Journal Covers

      Biochem. Biophys. Res. Commun. vol 309, issue 4, 2003. Bilobed structure of the Abl protein kinase domain. The upper lobe is chiefly b sheet (blue) and the lower lobe is chiefly a helix (red ribbons). The active site occurs in the cleft between the two lobes. The upper lobe is involved in anchoring and orienting ATP. The lower lobe is responsible for binding the peptide or protein substrate. 

      The Abl protein kinase occurs in an activated form in chronic myeloid leukemia and is the driving force of this neoplasm. Gleevec (imatinib, STI-571) inhibits the Abl family of protein kinases and is a very effective FDA approved drug for the treatment of this disorder. Moreover, Gleevec is approved for the treatment of gastrointestinal stromal tumors owing to its inhibition of the Kit protein tyrosine kinase that is the driving force for 85% of these malignancies. Gleevec is the quintessential targeted protein kinase inhibitor. Mutations within the kinase domain are the most commonly identified mechanisms associated with resistance to Gleevec and relapse. 

      Biochem. Biophys. Res. Commun. vol 319, issue 1, 2004. Binding of Tarceva to the epidermal growth factor receptor protein kinase domain. Tarceva occupies the ATP-binding site of the enzyme and is a competitive inhibitor. The dashed line indicates a hydrogen bond from the blue methionine residue at position 769 (Met769) in the primary structure of the receptor to N1 of Tarceva. The light blue circle above methionine 769 is a water molecule. Tarceva (erlotinib) and Iressa (gefitinib) inhibit the epidermal growth factor receptor protein-tyrosine kinase activity and are approved for the treatment of non-small cell lung cancer. However, because they extend the lives of such patients by only a few months, clearly other therapies are required.
      Biochem. Biophys. Res. Commun. vol 324, issue 4, 2004. Ribbon diagram illustrating the structure of human Src, a non-receptor protein-tyrosine kinase. AMP-PNP, which is an ATP analog, is bound at the active site and is shown in red. From the N- to C-terminus, Src contains a 14-carbon myristoyl group attached to an SH4 domain, a unique domain, an SH3 domain, an SH2 domain, an SH2-kinase linker, a protein-tyrosine kinase domain (the SH1 domain), and a C-terminal regulatory segment. SH2 (Src homology domain 2) binds to phosphotyrosine and SH3 (Src homology domain 3) binds to proline-rich segments. The SH2 domain binds to phosphotyrosine 527 in the C-terminal tail to form a latch, and the latch stabilizes the attachment of the SH2 domain to the large lobe. The SH3 domain contacts the linker that glues the domain to the small lobe. As a result of clamping the SH2 and SH3 domains to the back side of the kinase domain, the enzyme is locked in an inactive conformation. An equilibrium exists between the inactive (shown) and active conformation (not shown). The equilibrium favors the inactive conformation. The inactive form is destabilized by dephosphorylation of tyrosine 527 and by phosphorylation of the activation loop tyrosine 416. 

      The small and large lobes can adopt a range of relative orientations, opening or closing the active site cleft. Within each lobe is a polypeptide segment that has an active and a restrained conformation. In the small lobe, this segment is the major α-helix designated as the αC-helix shown above (it is preceded by minor A and B helices in protein kinase A).  The αC-helix in some kinases rotates and translates with respect to the rest of the lobe, making or breaking part of the active catalytic site. In the large lobe, the activation loop adjusts to make or break part of the catalytic site. In most kinases, phosphorylation of the activation loop stabilizes the active conformation; this corresponds to Tyr416 in Src. Src kinase and members of the Src-kinase family thus have two important phosphorylation sites; phosphorylation of Tyr416 is stimulatory and phosphorylation of Tyr527 is inhibitory.

      The G-rich loop forms part of the ATP-binding site. In dormant Src kinase, shown above, residues 413-418 of the activation loop form a short α-helix (the A-loop helix) between the small and large lobes of the kinase domain. As a result, the A-loop helix buries the side chain of Tyr416 (the site of activating phosphorylation) between the lobes of the kinase domain. Residues 404-411 of the activation loop push the αC-helix out of its active state so that Glu310 in the helix cannot form a critical salt bridge with Lys295 and the enzyme is inactive. This A-loop helix is an important autoinhibitory component. The helix precludes protein/peptide substrate recognition, it sequesters Tyr416, and it stabilizes the inactive conformation of the kinase domain. Asp386 functions as a base that abstracts a proton from tyrosine thereby facilitating its nucleophilic attack of the γ-phosphorus atom of MgATP; Asp386 is called the catalytic base. This base occurs in the Cat.(catalytic) loop, shown above, that generally has the sequence HRDLRAAN in non-receptor protein-tyrosine kinases including Src.

      Src and Src-family protein kinases are proto-oncogenes that play key roles in cell proliferation, survival, and migration. v-Src (a viral protein) is encoded by the chicken oncogene of Rous sarcoma virus, and Src (the cellular homologue) is encoded by a physiological gene, the first of the proto-oncogenes. Activated Src may play a role in the production of breast, colon, stomach, lung, pancreatic, nervous, and ovarian neoplasms. Inhibitors of Src are being sought for the treatment of these and other neoplasms.

Sometimes slight miscalculations can lead to adverse effects as shown above at a railroad station. 

 

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Updated 5 December 2006