The Structure of PI3K: Difference between revisions
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==Structure of PI3K== | ==Structure of PI3K== | ||
Class I PI3Ks, which are tightly regulated by tyrosine kinases, are composed of an 85kDa regulatory/adapter subunit (p85) and a 110kDa catalytic subunit (p110). <ref name="Flip"> PMID: 10525402</ref> | Class I [[PI3K|PI3Ks]], which are tightly regulated by tyrosine kinases, are composed of an 85kDa regulatory/adapter subunit (p85) and a 110kDa catalytic subunit (p110). <ref name="Flip"> PMID: 10525402</ref> | ||
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==Adapter Subunit== | ==Adapter Subunit== | ||
<StructureSection load='1dq8' size=' | <StructureSection load='1dq8' size='450' side='right' scene='User:David_Canner/Sandbox_P/Full/4' caption='Structure of PI3K p110, ([[3hhm]])'> | ||
===The p85 Adapter Subunit=== | ===The p85 Adapter Subunit=== | ||
Class IA PI3Ks are tightly associated with a 85 kDa regulatory subunit called p85.<ref name="Wymann"/> P85 contains a Src homology 3 (SH3) domain, a breakpoint-cluster region homology (BH) domain between two proline-rich regions, and two C-terminal SH2 domains separated by an inter-SH2 (iSH2) region, which tightly binds p85 to the catalytic subunit.<ref>PMID:1707345</ref> Since PI3K has multiple protein-interaction domains, p85 is able to interact with several signaling molecules simultaneously, allowing for significant fine tuning of PI3K activity. <ref name="Wymann"> PMID: 9838078</ref> | Class IA PI3Ks are tightly associated with a 85 kDa regulatory subunit called p85.<ref name="Wymann"/> P85 contains a Src homology 3 (SH3) domain, a breakpoint-cluster region homology (BH) domain between two proline-rich regions, and two C-terminal SH2 domains separated by an inter-SH2 (iSH2) region, which tightly binds p85 to the catalytic subunit.<ref>PMID:1707345</ref> Since PI3K has multiple protein-interaction domains, p85 is able to interact with several signaling molecules simultaneously, allowing for significant fine tuning of PI3K activity. <ref name="Wymann"> PMID: 9838078</ref> | ||
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All PI3K catalytic subunits possess intrinsic protein serine kinase activity. PI3K regulatory subunits can be phophorylated by the catalytic subunit (p110) at specific sites. For example, phophorylation of Ser 608, a residue located in an area of the iSH2 domain that is critical for PIP2 presentation to the catalytic subunit, results in a dramatic reduction in PI3K lipid kinase activity.<ref>PMID: 8313897</ref> Additionally, tyrosines 580 and 607 can be phosphorylated upon stimulation with insulin and growth factor along with <scene name='User:David_Canner/Sandbox_P/Tyr_508/1'>Tyr 508 upon PDGF receptor mediation</scene>. <ref name="Wymann"/> Phosphorylation of Tyr 688 in the CSH2 domain by Abl and Lck results in reduced affinity for phosphopeptides and subsequent activation of the catalytic domain. <ref>PMID:9461588 </ref> | All PI3K catalytic subunits possess intrinsic protein serine kinase activity. PI3K regulatory subunits can be phophorylated by the catalytic subunit (p110) at specific sites. For example, phophorylation of Ser 608, a residue located in an area of the iSH2 domain that is critical for PIP2 presentation to the catalytic subunit, results in a dramatic reduction in PI3K lipid kinase activity.<ref>PMID: 8313897</ref> Additionally, tyrosines 580 and 607 can be phosphorylated upon stimulation with insulin and growth factor along with <scene name='User:David_Canner/Sandbox_P/Tyr_508/1'>Tyr 508 upon PDGF receptor mediation</scene>. <ref name="Wymann"/> Phosphorylation of Tyr 688 in the CSH2 domain by Abl and Lck results in reduced affinity for phosphopeptides and subsequent activation of the catalytic domain. <ref>PMID:9461588 </ref> | ||
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==The Catalytic Subunit== | ==The Catalytic Subunit== | ||
===The Catalytic Subunit (P110) of Class 1 PI3Ks=== | ===The Catalytic Subunit (P110) of Class 1 PI3Ks=== | ||
The catalytic subunit, P110 has several isoforms that associate with different classes of PI3Ks. P110α, β, and δ associate with Class IA PI3Ks while p110γ associates with Class 1B PI3ks. <ref name="Wymann"/> The <scene name='User:David_Canner/Sandbox_P/Full/1'>p110α subunit contains several domains including</scene> an N-terminal adaptor-binding domain (ABD), a Ras binding domain (RBD) a C2 domain that likely binds to the cellular membrane, a helical domain (HD) with unknown function, and the actual catalytic kinase domain. <ref name="Amzel"> PMID: 19805105 </ref> The actions of these domains are coordinated by the nSH2 communicating domain in p85. | The catalytic subunit, P110 has several isoforms that associate with different classes of PI3Ks. P110α, β, and δ associate with Class IA PI3Ks while p110γ associates with Class 1B PI3ks. <ref name="Wymann"/> The <scene name='User:David_Canner/Sandbox_P/Full/1'>p110α subunit contains several domains including</scene> an N-terminal adaptor-binding domain (ABD), a Ras binding domain (RBD) a C2 domain that likely binds to the cellular membrane, a helical domain (HD) with unknown function, and the actual catalytic kinase domain. <ref name="Amzel"> PMID: 19805105 </ref> The actions of these domains are coordinated by the nSH2 communicating domain in p85. | ||
<html5media height="360" width="640">https://vimeo.com/540290912</html5media> | |||
The video above depicts the ATP binding pocket of PI3K. | |||
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The <scene name='User:David_Canner/Sandbox_P/Helical_overview/2'>helical domain in p110</scene>, whose function isn’t thoroughly understood, interacts with nSH2 via charge interactions. The HD residue, <scene name='User:David_Canner/Sandbox_P/Helical_domain/1'>Glu 542 forms a | The <scene name='User:David_Canner/Sandbox_P/Helical_overview/2'>helical domain in p110</scene>, whose function isn’t thoroughly understood, interacts with nSH2 via charge interactions. The HD residue, <scene name='User:David_Canner/Sandbox_P/Helical_domain/1'>Glu 542 forms a salt bridge with Arg 358 on NSH2 while Glu 545 interacts with NSH2 Lys 379</scene>. These residues are known hotspot mutations which are associated with various types of cancer. <ref name="Amzel"/> This loop in <scene name='User:David_Canner/Sandbox_P/Nsh2__and_helical_ligand_out/2'>the helical domain </scene> which contains the hotspots (residues 542-546) is located precisely where <scene name='User:David_Canner/Sandbox_P/Nsh2_ligand_just_ligand_full/1'> the phosphopeptide of NSH2 ligands, like PDGFR, bind to NSH2.</scene> The salt bridge formed between <scene name='User:David_Canner/Sandbox_P/Nsh2_disruption_of_salt/1'>Glu 542 and nSH2 is disrupted upon binding phosphorylated peptides</scene> like PDGFR, eliminating nSH2-mediated inhibition of p110α and activating the enzyme to phosphorylate PIP2 into PIP3. The hotspot mutation at Glu 542 accomplishes the same thing by eliminating the salt bridge and uninhibiting p110α. It is the <scene name='User:David_Canner/Sandbox_P/Kinase_with_atp_full/2'>kinase domain </scene> which <scene name='User:David_Canner/Sandbox_P/Kinase_with_atp_zoomed/3'>binds ATP to provide the phosphate group</scene> used to convert PIP2 into PIP3. <ref name="Amzel"/> | ||
===Model for Catalysis=== | ===Model for Catalysis=== | ||
Although no <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>crystal structure of PI3K</scene> with bound substate analog has been solved, a model for PIP2 phosphorylation has been developed and is generally supported. <ref name="Walker2">PMID:10580505</ref> In this model, the headgroup of PIP2 is <scene name='User:David_Canner/Sandbox_P/Catalytic_cavity/2'>positioned in a cavity</scene> between the <scene name='User:David_Canner/Sandbox_P/Catalytic_site/1'>C-terminal helix 12 of the kinase domain, the “activation” loop, and the “catalytic” loop</scene>. This puts the 5-phosphate of PIP2 near Lys 973 and the <scene name='User:David_Canner/Sandbox_P/Catalytic_site_atp_lys/1'>I-phosphate of ATP near Lys 807 and Lys 808</scene>. The <scene name='User:David_Canner/Sandbox_P/Catalytic_site_pip2/1'>basic residues Arg 947</scene> and Lys 973 can bind the 4-Phosphate of PIP2 and help provide the Class I PI3Ks with their specificity for PIP2. Once PIP2 and ATP are bound, it is believed <scene name='User:David_Canner/Sandbox_P/Catalytic_site_his/1'>His 948 rotates to interact with PIP2</scene>, deprotonating it at the C-3 Hydroxyl position creating a nucleophile. This nucleophile subsequently attacks the gamma phosphate of ATP producing PIP3. <ref name="Walker2"/> | Although no <scene name='User:David_Canner/Sandbox_P/Inhibitor_main/4'>crystal structure of PI3K</scene> with bound substate analog has been solved, a model for PIP2 phosphorylation has been developed and is generally supported. <ref name="Walker2">PMID:10580505</ref> In this model, the headgroup of PIP2 is <scene name='User:David_Canner/Sandbox_P/Catalytic_cavity/2'>positioned in a cavity</scene> between the <scene name='User:David_Canner/Sandbox_P/Catalytic_site/1'>C-terminal helix 12 of the kinase domain, the “activation” loop, and the “catalytic” loop</scene>. This puts the 5-phosphate of PIP2 near Lys 973 and the <scene name='User:David_Canner/Sandbox_P/Catalytic_site_atp_lys/1'>I-phosphate of ATP near Lys 807 and Lys 808</scene>. The <scene name='User:David_Canner/Sandbox_P/Catalytic_site_pip2/1'>basic residues Arg 947</scene> and Lys 973 can bind the 4-Phosphate of PIP2 and help provide the Class I PI3Ks with their specificity for PIP2. Once PIP2 and ATP are bound, it is believed <scene name='User:David_Canner/Sandbox_P/Catalytic_site_his/1'>His 948 rotates to interact with PIP2</scene>, deprotonating it at the C-3 Hydroxyl position creating a nucleophile. This nucleophile subsequently attacks the gamma phosphate of ATP producing PIP3. <ref name="Walker2"/> | ||
</StructureSection> | </StructureSection> | ||
==Additional Resources== | |||
* See [[Phosphoinositide 3-Kinases]] for the main page or [[PI3K Activation, Inhibition, & Medical Implications]] for PI3Ks medical importance. | |||
* See [[Cancer]] for additional information. | |||
* See [[Diabetes]] for additional information. | |||
==References== | ==References== | ||
