User:Alice Harmon/Sandbox 1: Difference between revisions

Line 9:

This article describes the general structure of protein kinase domains. It is based on the analysis of the primary structure of protein kinases by Hanks, Quinn, and Hunter <ref> PMID: 3291115</ref> in which the amino acid sequences of 65 protein kinases were aligned, and the revised analysis by Hanks and Hunter <ref> PMID: 7768349</ref>, and on the first three-dimensional structure of protein kinase to be published, that of protein kinase A (also called PKA or [[CAMP-dependent protein kinase]]) by Knighton et al.<ref> PMID: 1862342</ref>. The results described in these papers apply to the basic structure of the great range of eukaryotic protein kinases known today.

The crystal structure [[1atp]] contains the mouse PKA catalytic subunit (blue cartoon), inhibitor protein PKI (yellow cartoon), ATP (CPK wireframe), and two manganese ions (green spheres). The model at the left illustrates that 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 large lobe binds the protein substrate. the inhibitor peptide has an alanine substituted for the serine in the phosphorylation motif RRxS. All of the molecular scenes ~~below~~ include ATP, and some include the inhibitor peptide to illustrate kinase/substrate interactions.

The crystal structure [[1atp]] contains the mouse PKA catalytic subunit (blue cartoon), inhibitor protein PKI (yellow cartoon), ATP (CPK wireframe), and two manganese ions (green spheres). The model at the left illustrates that 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 cleft is located between them. The small lobe binds ATP and the large lobe binds the protein substrate modeled here by the inhibitor peptide, which has an alanine substituted for the serine in the phosphorylation motif RRxS. All of the molecular scenes include ATP, and some include the inhibitor peptide to illustrate kinase/substrate interactions.

=Twelve Conserved Subdomains=

Following is a tour of the twelve conserved subdomains (numbered starting at the amino terminal end of the catalytic domain) defined by Hanks and Hunter using ~~1PKA~~ as a model.

Following is a tour of the twelve conserved subdomains (numbered starting at the amino terminal end of the catalytic domain) defined by Hanks and Hunter and using 1atp as a model.

Line 48:

Two hydrophobic <scene name='55/555705/Both_spines/2'>"spines"</scene> (reviewed by Taylor and Kornev<ref> PMID: 20971646 </ref>) are important for the structure of active conformation of protein kinases. 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 it comprises residues (from top to bottom in the scene) 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'>The regulatory spine</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. This spine is assembled in the active conformation and disorganized in inactive conformations.

The <scene name='55/555705/Gatekeeper-subdomainv/2'>"gatekeeper"</scene> residue (chartreuse spacefill) is a part of subdomain V (blue) and it is located deep in the ATP-binding pocket (Subdomain I with its ATP binding loop are shown in yellow). The size of the gatekeeper residue determines the size of the binding pocket and it is thus a gatekeeper for which nucleotides, ATP analogs, and inhibitors can bind. In PKA and about 75% of all kinases it is a large residue, such as leucine, phenylalanine or methionine as seen here. In the remaining kinases, especially tyrosine kinases, the residue is larger, such as threonine or valine. The gatekeeper's location is <scene name='55/555705/Gatekeeper-spines/2'>between the two hydrophobic spines</scene> (gatekeeper is chartreuse, catalytic spine is blue, regulatory spine is orchid). Mutation of this residue in some ~~cancers~~ leads to activation of the kinase in the absence of phosphorylation of the activation loop. The gatekeeper's interaction with the two spines affects the orientation of the catalytic and magnesium binding loops.

The <scene name='55/555705/Gatekeeper-subdomainv/2'>"gatekeeper"</scene> residue (chartreuse spacefill) is a part of subdomain V (blue) and it is located deep in the ATP-binding pocket (Subdomain I with its ATP binding loop are shown in yellow). The size of the gatekeeper residue determines the size of the binding pocket and it is thus a gatekeeper for which nucleotides, ATP analogs, and inhibitors can bind. In PKA and about 75% of all kinases it is a large residue, such as leucine, phenylalanine or methionine as seen here. In the remaining kinases, especially tyrosine kinases, the residue is larger, such as threonine or valine. The gatekeeper's location is <scene name='55/555705/Gatekeeper-spines/2'>between the two hydrophobic spines</scene> (gatekeeper is chartreuse, catalytic spine is blue, regulatory spine is orchid). Mutation of this residue in some kinases leads to activation of the kinase in the absence of phosphorylation of the activation loop, and the unregulated kinase activity promotes cancer. The gatekeeper's interaction with the two spines affects the orientation of the catalytic and magnesium binding loops.

@@ Line 9: / Line 9: @@
 This article describes the general structure of protein kinase domains. It is based on the analysis of the primary structure of protein kinases by Hanks, Quinn, and Hunter <ref> PMID: 3291115</ref> in which the amino acid sequences of 65 protein kinases were aligned, and the revised analysis by Hanks and Hunter <ref> PMID: 7768349</ref>, and on the first three-dimensional structure of protein kinase to be published, that of protein kinase A (also called PKA or [[CAMP-dependent protein kinase]]) by Knighton et al.<ref> PMID: 1862342</ref>. The results described in these papers apply to the basic structure of the great range of eukaryotic protein kinases known today.
-The crystal structure [[1atp]] contains the mouse PKA catalytic subunit (blue cartoon), inhibitor protein PKI (yellow cartoon), ATP (CPK wireframe), and two manganese ions (green spheres). The model at the left illustrates that 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 large lobe binds the protein substrate. the inhibitor peptide has an alanine substituted for the serine in the phosphorylation motif RRxS. All of the molecular scenes below include ATP, and some include the inhibitor peptide to illustrate kinase/substrate interactions.
+The crystal structure [[1atp]] contains the mouse PKA catalytic subunit (blue cartoon), inhibitor protein PKI (yellow cartoon), ATP (CPK wireframe), and two manganese ions (green spheres). The model at the left illustrates that 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 cleft is located between them. The small lobe binds ATP and the large lobe binds the protein substrate modeled here by the inhibitor peptide, which has an alanine substituted for the serine in the phosphorylation motif RRxS. All of the molecular scenes include ATP, and some include the inhibitor peptide to illustrate kinase/substrate interactions.
 =Twelve Conserved Subdomains=
-Following is a tour of the twelve conserved subdomains (numbered starting at the amino terminal end of the catalytic domain) defined by Hanks and Hunter using 1PKA as a model.
+Following is a tour of the twelve conserved subdomains (numbered starting at the amino terminal end of the catalytic domain) defined by Hanks and Hunter and using 1atp as a model.
 <Structure load='1ATP' size='500' frame='true' align='right' caption='1atp - Protein kinase A catalytic subunit in complex with ATP (wireframe), manganese, and inhibitor peptide PKI' scene='55/555705/Pkaall/1' />
@@ Line 48: / Line 48: @@
 Two hydrophobic <scene name='55/555705/Both_spines/2'>"spines"</scene> (reviewed by Taylor and Kornev<ref> PMID: 20971646 </ref>) are important for the structure of active conformation of protein kinases. 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 it comprises residues (from top to bottom in the scene) 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'>The regulatory spine</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. This spine is assembled in the active conformation and disorganized in inactive conformations.
-The <scene name='55/555705/Gatekeeper-subdomainv/2'>"gatekeeper"</scene> residue (chartreuse spacefill) is a part of subdomain V (blue) and it is located deep in the ATP-binding pocket (Subdomain I with its ATP binding loop are shown in yellow).  The size of the gatekeeper residue determines the size of the binding pocket and it is thus a gatekeeper for which nucleotides, ATP analogs, and inhibitors can bind. In PKA and about 75% of all kinases it is a large residue, such as leucine, phenylalanine or methionine as seen here. In the remaining kinases, especially tyrosine kinases, the residue is larger, such as threonine or valine.  The gatekeeper's location is <scene name='55/555705/Gatekeeper-spines/2'>between the two hydrophobic spines</scene> (gatekeeper is chartreuse, catalytic spine is blue, regulatory spine is orchid). Mutation of this residue in some cancers leads to activation of the kinase in the absence of phosphorylation of the activation loop. The gatekeeper's interaction with the two spines affects the orientation of the catalytic and magnesium binding loops.
+The <scene name='55/555705/Gatekeeper-subdomainv/2'>"gatekeeper"</scene> residue (chartreuse spacefill) is a part of subdomain V (blue) and it is located deep in the ATP-binding pocket (Subdomain I with its ATP binding loop are shown in yellow).  The size of the gatekeeper residue determines the size of the binding pocket and it is thus a gatekeeper for which nucleotides, ATP analogs, and inhibitors can bind. In PKA and about 75% of all kinases it is a large residue, such as leucine, phenylalanine or methionine as seen here. In the remaining kinases, especially tyrosine kinases, the residue is larger, such as threonine or valine.  The gatekeeper's location is <scene name='55/555705/Gatekeeper-spines/2'>between the two hydrophobic spines</scene> (gatekeeper is chartreuse, catalytic spine is blue, regulatory spine is orchid). Mutation of this residue in some kinases leads to activation of the kinase in the absence of phosphorylation of the activation loop, and the unregulated kinase activity promotes cancer. The gatekeeper's interaction with the two spines affects the orientation of the catalytic and magnesium binding loops.