Sandbox Reserved 1508: Difference between revisions

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{{Sandbox_Reserved_ESBS}}

==The protein 5C04==

=='''The protein 5C04'''

== Headline text ==

==

<div align="justified">The protein 5C04 is classified as an oxidoreductase. We found it in the ''Mycobacterium tuberculosis'' organism, especially in the strain ATCC 25618/H37Rv. It can be expressed in ''Escherichia Coli'' bacteria. This is a pathogenic protein which is involved in the tuberculosis. Its pathogenicity is due to a specific mutation in the active site of peroxiredoxins.</div>

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At the active site of the enzyme, a pyrodoxal-phosphate cofactor is covalently linked to the Lysine 51, an invariant residue. A parallel β-sheet associated with three α-helices are part of the N terminal domain (residues 46 to 153). Two of those α-helices are part of the dimer interface and the third one is partly forming the entrance of the active site as on the other side of the β-sheet. On the other hand the C-terminal domain is made of 6-stranded mixed β-sheets surrounded by four α-helices (two on each sides) and of residues with a unique insertion of eight amino acids within them. (Ågren et al, 2008)

At the active site of the enzyme, a pyrodoxal-phosphate cofactor is covalently linked to the Lysine 51 <scene name='80/802682/Lys_51/1'>Lys 51</scene>, an invariant residue. A parallel β-sheet associated with three α-helices are part of the N terminal domain (residues 46 to 153). Two of those α-helices are part of the dimer interface and the third one is partly forming the entrance of the active site as on the other side of the β-sheet. On the other hand the C-terminal domain is made of 6-stranded mixed β-sheets surrounded by four α-helices (two on each sides) and of residues with a unique insertion of eight amino acids within them. (Ågren et al, 2008)

All those compounds allow the enzyme to have several conformations : an open one, a closed one (when a substrate is bound to the enzyme) and an inhibited form (when there is a chlorite bound at an allosteric site). (Ågren et al, 2008)

The cysteine are polar uncharged amino acids. It has the particularity to be easily oxidized to form a dimer containing disulfide bridge between two cysteine. Important protein nonpolar residues in the dimer interface have been shown. The proximity between this hydrophobic region and Cys residues allows this kind of substrates to lay most of their aliphatic carbon chains over the patch, supporting the direct interaction of the peroxide group with the reactive thiolate group (Zeida et al, 2015). There is a complex hydrogen bound network which is involved in the Thr and oxygen bonding.

Additionally, there is fatty acid, derived from hydroperoxide, involved in the reduction of the H2O2. Peroxidase involves a proton transfer from the both oxygens that occurs after transtion state.

The oxidized reactive cystein have an unprotonated form of sulfenic acid and a protonated form. The reduction mechanism of these subtrate is the same as for H2O2.

Sandbox Reserved 1508: Difference between revisions

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 {{Sandbox_Reserved_ESBS}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
-==The protein 5C04==
+=='''The protein 5C04'''
+== Headline text ==
+==
 <StructureSection load='5C04' size='340' side='right' caption='Caption for this structure' scene=''>
 <div align="justified">The protein 5C04 is classified as an oxidoreductase. We found it in the ''Mycobacterium tuberculosis'' organism, especially in the strain ATCC 25618/H37Rv. It can be expressed in ''Escherichia Coli'' bacteria. This is a pathogenic protein which is involved in the tuberculosis. Its pathogenicity is due to a specific mutation in the active site of peroxiredoxins.</div>
@@ Line 32: / Line 34: @@
-At the active site of the enzyme, a pyrodoxal-phosphate cofactor is covalently linked to the Lysine 51, an invariant residue.  A parallel β-sheet associated with three α-helices are part of the N terminal domain (residues 46 to 153). Two of those α-helices are part of the dimer interface and the third one is partly forming the entrance of the active site as on the other side of the β-sheet.  On the other hand the C-terminal domain is made of 6-stranded mixed  β-sheets surrounded by four α-helices (two on each sides) and of residues with a unique insertion of eight amino acids within them. (Ågren et al, 2008)
+At the active site of the enzyme, a pyrodoxal-phosphate cofactor is covalently linked to the Lysine 51 <scene name='80/802682/Lys_51/1'>Lys 51</scene>, an invariant residue.  A parallel β-sheet associated with three α-helices are part of the N terminal domain (residues 46 to 153). Two of those α-helices are part of the dimer interface and the third one is partly forming the entrance of the active site as on the other side of the β-sheet.  On the other hand the C-terminal domain is made of 6-stranded mixed  β-sheets surrounded by four α-helices (two on each sides) and of residues with a unique insertion of eight amino acids within them. (Ågren et al, 2008)
 All those compounds allow the enzyme to have several conformations : an open one, a closed one (when a substrate is bound to the enzyme) and an inhibited form (when there is a chlorite bound at an allosteric site). (Ågren et al, 2008)
-The cysteine are polar uncharged amino acids. It has the particularity to be easily oxidized to form a dimer containing disulfide bridge between two cysteine. Important protein nonpolar residues in the dimer interface have been shown. The proximity between this hydrophobic region and Cys residues allows this kind of substrates to lay most of their aliphatic carbon chains over the patch, supporting the direct interaction of the peroxide group with the reactive thiolate group (Zeida et al, 2015). There is a complex hydrogen bound network which is involved in the Thr and oxygen bonding.
+The cysteine are polar uncharged amino acids. It has the particularity to be easily oxidized to form  a dimer containing disulfide bridge between two cysteine. Important protein nonpolar residues in the dimer interface have been shown. The proximity between this hydrophobic region and Cys residues allows this kind of substrates to lay most of their aliphatic carbon chains over the patch, supporting the direct interaction of the peroxide group with the reactive thiolate group (Zeida et al, 2015). There is a complex hydrogen bound network which is involved in the Thr and oxygen bonding.
 Additionally, there is fatty acid, derived from hydroperoxide, involved in the reduction of the H2O2. Peroxidase involves a proton transfer from the both oxygens that occurs after transtion state.
 The oxidized reactive cystein have an unprotonated form of sulfenic acid and a protonated form. The reduction mechanism of these subtrate is the same as for H2O2.