User:Alice Harmon/Sandbox 1: Difference between revisions

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<scene name='55/555705/Subdomainvii/1'>Subdomain VII</scene> contains two beta strands link by 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 (Mn<sup>2+</sup> in the 1atp crystal structure) 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 several important features. The APE motif is located at the carboxyl end of this subdomain and the <scene name='55/555705/Ape/1'>glutamate </scene>(blue ball and stick) 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 and it provides an anchor for the movement of the activation loop (see below). 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 YRDLKPEN 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.

<scene name='55/555705/Subdomainviii/1'>Subdomain VIII</scene> contains several important features. The APE motif is located at the carboxyl end of this subdomain and the <scene name='55/555705/Ape/1'>glutamate </scene>(blue ball and stick) in this motif forms a salt bridge with an arginine (yellow ball and stick) in in Subdomain XI. This salt bridge is critical for forming the stable kinase core and it provides an anchor for the movement of the activation loop (see below). 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 YRDLKPEN 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.

<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> contains two beta strands link by 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 (Mn<sup>2+</sup> in the 1atp crystal structure) 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 several important features. The APE motif is located at the carboxyl end of this subdomain and the <scene name='55/555705/Ape/1'>glutamate  </scene>(blue ball and stick) 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 and it provides an anchor for the movement of the activation loop (see below). 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 YRDLKPEN 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.
+<scene name='55/555705/Subdomainviii/1'>Subdomain VIII</scene> contains several important features. The APE motif is located at the carboxyl end of this subdomain and the <scene name='55/555705/Ape/1'>glutamate  </scene>(blue ball and stick) in this motif forms a salt bridge with an arginine (yellow ball and stick) in in Subdomain XI. This salt bridge is critical for forming the stable kinase core and it provides an anchor for the movement of the activation loop (see below). 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 YRDLKPEN 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.
 <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.