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. 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 that occur during a catalytic cycle and in active and inactive enzymes, use the links below to compare inactive, unphosphorylated PKA [[4dfy]] (activation loop threonine is not phosphorylated), and active PKA in complex with ANP and PKI [[1atp]] (the same structure used above)~~, active apo PKA [[1j3h]]~~, shown in the left, middle, and right frames, respectively. 4dfy shows the structure of an inactive form of PKA, in which the internal structure is disorganized due to the lack of phosphorylation of threonine 197 in the activation loop. Phosphorylation is required for formation of hydrogen bonds that are critical for alignment of structures to form the active site. 1j3h and 1atp show the open and closed structures assumed by PKA during the catalytic cycle. Note that some residues in 1j3h and 4dfy are not depicted in the models, because they are disordered and not resolved in the structures.

To get an idea of the structural differences that occur during a catalytic cycle and in active and inactive enzymes, use the links below to compare inactive, unphosphorylated PKA [[4dfy]] (activation loop threonine is not phosphorylated), active apo PKA [[1j3h]], and active PKA in complex with ANP and PKI [[1atp]] (the same structure used above), shown in the left, middle, and right frames, respectively. 4dfy shows the structure of an inactive form of PKA, in which the internal structure is disorganized due to the lack of phosphorylation of threonine 197 in the activation loop. Phosphorylation of this residue is required for formation of hydrogen bonds that are critical for alignment of structures to form the active site. 1j3h and 1atp show the open and closed structures assumed by PKA during the catalytic cycle. Note that some residues in 1j3h and 4dfy are not depicted in the models, because they are disordered and not resolved in the structures.

Click on all three links with same number to compare the indicated features. Legends for each set of scenes are below. To reset the structures, reload the page.

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{|

| <applet load='4DFY' size='300' frame='true' align='right' caption='4dfy - apo unphosphorylated PKA, inactive' scene='55/555705/Unphospka/3' /> '''4dfy''' <scene name='55/555705/Unphospka_spacefill/2'>1. Inactive conformation</scene> <scene name='55/555705/Unphospka_spines/1'>2. Disassembled spines</scene> <scene name='55/555705/Unphoscritical/2'>3. Critical structures</scene>

| <applet load='1J3H' size='300' frame='true' align='right' caption='1j3h - apo PKA, open conformation' scene='55/555705/Apopka/2' /> '''1j3h''': <scene name='55/555705/Twistedlobes/2'>1. Open conformation</scene> <scene name='55/555705/Apo_spines/1'>2. Assembled, open spines</scene> <scene name='55/555705/Apo_critical/2'>3. Critical structures</scene>

| <applet load='1J3H' size='300' frame='true' align='right' caption='1j3h - apo PKA, open conformation' scene='55/555705/Apopka/2' /> '''1j3h''' <scene name='55/555705/Twistedlobes/2'>1. Open conformation</scene> <scene name='55/555705/Apo_spines/1'>2. Assembled, open spines</scene> <scene name='55/555705/Apo_critical/2'>3. Critical structures</scene>

| <applet load='1atp' size='300' frame='true' align='right' caption='1atp - PKA with ANP and PKI; closed and active' scene='55/555705/Pkaall/1' /> '''1atp:''' <scene name='55/555705/Closedlobes/4'>1. Closed, active conformation</scene> <scene name='55/555705/Both_spines/2'>2. Assembled, closed spines</scene> <scene name='55/555705/Pkacritical/2'>3. Critical structures</scene>

| <applet load='1atp' size='300' frame='true' align='right' caption='1atp - PKA with ANP and PKI; closed and active' scene='55/555705/Pkaall/1' /> '''1atp''' <scene name='55/555705/Closedlobes/4'>1. Closed, active conformation</scene> <scene name='55/555705/Both_spines/2'>2. Assembled, closed spines</scene> <scene name='55/555705/Pkacritical/2'>3. Critical structures</scene>

|}

'''Scene legends'''

1. In these 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. (The activation loop of the unphosphorylated PKA is disordered, and thus not represented in the crystal structure.) Note the difference in distance and alignment of these pairs of residues. The small lobe is rotated 18° relative to the active conformation. 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.

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 The kinase structure used in the above tour is that of the active conformation of PKA. 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 that occur during a catalytic cycle and in active and inactive enzymes, use the links below to compare inactive, unphosphorylated PKA [[4dfy]] (activation loop threonine is not phosphorylated), and active PKA in complex with ANP and PKI [[1atp]] (the same structure used above), active apo PKA [[1j3h]], shown in the left, middle, and right frames, respectively. 4dfy shows the structure of an inactive form of PKA, in which the internal structure is disorganized due to the lack of phosphorylation of threonine 197 in the activation loop. Phosphorylation is required for formation of hydrogen bonds that are critical for alignment of structures to form the active site. 1j3h and 1atp show the open and closed structures assumed by PKA during the catalytic cycle.  Note that some residues in 1j3h and 4dfy are not depicted in the models, because they are disordered and not resolved in the structures.
+To get an idea of the structural differences that occur during a catalytic cycle and in active and inactive enzymes, use the links below to compare inactive, unphosphorylated PKA [[4dfy]] (activation loop threonine is not phosphorylated), active apo PKA [[1j3h]], and active PKA in complex with ANP and PKI [[1atp]] (the same structure used above), shown in the left, middle, and right frames, respectively. 4dfy shows the structure of an inactive form of PKA, in which the internal structure is disorganized due to the lack of phosphorylation of threonine 197 in the activation loop. Phosphorylation of this residue is required for formation of hydrogen bonds that are critical for alignment of structures to form the active site. 1j3h and 1atp show the open and closed structures assumed by PKA during the catalytic cycle.  Note that some residues in 1j3h and 4dfy are not depicted in the models, because they are disordered and not resolved in the structures.
 Click on all three links with same number to compare the indicated features. Legends for each set of scenes are below. To reset the structures, reload the page.
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 {|
 | <applet load='4DFY' size='300' frame='true' align='right' caption='4dfy - apo unphosphorylated PKA, inactive' scene='55/555705/Unphospka/3' /><Br>'''4dfy'''<Br><scene name='55/555705/Unphospka_spacefill/2'>1. Inactive conformation</scene><br><scene name='55/555705/Unphospka_spines/1'>2. Disassembled spines</scene><br><scene name='55/555705/Unphoscritical/2'>3. Critical structures</scene>
-| <applet load='1J3H' size='300' frame='true' align='right' caption='1j3h - apo PKA, open conformation' scene='55/555705/Apopka/2' /><Br>'''1j3h''': <Br><scene name='55/555705/Twistedlobes/2'>1. Open conformation</scene><br><scene name='55/555705/Apo_spines/1'>2. Assembled, open spines</scene><br><scene name='55/555705/Apo_critical/2'>3. Critical structures</scene>
+| <applet load='1J3H' size='300' frame='true' align='right' caption='1j3h - apo PKA, open conformation' scene='55/555705/Apopka/2' /><Br>'''1j3h''' <Br><scene name='55/555705/Twistedlobes/2'>1. Open conformation</scene><br><scene name='55/555705/Apo_spines/1'>2. Assembled, open spines</scene><br><scene name='55/555705/Apo_critical/2'>3. Critical structures</scene>
-| <applet load='1atp' size='300' frame='true' align='right' caption='1atp - PKA with ANP and PKI; closed and active' scene='55/555705/Pkaall/1' /><Br>'''1atp:''' <Br><scene name='55/555705/Closedlobes/4'>1. Closed, active conformation</scene><br><scene name='55/555705/Both_spines/2'>2. Assembled, closed spines</scene><Br><scene name='55/555705/Pkacritical/2'>3. Critical structures</scene>
+| <applet load='1atp' size='300' frame='true' align='right' caption='1atp - PKA with ANP and PKI; closed and active' scene='55/555705/Pkaall/1' /><Br>'''1atp''' <Br><scene name='55/555705/Closedlobes/4'>1. Closed, active conformation</scene><br><scene name='55/555705/Both_spines/2'>2. Assembled, closed spines</scene><Br><scene name='55/555705/Pkacritical/2'>3. Critical structures</scene>
 |}
+'''Scene legends'''<br/>
 . In these 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. (The activation loop of the unphosphorylated PKA is disordered, and thus not represented in the crystal structure.)  Note the difference in distance and alignment of these pairs of residues. The small lobe is rotated 18° relative to the active conformation. 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.