Sandbox Reserved 1600: Difference between revisions

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Because there is no proton pump present, the proton transfer mechanism is facilitated by <scene name='83/838655/Bdoxidase_proton_pathways/1'>2 potential proton pathways</scene> via intracellular water molecules.

One potential proton pathway is formed from the <scene name='83/838655/Bdoxidase_helix_a_1-4/1'>four-helix bundle (a1-4)</scene> of CydA. It is called the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene>. The location of Glu108 in our structure ~~supports~~ the ~~proposal~~ that this glutamate residue is a redox state-dependent mediator of proton transfer. In other words, ~~its main role is to allow charge to be alleviated at this site.~~ <ref name =”Safarian” /> ~~With~~ the ~~CydA~~ pathway ~~leading to Glu101~~, ~~this residue~~ could be the protonatable group used ~~for charge compensation~~ upon heme b595 reduction. It is still unknown whether protons entering the CydA pathway can be transferred from Glu101 to Glu378, to allow the spread of the negative charge of a second electron used to reduce the two high-spin hemes. Proto- nation of Glu378 could alternatively also be accomplished by a proton accessing from the extracellular side. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation or whether Glu108 can be a branching point that is able to pass protons via the heme b595 propionates to the oxygen-binding site.

One potential proton pathway is formed from the <scene name='83/838655/Bdoxidase_helix_a_1-4/1'>four-helix bundle (a1-4)</scene> of CydA. It is called the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene>. The residues along this pathway help facilitate the movement of the protons. The location of Glu108 in our structure is a key residue in this pathway. Its location within the pathway and negative charge characteristic implies that this glutamate residue is a redox state-dependent mediator of proton transfer. In other words, it acts like a proton shuttle <ref name =”Safarian” />. The Glu101 residue, which is the last residue in this pathway, could be the protonatable group eventually used upon heme b595 reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether Glu108 can be a branching point that is able to pass protons via the heme b595 propionates to the oxygen-binding site.

Another potential entry site is related to the a1-4 four-helix bundle of CydB. Therefore, this is called the <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. In this pathway, Asp25 is thought to be the equivalent of the Glu108 in the CydA pathway <ref name =”Safarian” />. The other residues help facilitate the movement of the proton very similarly to the CydA pathway. There is less known about the CydB pathway, and therefore, the CydA pathway is the most accepted source of protons.

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= Biological Importance of Reducing O₂ =

Oxygen toxicity is a fatal problem among all organisms, but can easily occur in prokaryotes due to their low oxygen tolerance. In prokaryotes, the cytochrome Bd family functions to quickly reduce the concentration of O2 into H2O to protect the cell from detrimental effects. Without proper functioning of these enzymes, or if O2 concentrations are too high, the concentrations of the intermediates formed from the reduction reaction will increase and can be detrimental. As a result of the vitality of reducing O2 in prokaryotes, knowledge on Bd oxidases can help develop drugs that target these enzymes to combat bacterial infection <ref name=”Borisov”>PMID:21756872</ref>.

= Structure Similarity to bd oxidase found in ''E. coli'' =

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@@ Line 38: / Line 38: @@
 Because there is no proton pump present, the proton transfer mechanism is facilitated by <scene name='83/838655/Bdoxidase_proton_pathways/1'>2 potential proton pathways</scene> via intracellular water molecules.
-One potential proton pathway is formed from the <scene name='83/838655/Bdoxidase_helix_a_1-4/1'>four-helix bundle (a1-4)</scene> of CydA. It is called the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene>. The location of <font color='gold'><b>Glu108</b></font> in our structure supports the proposal that this glutamate residue is a redox state-dependent mediator of proton transfer. In other words, its main role is to allow charge to be alleviated at this site. <ref name =”Safarian” /> With the CydA pathway leading to Glu101, this residue could be the protonatable group used for charge compensation upon heme b595 reduction. It is still unknown whether protons entering the CydA pathway can be transferred from Glu101 to Glu378, to allow the spread of the negative charge of a second electron used to reduce the two high-spin hemes. Proto- nation of Glu378 could alternatively also be accomplished by a proton accessing from the extracellular side. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation or whether Glu108 can be a branching point that is able to pass protons via the heme b595 propionates to the oxygen-binding site.
+One potential proton pathway is formed from the <scene name='83/838655/Bdoxidase_helix_a_1-4/1'>four-helix bundle (a1-4)</scene> of CydA. It is called the <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene>. The residues along this pathway help facilitate the movement of the protons. The location of <font color='gold'><b>Glu108</b></font> in our structure is a key residue in this pathway. Its location within the pathway and negative charge characteristic implies that this glutamate residue is a redox state-dependent mediator of proton transfer. In other words, it acts like a proton shuttle <ref name =”Safarian” />. The Glu101 residue, which is the last residue in this pathway, could be the protonatable group eventually used upon heme b595 reduction. More research needs to be done to determine whether the CydA pathway is solely providing protons for charge compensation, or whether Glu108 can be a branching point that is able to pass protons via the heme b595 propionates to the oxygen-binding site.
 Another potential entry site is related to the a1-4 four-helix bundle of CydB. Therefore, this is called the <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. In this pathway, Asp25 is thought to be the equivalent of the Glu108 in the CydA pathway <ref name =”Safarian” />. The other residues help facilitate the movement of the proton very similarly to the CydA pathway. There is less known about the CydB pathway, and therefore, the CydA pathway is the most accepted source of protons.
@@ Line 53: / Line 53: @@
 = Biological Importance of Reducing O₂ =
-Oxygen toxicity is a fatal problem among all organisms, but can easily occur in prokaryotes due to their low oxygen tolerance. In prokaryotes, the cytochrome Bd family functions to quickly reduce the concentration of O2 into H2O to protect the cell from detrimental effects. Without proper functioning of these enzymes, or if O2 concentrations are too high, the concentrations of the intermediates formed from the reduction reaction will increase and can be detrimental. As a result of the vitality of reducing O2 in prokaryotes, knowledge on Bd oxidases can help develop drugs that target these enzymes to combat bacterial infection <ref name=”Borisov”>PMID:21756872</ref>.
 = Structure Similarity to bd oxidase found in ''E. coli'' =