SandboxPKA: Difference between revisions
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The fusion of the gene encoding c-Abl with the breakpoint cluster region (BCR) gene, results in the formation of a fusion protein, BCR-Abl, in which all of c-Abl is preserved without mutation, except for the “cap” region upstream of the SH3 domain. | The fusion of the gene encoding c-Abl with the breakpoint cluster region (BCR) gene, results in the formation of a fusion protein, BCR-Abl, in which all of c-Abl is preserved without mutation, except for the “cap” region upstream of the SH3 domain. | ||
<StructureSection load='1OPK' size='250' side='right' caption='c-Abl tyrosine kinase: SH3 | <StructureSection load='1OPK' size='250' side='right' caption='c-Abl tyrosine kinase: SH3 doamain is shown in red while SH2 domain is shown in purple. Catalytic domain is represented by blue. Also it is possible to observe myristoiled group in the N-terminal domain of c-Abl tyrosin kinase' scene='SandboxPKA/Abl1/4'> | ||
==='''Kinase domain'''=== | ==='''Kinase domain'''=== | ||
Protein kinases are characterized by an architecture that enables distal parts of the enzyme to be linked by conserved hydrophobic elements. Kynase domain is composed by N-lobe and a C-lobe, and the adenine ring of ATP is buried at the base of the cleft between the two lobes. | Protein kinases are characterized by an architecture that enables distal parts of the enzyme to be linked by conserved hydrophobic elements. Kynase domain is composed by N-lobe and a C-lobe, and the adenine ring of ATP is buried at the base of the cleft between the two lobes. | ||
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• '''Gly-rich loop (GxGxxG):''' this loop folds over the nucleotide and positions the γ-phosphate of ATP for catalysis and is the most flexible part of the N-lobe. | • '''Gly-rich loop (GxGxxG):''' this loop folds over the nucleotide and positions the γ-phosphate of ATP for catalysis and is the most flexible part of the N-lobe. | ||
• '''P- | • '''<scene name='Dasatinib/Mpl/4'>P-Loop Movement</scene>'''< often referred to as the Walker-A motif (GxxxxGKT/S) <Ref>[Ramakrishnan, C. et al. (2002) A conformational analysis of Walker motif A [GXXXXGKT (S)] in nucleotide-binding and other proteins. Protein Eng. 15, 783–798]</Ref>. In this loop there is a higly conserved residue (usually Lys) which is able to form a salt bridge with C-helix. | ||
• '''C-helix''': is a unique helix present in the N-lobe. It is very dynamic and plays a key role as a regulatory element in the protein kinase molecule. C-helix occupies a strategically important position between the two lobes. The C-helix connects many different parts of the molecule and serves as a ‘‘signal integration motif’’ <Ref>[Johnson, D.A. et al. (2001) Dynamics of cAMP-dependent protein kinase. Chem. Rev. 101, 2243–2270].</Ref> The C-helix contains another conserved residue, Glu or Asp, that bridges to Lys located in P-loop. This bridge is really important for catalysis process. | • '''C-helix''': is a unique helix present in the N-lobe. It is very dynamic and plays a key role as a regulatory element in the protein kinase molecule. C-helix occupies a strategically important position between the two lobes. The C-helix connects many different parts of the molecule and serves as a ‘‘signal integration motif’’ <Ref>[Johnson, D.A. et al. (2001) Dynamics of cAMP-dependent protein kinase. Chem. Rev. 101, 2243–2270].</Ref> The C-helix contains another conserved residue, Glu or Asp, that bridges to Lys located in P-loop. This bridge is really important for catalysis process. | ||
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The '''β-subdomain''' contains much of the catalytic machinery associated with transfer of the phosphate from ATP to the protein substrate, and is anchored through hydrophobic residues to the helical core. | The '''β-subdomain''' contains much of the catalytic machinery associated with transfer of the phosphate from ATP to the protein substrate, and is anchored through hydrophobic residues to the helical core. | ||
- The '''catalytic loop''' is composed by β6 and β7, whereas β8 and β9 strands flank DGF motif, where aspartic/glutamic residue is critical for recognizing one of the ATP-bound Mg++ ions | - The '''catalytic loop''' is composed by β6 and β7, whereas β8 and β9 strands flank DGF motif, where aspartic/glutamic residue is critical for recognizing one of the ATP-bound Mg++ ions | ||
- The ''' | - The '''<scene name='Dasatinib/Mact/1'>Activation Loop Movement</scene>''' contains Tyr412 responsible of activation of kinase activity. | ||
- The unactivated, autoinhibited conformation [in which the Asp-810-Phe-811-Gly-812 (DFG) triad at the beginning of the A-loop is in the “DFG-out”, can <scene name='Dasatinib/Mdfg/3'>move</scene> when ATP Tyr412 is phosphorlated, rising an active conformation. | |||
- The '''myristoyl group''' complement activation loop in turning on and off c-abl protein. It has been shown to be the key regulator of this kinase. | - The '''myristoyl group''' complement activation loop in turning on and off c-abl protein. It has been shown to be the key regulator of this kinase. | ||
==='''Catalytic domain'''=== | ==='''Catalytic domain'''=== | ||
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• '''Protein-binding pocket''': lamina-B domain | • '''Protein-binding pocket''': lamina-B domain | ||
The unactivated conformation ("DGF out") is due to Phe (in the DGF triad) is oriented near the ATP-binding pocket. When Tyr 412 is phosphorylated, “DFG-in” conformation buries the Phe away from the ATP-binding pocket and the A-loop extends over the C terminus of the catalytic domain). The protein can be considered to be in equilibrium among these conformations, with a shift to the activated form upon phosphorylation. | |||
</StructureSection> | </StructureSection> | ||