User:Kaitlyn Roberts/Sandbox 2
From Proteopedia
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=== Tertiary Structure === | === Tertiary Structure === | ||
The overall structure of the enzyme is a <scene name='87/877559/Tetramer/10'>tetramer</scene> structure or a <scene name='87/877559/Tetramer/11'>dimer of dimers</scene>. The functional building block of SOAT is a <scene name='87/877559/Dimer/3'>dimer</scene> which is made up of two identical <scene name='87/877559/Monomer/5'>monomer</scene> structures. The [https://en.wikipedia.org/wiki/Amino_acid residues] that form the dimer interface are mostly hydrophobic and interact with each other in a shape-complementary manner. Mutating residues within the dimer interface reduced the dimers to monomer fractions, indicating that the dimeric architecture is important for the activity of the enzyme. The dimerization of SOAT is mainly mediated by [https://en.wikipedia.org/wiki/Van_der_Waals_force extensive van der Waals interactions] between TM1 in one protomer and the [https://en.wikipedia.org/wiki/Lumen_(anatomy) lumenal segment] of TM6 and the [https://en.wikipedia.org/wiki/Cytosol cytosolic segment] of TM9 in the other. TM1, TM5, TM6 and TM9 from the two protomers enclose a deep hydrophobic pocket that is open to the lumenal side. Numerous hydrophobic residues on TM6 and TM9 from one protomer contact those on TM1 from the other protomer. On the intracellular side, hydrophobic residues on IH1 of each protomer interact with each other to stabilize the dimer.<ref name="Qian">PMID:32433614</ref> | The overall structure of the enzyme is a <scene name='87/877559/Tetramer/10'>tetramer</scene> structure or a <scene name='87/877559/Tetramer/11'>dimer of dimers</scene>. The functional building block of SOAT is a <scene name='87/877559/Dimer/3'>dimer</scene> which is made up of two identical <scene name='87/877559/Monomer/5'>monomer</scene> structures. The [https://en.wikipedia.org/wiki/Amino_acid residues] that form the dimer interface are mostly hydrophobic and interact with each other in a shape-complementary manner. Mutating residues within the dimer interface reduced the dimers to monomer fractions, indicating that the dimeric architecture is important for the activity of the enzyme. The dimerization of SOAT is mainly mediated by [https://en.wikipedia.org/wiki/Van_der_Waals_force extensive van der Waals interactions] between TM1 in one protomer and the [https://en.wikipedia.org/wiki/Lumen_(anatomy) lumenal segment] of TM6 and the [https://en.wikipedia.org/wiki/Cytosol cytosolic segment] of TM9 in the other. TM1, TM5, TM6 and TM9 from the two protomers enclose a deep hydrophobic pocket that is open to the lumenal side. Numerous hydrophobic residues on TM6 and TM9 from one protomer contact those on TM1 from the other protomer. On the intracellular side, hydrophobic residues on IH1 of each protomer interact with each other to stabilize the dimer.<ref name="Qian">PMID:32433614</ref> | ||
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- | === Active Site === | ||
- | The <scene name='87/877555/As_residues/4'>active site</scene> of this enzyme has 3 main residues that are essential for the catalytic activity of SOAT. <scene name='87/877555/As_acylcoa_interaction/1'>H460, W420, and N421</scene> work to stabilize the substrates as well as serve other roles in the mechanism of action. Many acyl transferases utilize histidine as the catalytic base. The conserved H460 is crucial for SOAT activity and is the putative catalytic residue. A single point mutation of the histidine at position 460 to alanine resulted in the complete abolition of enzymatic activity indicating its essential role in the mechanism. Along with H460, there are several other residues in the central cavity that are important for SOAT function. Most residues aligning the interior of the reaction chamber are highly conserved indicating that the local environment in the central cavity is important for the catalytic reaction. | ||
=== Tunnel System === | === Tunnel System === | ||
A main structural element of this enzyme is the tunnel systems. There are 3 main tunnels in each monomer: the cytosolic (C) tunnel opening to the cytosol, the transmembrane(T) tunnel opening to the membrane, and the lumenal(L) tunnel opens to the lumen. The C tunnel opens to the cytosol of the cell and is the entrance site for the Acyl CoA into the active site. Surface representations of SOAT indicate that there are 2 alpha helices that block the entrance to the C tunnel, therefore a conformational change needs to occur to move the 2 helices so the substrate can enter the tunnel. The T tunnel opens into the membrane and is where cholesterol enters to have access to the active site. The two substrates are catalyzed by the H460 in the active site to form the cholesteryl ester. The products then leave via different pathways. The CoA-SH in the C tunnel leaves via that tunnel and is released back into the cytosol. The cholesteryl ester then leaves via either the T tunnel into the membrane or through the L tunnel into the lumen of the cell. | A main structural element of this enzyme is the tunnel systems. There are 3 main tunnels in each monomer: the cytosolic (C) tunnel opening to the cytosol, the transmembrane(T) tunnel opening to the membrane, and the lumenal(L) tunnel opens to the lumen. The C tunnel opens to the cytosol of the cell and is the entrance site for the Acyl CoA into the active site. Surface representations of SOAT indicate that there are 2 alpha helices that block the entrance to the C tunnel, therefore a conformational change needs to occur to move the 2 helices so the substrate can enter the tunnel. The T tunnel opens into the membrane and is where cholesterol enters to have access to the active site. The two substrates are catalyzed by the H460 in the active site to form the cholesteryl ester. The products then leave via different pathways. The CoA-SH in the C tunnel leaves via that tunnel and is released back into the cytosol. The cholesteryl ester then leaves via either the T tunnel into the membrane or through the L tunnel into the lumen of the cell. | ||
- | == Catalytic Mechanism == | + | === Active Site === |
+ | The <scene name='87/877555/As_residues/4'>active site</scene> of this enzyme has 3 main residues that are essential for the catalytic activity of SOAT. <scene name='87/877555/As_acylcoa_interaction/1'>H460, W420, and N421</scene> work to stabilize the substrates as well as serve other roles in the mechanism of action. Many acyl transferases utilize histidine as the catalytic base. The conserved H460 is crucial for SOAT activity and is the putative catalytic residue. A single point mutation of the histidine at position 460 to alanine resulted in the complete abolition of enzymatic activity indicating its essential role in the mechanism. Along with H460, there are several other residues in the central cavity that are important for SOAT function. Most residues aligning the interior of the reaction chamber are highly conserved indicating that the local environment in the central cavity is important for the catalytic reaction. | ||
+ | |||
+ | === Catalytic Mechanism === | ||
The distal-most nitrogen on H460 acts as a base catalyst to deprotonate the hydroxyl group of a cholesterol molecule. This leaves the cholesterol oxygen with a negative charge, making it a good nucleophile. The [https://en.wikipedia.org/wiki/Nucleophile nucleophilic] oxygen attacks the Acyl CoA substrate at the carbonyl carbon, kicking electron density up to the carbonyl oxygen. Shown in brackets, the transition state is stabilized by N421 and newly protonated H460. | The distal-most nitrogen on H460 acts as a base catalyst to deprotonate the hydroxyl group of a cholesterol molecule. This leaves the cholesterol oxygen with a negative charge, making it a good nucleophile. The [https://en.wikipedia.org/wiki/Nucleophile nucleophilic] oxygen attacks the Acyl CoA substrate at the carbonyl carbon, kicking electron density up to the carbonyl oxygen. Shown in brackets, the transition state is stabilized by N421 and newly protonated H460. | ||
[[Image:SOATmech1.png|400 px|right|thumb|Figure 1. Mech 1]] | [[Image:SOATmech1.png|400 px|right|thumb|Figure 1. Mech 1]] | ||
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[[Image:SOATmech2.png|400 px|right|thumb|Figure 2. Mech 2]] | [[Image:SOATmech2.png|400 px|right|thumb|Figure 2. Mech 2]] | ||
- | + | == Inhibitors == | |
CI-976 inhibits SOAT activity in a dose-dependent manner. The location of CI-976 is found right in the <scene name='87/877559/Active_site_overview/1'>catalytic center</scene> with its large trimethoxyphenyl head sandwiched right between the catalytic residues <scene name='87/877559/Residues_and_inhibitor/17'>H460, W420, and N421</scene>. This suggests that CI-976 inhibits the enzyme by preventing the loading of the substrate into the catalytic center, which makes sense given the competitive behavior of CI-976. Mutations of CI-976 interaction residues, N421A, H460A, and H460N greatly diminish the enhancement effect of CI976 on the thermostability of the SOAT dimer. | CI-976 inhibits SOAT activity in a dose-dependent manner. The location of CI-976 is found right in the <scene name='87/877559/Active_site_overview/1'>catalytic center</scene> with its large trimethoxyphenyl head sandwiched right between the catalytic residues <scene name='87/877559/Residues_and_inhibitor/17'>H460, W420, and N421</scene>. This suggests that CI-976 inhibits the enzyme by preventing the loading of the substrate into the catalytic center, which makes sense given the competitive behavior of CI-976. Mutations of CI-976 interaction residues, N421A, H460A, and H460N greatly diminish the enhancement effect of CI976 on the thermostability of the SOAT dimer. | ||
Revision as of 13:11, 13 April 2021
Human Sterol O-acyltransferase
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References
- ↑ Guan C, Niu Y, Chen SC, Kang Y, Wu JX, Nishi K, Chang CCY, Chang TY, Luo T, Chen L. Structural insights into the inhibition mechanism of human sterol O-acyltransferase 1 by a competitive inhibitor. Nat Commun. 2020 May 18;11(1):2478. doi: 10.1038/s41467-020-16288-4. PMID:32424158 doi:http://dx.doi.org/10.1038/s41467-020-16288-4
- ↑ Qian H, Zhao X, Yan R, Yao X, Gao S, Sun X, Du X, Yang H, Wong CCL, Yan N. Structural basis for catalysis and substrate specificity of human ACAT1. Nature. 2020 May;581(7808):333-338. doi: 10.1038/s41586-020-2290-0. Epub 2020 May, 13. PMID:32433614 doi:http://dx.doi.org/10.1038/s41586-020-2290-0
Student Contributors
- Kylie Pfifer
- Stepahnie Pellegrino
- Kaitlyn Roberts