Sandbox Reserved 1108: Difference between revisions

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{{Sandbox_ESBS_2019}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
{{Sandbox_ESBS_2019}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
==Your Heading Here (maybe something like 'Structure')==
==4iv6==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
<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 &lt; and &gt; signs.
4iv6 is an  enzyme ''Mycobacterium tuberculosis'' which get his structure analyzed by Baugh et al. [https://www.ncbi.nlm.nih.gov/pubmed/25613812] with other enzymes homologue in order to fight ''Mycobacterium tuberculosis'' relative infections.
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 ==
== Function ==
==Primary and Secondary structure==
4iv6 functions were not studied and only structural infos are disponible.
Nevertheless we can consider datas from other E.C.1.3.8.1[https://enzyme.expasy.org/EC/1.3.8.1] which came from other organisms.
E.C.1.3.8.1[https://enzyme.expasy.org/EC/1.3.8.1] is communly found in following pathways with various functions:
 
[[Analine metabolism]]:[https://www.brenda-enzymes.info/pathway_index.php?pathway=alanine%20metabolism&ecno=1.3.8.1]
 
[[Butanoate metabolism]]:[https://www.genome.jp/kegg-bin/show_pathway?map00650+1.3.8.1]
 
[[Lipids metabolism]] : [https://www.brenda-enzymes.info/pathway_index.php?pathway=lipid%20metabolism&ecno=1.3.8.1][https://www.genome.jp/kegg-bin/show_pathway?map00071+1.3.8.1]
 
[[Valine Leucine and isoleucine pathways]]:[https://www.genome.jp/kegg-bin/show_pathway?map00280+1.3.8.1]
 
 
==Primary and Secondary structure<ref>http://www.rcsb.org/structure/4IV6</ref>==
 
Isovaleryl-CoA dehydrogenase is the assembly of '''<scene name='82/829361/2asymunit/1'>two asymmetric units</scene>''' each composed of '''two chains <scene name='82/829361/Chainea_asymunit/2'>A</scene> and <scene name='82/829361/Chaineb_asymunit/1'>B</scene>'''. Each of the two chains A and B are composed of 388 amino acids. An asymmetric unit is therefore composed of 776 amino acids and has a molecular weight of 86233.70 Da.
1% of the unit's amino acid have incomplete sidechains, which means that there are 11 missing residue in the assymetric unit.<ref>https://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4iv6</ref>
 
The A chain is made up of <scene name='82/829361/Helixalphachaina_asymunit/1'>17 helices</scene> (involving 221 residues) and <scene name='82/829361/Betasheetchaina_asymunit/1'>14 beta-sheets</scene> (61 residues).
Chain B is formed of <scene name='82/829361/Helixchainb_asymunit/1'>17 helices</scene> (involving 218 residues) and <scene name='82/829361/Betasheetchainb_asymunit/1'>14 beta-sheets</scene> (62 residues).
 
==Tertiary structures==
==Tertiary structures==
==Enzymatic reaction==
 
The two chains A and B of the isovaleryl-CoA dehydrogenase are linked by a <scene name='82/829361/Ligand_asymunit/1'>ligand</scene> (Dihydroflavine-Adenine Dinucleotide also known as [https://pubchem.ncbi.nlm.nih.gov/compound/Dihydroflavine-adenine-dinucleotide FADH2] ).
 
The protein is a tetramer, the surface between the two monomers of a single dimer of an acyl-CoA dehydrogenase contains the FAD binding sites and has extensive bonding interactions. There are 2 active sites in the tetramer, each of these 2 sites contains a FAD molecule and an acyl-CoA substrate binding site. <ref>https://en.wikipedia.org/wiki/Flavin_adenine_dinucleotide</ref>
 
==Enzymatic reaction<ref>http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=4iv6</ref><ref>https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=1.3.8.1</ref><ref>https://enzyme.expasy.org/EC/1.3.8.1</ref>==


[[Enzyme accepted name]]: Short-chain acyl-CoA dehydrogenase
[[Enzyme accepted name]]: Short-chain acyl-CoA dehydrogenase
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[[Products]]: a short-chain trans-2,3-dehydroacyl-CoA + reduced electron-transfer flavoprotein
[[Products]]: a short-chain trans-2,3-dehydroacyl-CoA + reduced electron-transfer flavoprotein


[[Pathways]]: Fatty acid degradation
[[Informed Pathways]]: Fatty acid degradation


[[Other information]]:
[[Other information]]:


The enzyme from beef liver can accept acyl-chain lengths from 3 to 8 carbon atoms. From different organism the range can vary so we ignore if M.tuberculosis gets the same lengths resolution.
The enzyme from beef liver can accept acyl-chain lengths from 3 to 8 carbon atoms. From different organism the range can vary so we ignore if ''Mycobacterium tuberculosis'' gets the same lengths resolution.


The highest activity reported for beef liver enzyme was for substrates with 4 and 5 carbon acyl-chain lengths.
The highest activity reported for beef liver enzyme was for substrates with 4 and 5 carbon acyl-chain lengths.
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4iv6 which belong to ''Mycobacterium tuberculosis'' was studied with other protein homolog.
4iv6 which belong to ''Mycobacterium tuberculosis'' was studied with other protein homolog.
They were chosen to be studied as potential TB-Drugs target
They were chosen to be studied as potential TB-Drugs target
Studies have been made on homolog similarities aimed on their active site because with the knowledges of many homolog active site structure and how they work, we can design a inhibitor of those enzyme which can stop essential reaction and reduce or stop ''M.tuberculosis'' infection.
Studies have been made on homolog similarities aimed on their active site because with the knowledges of many homolog active site structure and how they work, we can design a inhibitor of those enzyme which can stop essential reaction and reduce or stop ''Mycobacterium tuberculosis'' infection.
This strategy is called an « Homolog-rescue strategy ».
This strategy is called an « Homolog-rescue strategy ».
This strategy can be generalized for other drug target for other diseases.
This strategy can be generalized for other drug target for other diseases.




== Structural highlights ==
== Structural highlights summary ==
 
<scene name='82/829361/Biological_unit/1'>Biological unit</scene>
<scene name='82/829361/Biological_unit/1'>Biological unit</scene>


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.
<scene name='82/829361/2asymunit/1'>Asymmetric units</scene>
 
<scene name='82/829361/Betasheetchaina_asymunit/1'>Beta-sheets</scene>
 
<scene name='82/829361/Helixalphachaina_asymunit/1'>Helices</scene>
 
<scene name='82/829361/Secondary_structure/1'>Secondary structure</scene> 
 
<scene name='82/829361/Chainea_asymunit/2'>A chain</scene>
 
<scene name='82/829361/Chaineb_asymunit/1'>B chain</scene>
 
<scene name='82/829361/Hydrophobic/1'>Hydrophobic region</scene>


</StructureSection>
</StructureSection>
== References ==
== References ==
<references/>
<references/>
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