy et al. 1986). B. Sites of drug resistance mutations in Bcr-Abl, mapped onto a crystal structure of the auto-inhibited form of c-Abl (PDB code 1OPL). Mutation sites marked by a black sphere were identified in the first major survey of clinically observed resistance mutations to imatinib (Shah et al. 2002), and are given in human c-Abl isoform 1b numbering with the isoform 1a numbering in parentheses: M263(244)V, G269(250)E, Q271(252)H/R, Y272(253)F/H, E274(255)K, T334(315)I, F336(317)L, M370(351)T, E374(355)G, F378(359)V, L406(387)M, H415(396)R. Mutation sites marked by an orange sphere are examples of mutations distal to the imatinib binding site that confer resistance in a cell-based assay for oncogenic transformation (Azam et al. 2003): E298(279)K, V357(338)G, V358(339)A/G, A363(344)V, G391(372)R, G482(463)D, M491(472)I, F505(486)S, E513(494)A, I521(502)M, E528(509)D. C. Disease-related mutations in Btk, mapped onto a model of full-length Btk (left) from (Wang et al. 2015) (also see structures with PDB codes 4Y93 and 4XI2), a crystal structure of the Saraste dimer of the PH-TH module (top right, PDB code 4Y94), and a crystal structure of the Btk kinase domain bound to ibrutinib (bottom right, PDB code 5P9J). Residue numbering corresponds to that of the human Btk sequence. Sites of some inactivating mutations in XLA are shown as black spheres (R307G/K/T, L369F, R372G, G414R, R525K/G) or black ball and stick model in the case of R28H. The site of N-terminal truncation in an oncogenic form of Btk (Met 89), the critical cysteine (Cys 481) that reacts with the drug ibrutinib, and other sites of resistance mutations (T474I and L528W) are shown in orange (see colour version of this figure at www.tandfonline.com/ibmg).
See this image and copyright information in PMC

References

    1. Adrián FJ, Ding Q, Sim T, Velentza A, Sloan C, Liu Y, Zhang G, Hur W, Ding S, Manley P, et al. 2006. Allosteric inhibitors of Bcr-abl-dependent cell proliferation. Nat Chem Biol. 2:95–102. - PubMed
    1. Agafonov RV, Wilson C, Otten R, Buosi V, Kern D. 2014. Energetic dissection of Gleevec’s selectivity toward human tyrosine kinases. Nat Struct Mol Biol. 21:848–853. - PMC - PubMed
    1. Aleem SU, Craddock BP, Miller WT. 2015. Constitutive activity in an ancestral form of abl tyrosine kinase. PLoS One. 10:e0131062. - PMC - PubMed
    1. Andreotti AH, Joseph RE, Conley JM, Iwasa J, Berg LJ. 2018. Multidomain control over TEC kinase activation state tunes the T cell response. Annu Rev Immunol. 36:549–578. - PubMed
    1. Arbesú M, Maffei M, Cordeiro TN, Teixeira JMC, Pérez Y, Bernadó P, Roche S, Pons M. 2017. The unique domain forms a fuzzy intramolecular complex in Src family kinases. Structure. 25:630–640.e4. - PubMed

Publication types

Substances

LinkOut - more resources