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| = FadD13 = | | {{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> |
| | ==Your Protein Name here== |
| | <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> |
| | This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs. |
| | You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue. |
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| <StructureSection load='3r44' size='340' side='right' caption='3R44' scene=''>
| | == Biological Function == |
| == Introduction ==
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| ''<scene name='69/694230/Fadd13_subunits/5'>FadD13</scene>'' ''Mycobacterium Tuberculosis'' is an ACSVL (Acyl-CoA synthetases very long) peripheral membrane protein<ref>PMID: 17762044</ref>. ACS proteins activate [http://en.wikipedia.org/wiki/Lipid lipids] and [http://en.wikipedia.org/wiki/Fatty_acid fatty acids] before going into [http://en.wikipedia.org/wiki/Metabolic_pathway metabolic pathways]. FadD13 is soluble unlike other ACSVL proteins. FadD13 contains a hydrophobic tunnel for fatty acids to bind to, as well as an arginine rich lid loop that binds to the cell membrane. The binding of ATP causes structural changes promoting the binding of the hydrophobic substrates. Formation of an acyl-adenylate intermediate induces a 140 degree rotation of the small domain and binding of [http://en.wikipedia.org/wiki/Coenzyme_A CoA] for production of the final product, a fatty acyl-CoA thioester<ref>PMID: 19345228</ref>. Shown below is the general mechanism for ACS proteins.
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| [[Image:FadD13 steps.png|390 px|thumb|left|Figure 1 shows the general outline of the binding of ATP and acyl substrates to an ACSVL enzyme. This is the accepted mechanism for these types of proteins.<ref name="Anderson 2012"/>]]
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| == Background == | | == Structural Overview == |
| ''Mycobacterium Tuberculosis'' is the causative agent of [http://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] commonly abbreviated TB. TB causes approximately 1.4 million deaths every year. The cost for treatment of patients with TB between the years 2010-2015 was approximately 16 billion dollars. TB is spread through the air, not by contact. There are two forms of TB, latent TB and TB disease.
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| == Structural Highlights == | | == Mechanism of Action == |
| 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"/>.
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| ===Active Site===
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| 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>
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| ===Hydrophobic Tunnel===
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| 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 to the enzyme to be activated.
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| ===Surface Patch===
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| 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>.
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| [[Image:Proposed Mechanism.png|390 px|thumb|left|Figure 2 shows the proposed mechanism for an ACSVL protein bound to the membrane<ref name="Anderson 2012"/>]]
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| == Function ==
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| The FadD13 enzyme functions to activate lipids. Once the lipids are activated, they can continue on into metabolic pathways. This is done by ATP/AMP binding to the <scene name='69/694230/Fadd13_subunits/12'>ATP/AMP binding region</scene>. Once ATP/AMP is bound, the long lipid chain up to 26 carbons may bind in the <scene name='69/694230/Fadd13_subunits/13'>hydrophobic tunnel</scene> of the enzyme. Upon binding of the substrate, the C terminal swings up to close off the tunnel. From there CoA can bind to produce the final product, an acyl-CoA Thioester. The lipid can now move transversely throughout the membrane and throughout the rest of the cell. Figure 2 shows the proposed mechanism for ACSVL proteins<ref name="Anderson 2012"/>.
| | == Zinc Ligand(s) == |
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| ==Future Work== | | == Other Ligands == |
| Currently there is no crystal structure available for FadD13 complexes with lipids. Therefore the the mechanism that researchers proposed in (figure 2) is just based on the biochemical and structural information that they have been able to gather. The reason for the lack of a crystal structure for FadD13 complexes with ligands is due to the need for membrane interaction. The membrane interaction is required to induece a substrate binding conformation of the hydrophobic channel. In the future, researchers would like to develop a crystal structure of FadD13 peripherally bound to the membrane to gain a better understanding of how substrates bind. Despite the lack of a crystal structure, the proposed mechanism that researches developed (figure 2) could help synthesize inhibitors and locate certain locations for drug inhibitors to bind.<ref name="Anderson 2012"/>
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| | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. |
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| ==Relevant Pages==
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| * [http://proteopedia.org/wiki/index.php/3t5b 3T5B]
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| * [http://proteopedia.org/wiki/index.php/3t5c 3T5C]
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| </StructureSection> | | </StructureSection> |
| == References == | | == References == |
| {{reflist}}
| | <references/> |