User:Alice Harmon/Sandbox 1: Difference between revisions

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<scene name='55/555705/Subdomainvii/1'>Subdomain VII</scene>, the Mg-binding loop with the DFG motif. The <scene name='55/555705/Dfg/2'>Aspartate in this motif (blue ball and stick)</scene> chelates a Mg<sup>2+</sup> ion that bridges the gamma and beta phosphates of ATP and positions the gamma phosphate for transfer to the substrate.

<scene name='55/555705/Subdomainviii/1'>Subdomain VIII</scene> contains the APE motif. The <scene name='55/555705/Ape/1'>glutamate in this motif (blue ball and stick) </scene>glutamate in this motif forms a salt bridge with an arginine (yellow ball and stick) in in Subdomain X1. This salt bridge is critical for forming the stable kinase core. In many protein kinases there is a phosphorylatable residue seven to ten residues upstream of the APE motif. In PKA it is a <scene name='55/555705/Phosphothreonine/1'>phosphothreonine</scene> (blue ball and stick with the phosphate in CPK), which forms an ionic bond with the arginine (yellow ball and stick) in the HRDLKPEN motif of the catalytic loop and helps to position it for catalysis. Between the phosphorylated residue and the APE motif lies the <scene name='55/555705/Pplus1/1'>P+1 loop</scene> which interacts with the residue adjacent to the phosphorylated residue of the peptide substrate.

<scene name='55/555705/Subdomainviii/1'>Subdomain VIII</scene> contains the APE motif. The <scene name='55/555705/Ape/1'>glutamate in this motif (blue ball and stick) </scene>glutamate in this motif forms a salt bridge with an arginine (yellow ball and stick) in in Subdomain X1. This salt bridge is critical for forming the stable kinase core. In many protein kinases there is a phosphorylatable residue seven to ten residues upstream of the APE motif. In PKA it is a <scene name='55/555705/Phosphothreonine/1'>phosphothreonine</scene> (blue ball and stick with the phosphate in CPK), which forms an ionic bond with the arginine (yellow ball and stick) in the HRDLKPEN motif of the catalytic loop and helps to position it for catalysis. Kinases that don't have a phosphorylatable residue in this loop often have an acididc residue that can form the salt bridge. Between the phosphorylated residue and the APE motif lies the <scene name='55/555705/Pplus1/1'>P+1 loop</scene> which interacts with the residue adjacent to the phosphorylated residue of the peptide substrate.

The <scene name='55/555705/Activationloop/1'>activation loop</scene> has been defined by three dimensional structures of protein kinases and biochemical studies. It comprises amino acid residues between the DFG motif in subdomain VII to the APE motif in subdomain VIII.

The <scene name='55/555705/Activationloop/1'>activation loop</scene> has been defined by three dimensional structures of protein kinases and biochemical studies. It comprises amino acid residues between the DFG motif in subdomain VII to the APE motif in subdomain VIII. As it's name implies, it is involved in switching the activity of the kinase on and off. When the phosphorylatable residue in subdomain VIII (see above) is phosphorylated, the activation loop is positioned such that the active site cleft is accessible and the DFG motif is properly positioned for catalysis.

<scene name='55/555705/Subdomainix/1'>Subdomain IX</scene> is a very hydrophobic alpha helix (helix F in bovine PKA). It contains and invariant aspartate residue that is discussed below.

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 <scene name='55/555705/Subdomainvii/1'>Subdomain VII</scene>, the Mg-binding loop with the DFG motif. The <scene name='55/555705/Dfg/2'>Aspartate in this motif (blue ball and stick)</scene> chelates a Mg<sup>2+</sup> ion that bridges the gamma and beta phosphates of ATP and positions the gamma phosphate for transfer to the substrate.
-<scene name='55/555705/Subdomainviii/1'>Subdomain VIII</scene> contains the APE motif. The <scene name='55/555705/Ape/1'>glutamate in this motif (blue ball and stick) </scene>glutamate in this motif forms a salt bridge with an arginine (yellow ball and stick) in in Subdomain X1. This salt bridge is critical for forming the stable kinase core. In many protein kinases there is a phosphorylatable residue seven to ten residues upstream of the APE motif. In PKA it is a <scene name='55/555705/Phosphothreonine/1'>phosphothreonine</scene> (blue ball and stick with the phosphate in CPK), which forms an ionic bond with the arginine (yellow ball and stick) in the HRDLKPEN motif of the catalytic loop and helps to position it for catalysis.  Between the phosphorylated residue and the APE motif lies the <scene name='55/555705/Pplus1/1'>P+1 loop</scene> which interacts with the residue adjacent to the phosphorylated residue of the peptide substrate.
+<scene name='55/555705/Subdomainviii/1'>Subdomain VIII</scene> contains the APE motif. The <scene name='55/555705/Ape/1'>glutamate in this motif (blue ball and stick) </scene>glutamate in this motif forms a salt bridge with an arginine (yellow ball and stick) in in Subdomain X1. This salt bridge is critical for forming the stable kinase core. In many protein kinases there is a phosphorylatable residue seven to ten residues upstream of the APE motif. In PKA it is a <scene name='55/555705/Phosphothreonine/1'>phosphothreonine</scene> (blue ball and stick with the phosphate in CPK), which forms an ionic bond with the arginine (yellow ball and stick) in the HRDLKPEN motif of the catalytic loop and helps to position it for catalysis.  Kinases that don't have a phosphorylatable residue in this loop often have an acididc residue that can form the salt bridge. Between the phosphorylated residue and the APE motif lies the <scene name='55/555705/Pplus1/1'>P+1 loop</scene> which interacts with the residue adjacent to the phosphorylated residue of the peptide substrate.
-The <scene name='55/555705/Activationloop/1'>activation loop</scene> has been defined by three dimensional structures of protein kinases and biochemical studies. It comprises amino acid residues between the DFG motif in subdomain VII to the APE motif in subdomain VIII.
+The <scene name='55/555705/Activationloop/1'>activation loop</scene> has been defined by three dimensional structures of protein kinases and biochemical studies. It comprises amino acid residues between the DFG motif in subdomain VII to the APE motif in subdomain VIII. As it's name implies, it is involved in switching the activity of the kinase on and off. When the phosphorylatable residue in subdomain VIII (see above) is phosphorylated, the activation loop is positioned such that the active site cleft is accessible and the DFG motif is properly positioned for catalysis.
 <scene name='55/555705/Subdomainix/1'>Subdomain IX</scene> is a very hydrophobic alpha helix (helix F in bovine PKA). It contains and invariant aspartate residue that is discussed below.