Sandbox Reserved 1063: Difference between revisions
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FadD13 is composed of 503 amino acids which are divided into two domains. The larger of the two domains is the N-terminal domain composed of <scene name='69/694230/Fadd13_subunits/8'>residues 1-395</scene> shown in blue. The smaller of the two domains is the C-terminal domain composed of <scene name='69/694230/Fadd13_subunits/10'>residues 402-503</scene> shown in yellow. These two domains are held together by a flexible 6 amino acid linker (<scene name='69/694230/Fadd13_subunits/11'>residues 396-401</scene>) shown in black<ref name="Anderson 2012"/>. Research has also shown that altering V209D, D382A, and W377A effects the structual stability of FadD13. <scene name='69/694230/Fadd13_subunits/18'>Val 209</scene> and <scene name='69/694230/Fadd13_subunits/19'>Asp 382</scene> showed marginally reduced cytoplasmic expression, while <scene name='69/694230/Fadd13_subunits/17'>Trp 377</scene> showed a noteworthy low cytosolic expression<ref name="Khare 2009"/>. | FadD13 is composed of 503 amino acids which are divided into two domains. The larger of the two domains is the N-terminal domain composed of <scene name='69/694230/Fadd13_subunits/8'>residues 1-395</scene> shown in blue. The smaller of the two domains is the C-terminal domain composed of <scene name='69/694230/Fadd13_subunits/10'>residues 402-503</scene> shown in yellow. These two domains are held together by a flexible 6 amino acid linker (<scene name='69/694230/Fadd13_subunits/11'>residues 396-401</scene>) shown in black<ref name="Anderson 2012"/>. Research has also shown that altering V209D, D382A, and W377A effects the structual stability of FadD13. <scene name='69/694230/Fadd13_subunits/18'>Val 209</scene> and <scene name='69/694230/Fadd13_subunits/19'>Asp 382</scene> showed marginally reduced cytoplasmic expression, while <scene name='69/694230/Fadd13_subunits/17'>Trp 377</scene> showed a noteworthy low cytosolic expression<ref name="Khare 2009"/>. | ||
===Active Site=== | ===Active Site=== | ||
The active site of FadD13 is composed of an <scene name='69/694230/Fadd13_subunits/12'>ATP/AMP binding region</scene>. This region is comprised of residues 164-TSGTTGHPKG173-173 shown in red which binds to the phosphate group, and residues 298-VQGYALTE-305 shown in blue which binds to the adenine group. Research has also shown that <scene name='69/694230/Fadd13_subunits/16'>Ser 404</scene> plays a major role in binding of CoA. Ser 404 was shown to have a 4-fold enhancement for the Km value of CoA.<ref name="Khare 2009">DOI: 10.1371/journal.pone.0008387</ref> | The active site of FadD13 is composed of an <scene name='69/694230/Fadd13_subunits/12'>ATP/AMP binding region</scene>. This region is comprised of residues 164-TSGTTGHPKG173-173 shown in red (show atoms by color?) which binds to the phosphate group, and residues 298-VQGYALTE-305 shown in blue which binds to the adenine group. Research has also shown that <scene name='69/694230/Fadd13_subunits/16'>Ser 404</scene> plays a major role in binding of CoA. Ser 404 was shown to have a 4-fold enhancement for the Km value of CoA.<ref name="Khare 2009">DOI: 10.1371/journal.pone.0008387</ref> | ||
===Hydrophobic Tunnel=== | ===Hydrophobic Tunnel=== | ||
FadD13 has a distinct hydrophobic tunnel that starts at the active site and is capped by | FadD13 has a distinct hydrophobic tunnel that starts at the active site and is capped by a positively charged surface patch.The <scene name='69/694230/Fadd13_subunits/13'>hydrophobic tunnel</scene> is found inside the N-terminal domain. It is composed of six beta sheets (beta 9-14) shown in green and two alpha helices (alpha 8-9) shown in red.The hydrophobic tunnel allows large lipids/fatty acids, up to 26 carbons, to bind. | ||
===Surface Patch=== | ===Surface Patch=== | ||
FadD13 has an arginine and aromatic rich surface patch that allows it to be a [http://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral-membrane protein]<ref name="Khare 2009"/>.The hydrophobic tunnel is capped by the arginine and aromatic rich <scene name='69/694230/Fadd13_subunits/14'>lid loop</scene> shown in yellow that is involved in the peripheral binding of the enzyme to the membrane. Based on the structural information present and biochemical information, it is likely that the lid loop opens up upon contact with the membrane. This would allow for the substrate to bind and have the lipid tail to reside in the membrane during catalysis (figure 2)<ref name="Anderson 2012"/>. Six key arginine residues, <scene name='69/694230/Fadd13_subunits/15'>Arg 9, 17, 195, 197, 199, and 244</scene> create a positively charged surface that is likely involved in initially recruiting FadD13 to the membrane. When these residues were replaced with hyrdrophobic alanine residues, membrane binding increased. This points to the important role of hydrophobic interactions in keeping the protein bound at the membrane<ref name="Anderson 2012">PMID: 22560731</ref>. | FadD13 has an arginine and aromatic rich surface patch that allows it to be a [http://en.wikipedia.org/wiki/Peripheral_membrane_protein peripheral-membrane protein]<ref name="Khare 2009"/>.The hydrophobic tunnel is capped by the arginine and aromatic rich <scene name='69/694230/Fadd13_subunits/14'>lid loop</scene> shown in yellow that is involved in the peripheral binding of the enzyme to the membrane. Based on the structural information present and biochemical information, it is likely that the lid loop opens up upon contact with the membrane. This would allow for the substrate to bind and have the lipid tail to reside in the membrane during catalysis (figure 2)<ref name="Anderson 2012"/>. Six key arginine residues, <scene name='69/694230/Fadd13_subunits/15'>Arg 9, 17, 195, 197, 199, and 244</scene> create a positively charged surface that is likely involved in initially recruiting FadD13 to the membrane. When these residues were replaced with hyrdrophobic alanine residues, membrane binding increased. This points to the important role of hydrophobic interactions in keeping the protein bound at the membrane<ref name="Anderson 2012">PMID: 22560731</ref>. | ||