User:Alice Harmon/Sandbox 1: Difference between revisions
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the activation loop, the P+1 loop. | the activation loop, the P+1 loop. | ||
<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. | <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/Subdomainix/1'>Subdomain IX</scene> | <scene name='55/555705/Subdomainix/1'>Subdomain IX</scene> | ||
<scene name='55/555705/Subdomainx/1'>Subdomain X</scene> and <scene name='55/555705/Subdomainxi/1'>Subdomain XI</scene> bind substrate proteins and forms the kinase core. | <scene name='55/555705/Subdomainx/1'>Subdomain X</scene> and <scene name='55/555705/Subdomainxi/1'>Subdomain XI</scene> bind substrate proteins and forms the kinase core. | ||
Revision as of 23:44, 16 August 2013
Protein Kinase
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contains two beta strands connected by the glycine rich ATP-binding loop with the motif shown in ball and stick.
contains an that interacts with the phosphates of ATP.
connects to many parts of the kinase and its orientation is critical for activity. In the active conformation of the kinase the invariant in Subdomain III forms a salt bridge with the invariant lysine of Subdomain II (yellow ball and stick). This salt bridge couples subdomain III to ATP.
contains a beta strand and contributes to the core structure of the small lobe.
links the small and large lobes. It contributes residues to the and also for . In PKA Glu 127 (blue ball and stick) interacts with both the ribose of ATP and the first Arg (yellow ball and stick) in the phosphorylation motif RRxS of the peptide substrate.
is helix in the large lobe.
contains the catalytic loop with the conserved motif HRDLKxxN. The is the catalytic base that accepts the hydrogen removed from the hydroxyl group being phosphorylated. CHECK THIS FOR ACCURACY. Note the proximity of the glutamate residue to peptide residue that will be phosphorylated, here represented by an alanine (yellow ball and stick) in the inhibitor peptide.
, the Mg-binding loop with the DFG motif. The chelates a Mg2+ ion that bridges the gamma and beta phosphates of ATP and positions the gamma phosphate for transfer to the substrate.
the activation loop, the P+1 loop.
contains the APE motif. The 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 (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 which interacts with the residue adjacent to the phosphorylated residue of the peptide substrate.
and bind substrate proteins and forms the kinase core.