Sandbox Reserved 433
From Proteopedia
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==Overall Structure== | ==Overall Structure== | ||
| - | The overall structure of GSK-3β has two phosphorylation sites that are involved in catalysis. One of these sites is Ser 9, resulting in the inactivation of GSK-3β. The second phosphorylation site is Tyr 216, located on the activation loop ( | + | The overall structure of GSK-3β has two phosphorylation sites that are involved in catalysis. One of these sites is Ser 9, resulting in the inactivation of GSK-3β. The second phosphorylation site is Tyr 216, located on the activation loop (<span style="color:green">'''green'''</span> ), and is responsible for the increase in catalytic activity. GSK-3β has the characteristic two-domain kinase fold, containing a N-terminal β-strand domain (<span style="color:Blue">'''light blue, residues 25-138'''</span>) and a C-terminal α-helical domain (<span style="color:red">'''red, residues 139-343'''</span>). There is an interface between the α and β domains, at which the ATP-binding site is located, encircled by the hinge and the glycine-rich loop. The activation loop (<span style="color:purple">'''purple'''</span>) runs along the surface of the substrate-binding groove. There are 39 residues in the C-terminus end that are outside the main kinase fold. These residues form a small domain that closely packs next to the α-helical domain. The β-strand domain is formed by seven β-strands that run in an antiparallel formation. Strands 2-6 form a β-barrel, through which a short α helix (<span style="color:orange">'''yellow, residues 96-102'''</span>) aligns against the β-barrel. <ref>PMID: 11427888</ref>. |
<scene name='48/483890/Overall_structure_of_gsk-3beta/3'>Green Scene for Overall Structure</scene> | <scene name='48/483890/Overall_structure_of_gsk-3beta/3'>Green Scene for Overall Structure</scene> | ||
==Binding Interactions== | ==Binding Interactions== | ||
| - | Before GSK-3β can phosphorylate a substrate, the β and α domains of the protein must align. To ensure alignment of the domains, which can either promote or decrease catalysis, GSK-3β utilizes phosphorylated residues. As mentioned in overall structure, phosphorylation of Ser 9 inhibits the catalytic ability of GSK-3β, while phosphorylation of Tyr 216 promotes catalysis by 200 fold. When Ser 9 is phosphorylated, the N-terminus of the protein acts as a pseudo-substrate, binding to the active site and preventing any catalytic activity from occurring. The inhibitor staurosporine, prevents catalytic activity by binding slightly above the active site of GSK-3β while rotating the N-terminal domain of the protein back in order to occupy a prefered binding mode. More details on the binding of staurosporine can be read in the Additional Features section. When Tyr 216 is phosphorylated, the polar residues Arg 96, Arg 180, and Lys 205 all rearranged, due to electrostatic interactions to point towards the phosphorylated molecule, allowing for the protein to fold into its active form<ref | + | Before GSK-3β can phosphorylate a substrate, the β and α domains of the protein must align. To ensure alignment of the domains, which can either promote or decrease catalysis, GSK-3β utilizes phosphorylated residues. As mentioned in overall structure, phosphorylation of Ser 9 inhibits the catalytic ability of GSK-3β, while phosphorylation of Tyr 216 promotes catalysis by 200 fold. When Ser 9 is phosphorylated, the N-terminus of the protein acts as a pseudo-substrate, binding to the active site and preventing any catalytic activity from occurring. The inhibitor staurosporine, prevents catalytic activity by binding slightly above the active site of GSK-3β while rotating the N-terminal domain of the protein back in order to occupy a prefered binding mode. More details on the binding of staurosporine can be read in the Additional Features section. When Tyr 216 is phosphorylated, the polar residues Arg 96, Arg 180, and Lys 205 all rearranged, due to electrostatic interactions to point towards the phosphorylated molecule, allowing for the protein to fold into its active form.<ref>PMID: 11427888</ref> |
| - | To influence binding of substrates, a salt bridge must form between Glu 97 and Lys 85 located in the active site. GSK-3β recognizes a sequence on the substrate containing two serine molecules separated by three residues (SXXXS). If the last serine in the sequence is phosphorylated prior to its encounter with GSK-3β, also known as primed phosphorylation, then the catalytic rate increases by 100-1000 fold. Catalytic activity of primed phosphorylated substrates increases catalytic activity by replacing the phosphate ion that aligns the Arg 96, Arg 180, and Lys 205 residues. Although not all substrates that GSK-3β phosphorylated require primed phosphorylation, substrates that do have a primed serine increase catalytic activity by utilizing electrostatic interactions to hold the protein in its active form<ref | + | To influence binding of substrates, a salt bridge must form between Glu 97 and Lys 85 located in the active site. GSK-3β recognizes a sequence on the substrate containing two serine molecules separated by three residues (SXXXS). If the last serine in the sequence is phosphorylated prior to its encounter with GSK-3β, also known as primed phosphorylation, then the catalytic rate increases by 100-1000 fold. Catalytic activity of primed phosphorylated substrates increases catalytic activity by replacing the phosphate ion that aligns the Arg 96, Arg 180, and Lys 205 residues. Although not all substrates that GSK-3β phosphorylated require primed phosphorylation, substrates that do have a primed serine increase catalytic activity by utilizing electrostatic interactions to hold the protein in its active form.<ref>PMID: 11427888</ref> |
<scene name='48/483890/Binding_interactions/1'> Alignment of Arg 96, Arg 180, and Lys 205</scene> when Tyr 216 is phosphorylated, due to the electrostatic interactions between the residues and the phosphate ion.<span style="color:Blue">'''Blue atoms'''</span> - cationic side chains <span style="color:Grey">'''White atoms'''</span> - amino acid backbone | <scene name='48/483890/Binding_interactions/1'> Alignment of Arg 96, Arg 180, and Lys 205</scene> when Tyr 216 is phosphorylated, due to the electrostatic interactions between the residues and the phosphate ion.<span style="color:Blue">'''Blue atoms'''</span> - cationic side chains <span style="color:Grey">'''White atoms'''</span> - amino acid backbone | ||
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GSK-3 beta has various inhibiters; one example is AMP-PMP. These inhibitors bind to the N-terminus of the ligand on the GSK-3 beta complex, a result of the classical binding mechanism for a protein kinase. However, in the case of staurosporine (another inhibitor), it is unable to classically bind to the N-terminus of the ligand on the GSK-3 beta complex. This is because, in a GSK-3 beta complex with staurosporine, the ligand in question has an incompatible angle at the N-terminus, thus failing to undergo classical binding<ref name="paper" />. | GSK-3 beta has various inhibiters; one example is AMP-PMP. These inhibitors bind to the N-terminus of the ligand on the GSK-3 beta complex, a result of the classical binding mechanism for a protein kinase. However, in the case of staurosporine (another inhibitor), it is unable to classically bind to the N-terminus of the ligand on the GSK-3 beta complex. This is because, in a GSK-3 beta complex with staurosporine, the ligand in question has an incompatible angle at the N-terminus, thus failing to undergo classical binding<ref name="paper" />. | ||
| - | What type of bonding does GSK-3 beta exhibit with staurosporine, and which of its residues form this type of bond? | + | What type of bonding does GSK-3 beta exhibit with staurosporine, and which of its residues form this type of bond? If needed, a green screen of the complex can be found below. |
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<scene name='48/483890/Ligand_bonding_type/1'>View Complex</scene> | <scene name='48/483890/Ligand_bonding_type/1'>View Complex</scene> | ||
Revision as of 00:35, 6 April 2015
| This Sandbox is Reserved from January 19, 2016, through August 31, 2016 for use for Proteopedia Team Projects by the class Chemistry 423 Biochemistry for Chemists taught by Lynmarie K Thompson at University of Massachusetts Amherst, USA. This reservation includes Sandbox Reserved 425 through Sandbox Reserved 439. |
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