User:Alice Harmon/Sandbox 1: Difference between revisions

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This article is based on the pioneering analysis of the primary structure of protein kinases by Hanks, Quinn, and Hunter based upon the alignment of amino acid sequences of 65 protein kinases, and revised by Hanks and Hunter in 1995, and on the first three dimensional structure of protein kinase, that of PKA, to be published. The results described in these papers applies to the great range of protein kinases known today.

The catalytic domains of eukaryotic protein kinases have a small lobe and a large lobe (seen at the top and bottom of the model, respectively), and the catalytic site is located in a cleft between them. The small lobe binds ATP and the small lobe binds the protein substrate. The crystal structure includes ATP.~~2Mg2~~+ and the inhibitor peptide that has an alanine substituted for serine in a substrate's phosphorylation motif RRxS. All of the molecular scenes below include ATP, and some include the inhibitor peptide to illustrate kinase/substrate interactions.

The catalytic domains of eukaryotic protein kinases have a small lobe and a large lobe (seen at the top and bottom of the model, respectively), and the catalytic site is located in a cleft between them. The small lobe binds ATP and the small lobe binds the protein substrate. The crystal structure includes ATP.2Mg<sup>2+</sup> and the inhibitor peptide that has an alanine substituted for serine in a substrate's phosphorylation motif RRxS. All of the molecular scenes below include ATP, and some include the inhibitor peptide to illustrate kinase/substrate interactions.

Here, the twelve conserved subdomains (numbered starting at the amino terminal end of the domain) defined by Hanks and Hunter are examined using PKA as the model protein.

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<scene name='55/555705/Subdomainiv/1'>Subdomain IV</scene> contains a beta strand and contributes to the core structure of the small lobe.

<scene name='55/555705/Subdomainv/1'>Subdomain V</scene> links the small and large lobes~~. It~~ contributes residues to the <scene name='55/555705/Atppocket/1'>ATP binding pocket</scene> and also for <scene name='55/555705/Glu127/1'>peptide substrate binding</scene>. 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.

<scene name='55/555705/Subdomainv/1'>Subdomain V</scene> contains a hydrophobic beta strand in the small lobe and an alpha helix in the large lobe. The sequence that links these two secondary structures not only links together the small and large lobes of the kinase, but also contributes residues to the <scene name='55/555705/Atppocket/1'>ATP binding pocket</scene> and also for <scene name='55/555705/Glu127/1'>peptide substrate binding</scene>. 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 a peptide substrate.

<scene name='55/555705/Subdomainvia/1'>Subdomain VIa</scene> is a long alpha helix in the large lobe.

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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.

~~the activation loop,~~ the P+1 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. 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 (F in bovine PKA).

<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.

The activation segment has been defined by three dimensional structures of protein kinases and biochemical studies. It is a looping structure comprising amino acid residues between the DFG motif in subdomain VII to the invariant D in subdomain IX.

<scene name='55/555705/Subdomainx/1'>Subdomain X</scene> and <scene name='55/555705/Subdomainxi/1'>Subdomain XI</scene> contain three alpha helices (G, H, and I in bovine PKA) that form the kinase core and which are involved in binding substrate proteins.

Two hydrophobic "spines" are important for the structure of active conformation of protein kinases (Taylor TIBS 2010). They are composed of amino acid residues that are non-contiguous in the primary structure.<scene name='55/555705/Spine1/1'> The catalytic spine </scene>includes the adenine ring of ATP. In PKA the residues are A70, V57, ATP, L173, I174, L172, M128, M231, and L227, and it is directly anchored to amino end of helix F (Subdomain IX) <scene name='55/555705/Spine2/1'>Spine two</scene> contains residues L106, L95, F185, Y164, and it is anchored to helix F via a hydrogen bond between the invariant aspartate in helix F (yellow ball and stick) and the backbone nitrogen of Y164.

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 This article is based on the pioneering analysis of the primary structure of protein kinases by Hanks, Quinn, and Hunter based upon the alignment of amino acid sequences of 65 protein kinases, and revised by Hanks and Hunter in 1995, and on the first three dimensional structure of protein kinase, that of PKA, to be published. The results described in these papers applies to the great range of protein kinases known today.
-The catalytic domains of eukaryotic protein kinases have a small lobe and a large lobe (seen at the top and bottom of the model, respectively), and the catalytic site is located in a cleft between them. The small lobe binds ATP and the small lobe binds the protein substrate. The crystal structure includes ATP.2Mg2+ and the inhibitor peptide that has an alanine substituted for serine in a substrate's phosphorylation motif RRxS. All of the molecular scenes below include ATP, and some include the inhibitor peptide to illustrate kinase/substrate interactions.
+The catalytic domains of eukaryotic protein kinases have a small lobe and a large lobe (seen at the top and bottom of the model, respectively), and the catalytic site is located in a cleft between them. The small lobe binds ATP and the small lobe binds the protein substrate. The crystal structure includes ATP.2Mg<sup>2+</sup> and the inhibitor peptide that has an alanine substituted for serine in a substrate's phosphorylation motif RRxS. All of the molecular scenes below include ATP, and some include the inhibitor peptide to illustrate kinase/substrate interactions.
 Here, the twelve conserved subdomains (numbered starting at the amino terminal end of the domain) defined by Hanks and Hunter are examined using PKA as the model protein.
@@ Line 19: / Line 19: @@
 <scene name='55/555705/Subdomainiv/1'>Subdomain IV</scene> contains a beta strand and contributes to the core structure of the small lobe.
-<scene name='55/555705/Subdomainv/1'>Subdomain V</scene> links the small and large lobes. It contributes residues to the <scene name='55/555705/Atppocket/1'>ATP binding pocket</scene> and also for <scene name='55/555705/Glu127/1'>peptide substrate binding</scene>. 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.
+<scene name='55/555705/Subdomainv/1'>Subdomain V</scene> contains a hydrophobic beta strand in the small lobe and an alpha helix in the large lobe. The sequence that links these two secondary structures not only links together the small and large lobes of the kinase, but also contributes residues to the <scene name='55/555705/Atppocket/1'>ATP binding pocket</scene> and also for <scene name='55/555705/Glu127/1'>peptide substrate binding</scene>. 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 a peptide substrate.
 <scene name='55/555705/Subdomainvia/1'>Subdomain VIa</scene> is a long alpha helix in the large lobe.
@@ Line 27: / Line 27: @@
 <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.
-the activation loop, the P+1 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.  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 (F in bovine PKA).
+<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.
+The activation segment has been defined by three dimensional structures of protein kinases and biochemical studies. It is a looping structure comprising amino acid residues between the DFG motif in subdomain VII to the invariant D in subdomain IX.
 <scene name='55/555705/Subdomainx/1'>Subdomain X</scene> and <scene name='55/555705/Subdomainxi/1'>Subdomain XI</scene> contain three alpha helices (G, H, and I in bovine PKA) that form the kinase core and which are involved in binding substrate proteins.
 Two hydrophobic "spines" are important for the structure of active conformation of protein kinases (Taylor TIBS 2010). They are composed of amino acid residues that are non-contiguous in the primary structure.<scene name='55/555705/Spine1/1'> The catalytic spine </scene>includes the adenine ring of ATP. In PKA the residues are A70, V57, ATP, L173, I174, L172, M128, M231, and L227, and it is directly anchored to amino end of helix F (Subdomain IX)  <scene name='55/555705/Spine2/1'>Spine two</scene> contains residues L106, L95, F185, Y164, and it is anchored to helix F via a hydrogen bond between the invariant aspartate in helix F (yellow ball and stick) and the backbone nitrogen of Y164.