User:Alice Harmon/Sandbox 1: Difference between revisions

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The kinase structure used in the above tour is that of the active conformation of PKA. Following is a comparison of this active conformation, with its particular arrangement of structural elements, to the inactive conformation. While active conformations of protein kinases are very similar, there is great variation in the inactive conformations of protein kinases, but all involve misalignment of one or more of the structures, subdomain III (C-helix in PKA) and the catalytic, magnesium binding, and activation loops<ref name = "TaylorTIBS"/>.

To get an idea of the structural differences in active and inactive kinase domains, on the left is PKA in complex with ANP and PKI ([[1atp]]], the same structure used above), and on the right is inactive apo-PKA [[~~1J3H~~]].

To get an idea of the structural differences in active and inactive kinase domains, on the left is PKA in complex with ANP and PKI ([[1atp]]], the same structure used above), and on the right is inactive apo-PKA [[1j3h]].

<Structure load='1J3H' size='350' frame='true' align='right' caption='1j3h - apo-PKA' scene='55/555705/Apopka/2' /><scene name='55/555705/Twistedlobes/2'>Open, inactive conformation</scene> (right). <Structure load='1atp' size='350' frame='true' align='right' caption='1atp - PKA with ANP and PKI' scene='55/555705/Pkaall/1' /><scene name='55/555705/Closedlobes/4'>Closed, active conformation</scene> (left).

<Structure load='1J3H' size='350' frame='true' align='right' caption='1j3h - apo-PKA, open and inactive' scene='55/555705/Apopka/2' /><scene name='55/555705/Twistedlobes/2'>Open, inactive conformation</scene> (right). <Structure load='1atp' size='350' frame='true' align='right' caption='1atp - PKA with ANP and PKI; closed and active' scene='55/555705/Pkaall/1' /><scene name='55/555705/Closedlobes/4'>Closed, active conformation</scene> (left).

In theses scenes the catalytic domains are shown in spacefill, with the large lobe in silver and the small lobe in blue. To aid viewing, The N and C terminal sequences are in cartoon. Stop the rotation and use your mouse to get a good look at the catalytic cleft, which in 1ATP is closed around ANP. Two sets of residues are shown in yellow and red, respectively, to show the degree to which the cleft opens, and the two lobes twist with respect to each other. The yellow residues are Gly52 from the GxGxxG motif and Thr 201 in the activation loop. The red residues are His 87 in subdomain III (the C helix) and phosphorthreonine 197 in the activation loop. Note the difference in distance and alignment of these pairs of residues. In the closed, active conformation His 87 and phosphoThr 197 have an ionic interaction, whereas in the ~~openconformation~~ they are too far away from each other to interact.

In theses scenes the catalytic domains are shown in spacefill, with the large lobe in silver and the small lobe in blue. To aid viewing, The N and C terminal sequences are in cartoon. Stop the rotation and use your mouse to get a good look at the catalytic cleft, which in 1ATP is closed around ANP. Two sets of residues are shown in yellow and red, respectively, to show the degree to which the cleft opens, and the two lobes twist with respect to each other. The yellow residues are Gly52 from the GxGxxG motif and Thr 201 in the activation loop. The red residues are His 87 in subdomain III (the C helix) and phosphorthreonine 197 in the activation loop. Note the difference in distance and alignment of these pairs of residues. In the closed, active conformation His 87 and phosphoThr 197 have an ionic interaction, whereas in the open conformation they are too far away from each other to interact.

=References=

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 The kinase structure used in the above tour is that of the active conformation of PKA. Following is a comparison of this active conformation, with its particular arrangement of structural elements, to the inactive conformation. While active conformations of protein kinases are very similar, there is great variation in the inactive conformations of protein kinases, but all involve misalignment of one or more of the structures, subdomain III (C-helix in PKA) and the catalytic, magnesium binding, and activation loops<ref name = "TaylorTIBS"/>.
-To get an idea of the structural differences in active and inactive kinase domains, on the left is PKA in complex with ANP and PKI ([[1atp]]], the same structure used above), and on the right is inactive apo-PKA [[1J3H]].
+To get an idea of the structural differences in active and inactive kinase domains, on the left is PKA in complex with ANP and PKI ([[1atp]]], the same structure used above), and on the right is inactive apo-PKA [[1j3h]].
-<Structure load='1J3H' size='350' frame='true' align='right' caption='1j3h - apo-PKA' scene='55/555705/Apopka/2' /><scene name='55/555705/Twistedlobes/2'>Open, inactive conformation</scene> (right). <Structure load='1atp' size='350' frame='true' align='right' caption='1atp - PKA with ANP and PKI' scene='55/555705/Pkaall/1' /><scene name='55/555705/Closedlobes/4'>Closed, active conformation</scene> (left).
+<Structure load='1J3H' size='350' frame='true' align='right' caption='1j3h - apo-PKA, open and inactive' scene='55/555705/Apopka/2' /><scene name='55/555705/Twistedlobes/2'>Open, inactive conformation</scene> (right). <Structure load='1atp' size='350' frame='true' align='right' caption='1atp - PKA with ANP and PKI; closed and active' scene='55/555705/Pkaall/1' /><scene name='55/555705/Closedlobes/4'>Closed, active conformation</scene> (left).
-In theses scenes the catalytic domains are shown in spacefill, with the large lobe in silver and the small lobe in blue. To aid viewing, The N and C terminal sequences are in cartoon. Stop the rotation and use your mouse to get a good look at the catalytic cleft, which in 1ATP is closed around ANP. Two sets of residues are shown in yellow and red, respectively, to show the degree to which the cleft opens, and the two lobes twist with respect to each other. The yellow residues are Gly52 from the GxGxxG motif and Thr 201 in the activation loop. The red residues are His 87 in subdomain III (the C helix) and phosphorthreonine 197 in the activation loop.  Note the difference in distance and alignment of these pairs of residues. In the closed, active conformation His 87 and phosphoThr 197 have an ionic interaction, whereas in the openconformation they are too far away from each other to interact.
+In theses scenes the catalytic domains are shown in spacefill, with the large lobe in silver and the small lobe in blue. To aid viewing, The N and C terminal sequences are in cartoon. Stop the rotation and use your mouse to get a good look at the catalytic cleft, which in 1ATP is closed around ANP. Two sets of residues are shown in yellow and red, respectively, to show the degree to which the cleft opens, and the two lobes twist with respect to each other. The yellow residues are Gly52 from the GxGxxG motif and Thr 201 in the activation loop. The red residues are His 87 in subdomain III (the C helix) and phosphorthreonine 197 in the activation loop.  Note the difference in distance and alignment of these pairs of residues. In the closed, active conformation His 87 and phosphoThr 197 have an ionic interaction, whereas in the open conformation they are too far away from each other to interact.
 =References=
 <references/>