Sandbox Reserved 1108

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==4iv6==
==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=''>
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This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.
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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.
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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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== Function ==
== Function ==
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4iv6 functions were not studied and only structural infos are disponible.
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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.
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E.C.1.3.8.1[https://enzyme.expasy.org/EC/1.3.8.1] is communly found in following pathways with various functions:
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[[Analine metabolism]]:[https://www.brenda-enzymes.info/pathway_index.php?pathway=alanine%20metabolism&ecno=1.3.8.1]
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[[Butanoate metabolism]]:[https://www.genome.jp/kegg-bin/show_pathway?map00650+1.3.8.1]
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[[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]
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[[Valine Leucine and isoleucine pathways]]:[https://www.genome.jp/kegg-bin/show_pathway?map00280+1.3.8.1]
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==Primary and Secondary structure<ref>http://www.rcsb.org/structure/4IV6</ref>==
==Primary and Secondary structure<ref>http://www.rcsb.org/structure/4IV6</ref>==
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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>''' 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] ). 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.
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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.
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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).
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).
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==Tertiary structures==
==Tertiary structures==
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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] ).
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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>
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==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>==
==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>==
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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
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[[Pathways]]: Fatty acid degradation
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[[Informed Pathways]]: Fatty acid degradation
[[Other information]]:
[[Other information]]:
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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.
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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
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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.
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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.
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== Structural highlights ==
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== Structural highlights summary ==
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<scene name='82/829361/Biological_unit/1'>Biological unit</scene>
<scene name='82/829361/Biological_unit/1'>Biological unit</scene>
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<scene name='82/829361/Asymetrical_unit/2'>Asymetrical unit</scene> :Light Grey:1st sub-unit, Light green:2nd sub-unit, Blue and red:FDA
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<scene name='82/829361/2asymunit/1'>Asymmetric units</scene>
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<scene name='82/829361/Betasheetchaina_asymunit/1'>Beta-sheets</scene>
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<scene name='82/829361/Helixalphachaina_asymunit/1'>Helices</scene>
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<scene name='82/829361/Secondary_structure/1'>Secondary structure</scene>
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<scene name='82/829361/Chainea_asymunit/2'>A chain</scene>
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<scene name='82/829361/Secondary_structure/1'>Secondary structure</scene> : Red: helix alpha, Blue:FDA, Yellow: Beta sheet
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<scene name='82/829361/Chaineb_asymunit/1'>B chain</scene>
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<scene name='82/829361/Hydrophobic/1'>Hydrophobic region</scene> : Green: FDA, Purple: Polar region, Light grey: Hydrophobic region
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<scene name='82/829361/Hydrophobic/1'>Hydrophobic region</scene>
</StructureSection>
</StructureSection>
== References ==
== References ==
<references/>
<references/>

Current revision

This Sandbox is Reserved from 25/11/2019, through 30/9/2020 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1091 through Sandbox Reserved 1115.
To get started:
  • Click the edit this page tab at the top. Save the page after each step, then edit it again.
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4iv6

Caption for this structure

Drag the structure with the mouse to rotate

References

  1. ↑ http://www.rcsb.org/structure/4IV6
  2. ↑ https://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4iv6
  3. ↑ https://en.wikipedia.org/wiki/Flavin_adenine_dinucleotide
  4. ↑ http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=4iv6
  5. ↑ https://www.ebi.ac.uk/intenz/query?cmd=SearchEC&ec=1.3.8.1
  6. ↑ https://enzyme.expasy.org/EC/1.3.8.1
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