Sandbox Reserved 1638
From Proteopedia
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{{Sandbox_Reserved_BHall_F20}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | {{Sandbox_Reserved_BHall_F20}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --> | ||
| - | == | + | ==Structure== |
| - | <StructureSection load='6X0J | + | <StructureSection load='6X0J' 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. | 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. | 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. | ||
== Function of your Protein == | == Function of your Protein == | ||
| + | <scene name='86/861620/Regular_protein/1'>SidA catalyzes NADPH-dependent hydroxylation of ornithine through oxidative mechanisms.</scene> SidA acts as both a receptor and an enzyme. As a receptor it extracts metals such as iron and takes it into cells. It is also an enzyme because it uses the FAD in the reactions. | ||
== Biological relevance and broader implications == | == Biological relevance and broader implications == | ||
| - | + | SidA is from Aspergillus fumigatus and is a fungal disease drug target that is involved in the production of hydromate-containing siderophores, that are used by a pathogen to take iron. This protein affects the lungs and can be fatal in humans and animals. Because iron is the host organism, it is sequestered by the iron-building proteins which makes it a restricted nutrient for SidA. This is relevant because they are finding new information about configurational dynamics in flavin-dependent monooxygenases. We are using this to understand all of the different active sites and their conformations during the catalytic cycle. This results in the fine-tuning of inhibitor discovery efforts. | |
== Important amino acids == | == Important amino acids == | ||
| - | + | The important amino acids to pay attention to are Tyr324, Tyr276, Ser325, Asn323, and Asn275. Tyr324 is important because it moves over by 10A and shifts away from the active site. We have a triad which consists of Asn323, -FTyr324, and -Ser325. <scene name='86/861620/Protein_view_2_residues/1'>The important residues to pay attention to are 1-28</scene>. This image attacked to residues shows the residue amino acids to pay attention to. Our ligands are displayed in the next section but we see how some are and aren't bound. | |
== Structural highlights == | == Structural highlights == | ||
| - | + | <scene name='86/861620/Ligand_only/1'>Our structure has but also doesn't have ligands</scene>. The ligands it does have are NADPH and FAD and they're bound, just not to the substrate. There are 4 crystal structures formed. <scene name='86/861620/Secondary/1'>Our secondary structures are in orange and show the polypeptide chains in a helices.</scene> <scene name='86/861620/Cartoon/1'>You can see clearly the inside and outside of the protein.</scene> The outside green, pink, blue, and yellow show the beta sheets and helices in the secondary structure, about 90% helices and 10% beta. The important parts to recognize are the purple helices. <scene name='86/861620/Hydrophobic/1'>These are considered to be polar and hydrophobic.</scene> | |
== Other important features == | == Other important features == | ||
| + | One feature is that <scene name='86/861620/Charge/1'>His is light blue and shows</scene> that the Pka is 6.0. The charges would either be red or blue and it doesn't look like those are present. The other important feature is that there are <scene name='86/861620/Chains/1'>four separate chains</scene>. They are clearly marked by four separate colors and show different branches in the middle. | ||
| - | 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. | ||
| - | </StructureSection> | + | <ref>PMID:32723870</ref></StructureSection> |
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
| This Sandbox is Reserved from 09/18/2020 through 03/20/2021 for use in CHEM 351 Biochemistry taught by Bonnie Hall at Grand View University, Des Moines, IA. This reservation includes Sandbox Reserved 1628 through Sandbox Reserved 1642. |
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Structure
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References
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
- ↑ Campbell AC, Stiers KM, Martin Del Campo JS, Mehra-Chaudhary R, Sobrado P, Tanner JJ. Trapping conformational states of a flavin-dependent N-monooxygenase in crystallo reveals protein and flavin dynamics. J Biol Chem. 2020 Jul 28. pii: RA120.014750. doi: 10.1074/jbc.RA120.014750. PMID:32723870 doi:http://dx.doi.org/10.1074/jbc.RA120.014750
