Sandbox Reserved 1600: Difference between revisions

Line 6:

There are two main types of respiratory cytochrome oxidases: the heme/copper oxidases and the heme-only cytochrome bd quinol oxidase, which is what bd oxidase falls under.<ref name=”Das”>PMID:15743950</ref> Heme-only cytochrome bd quinol oxidases are associated with microaerobic dioxygen respiration, and they have a high affinity for oxygen.

The [https://www.uniprot.org/proteomes/UP000001578 ''G. thermodenitrificans''] is a facultative aerobic thermophilic bacterium that utilizes the bd oxidase mechanism. The oxygen enters the enzyme through the selective <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen entry site</scene> that funnels the extracellular oxygen to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> in the active site. The electrons for the reaction are provided by ubiquinone molecule bound to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene>. The protons for the reaction are provided by one of two <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene>, either the <scene name='83/838655/Bdoxidase_cyda_pathway/6'>CydA pathway</scene>or <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. Both of the proton pathways utilize the intracellular water molecules for the proton source, and shuttle them to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>.

The [https://www.uniprot.org/proteomes/UP000001578 ''G. thermodenitrificans''] is a facultative aerobic thermophilic bacterium that utilizes the bd oxidase mechanism. The oxygen enters the enzyme through the selective <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen entry site</scene> that funnels the extracellular oxygen to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> in the active site. The electrons for the reaction are provided by ubiquinone molecule bound to the <scene name='83/838655/Bdoxidase_q_loop/3'>Q loop</scene>. The protons for the reaction are provided by one of two <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene>, either the <scene name='83/838655/Bdoxidase_cyda_pathway/6'>CydA pathway</scene>or <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. Both of the proton pathways utilize the intracellular water molecules for the proton source, and shuttle them to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>.

=Structure=

The focus of this page is to explain the structure and function of the [https://www.rcsb.org/structure/5DOQ ''G. thermodenitrificans’'' bd oxidase]. The <scene name='83/838655/Bdoxidase_structure_full/4'>overall structure</scene> contains <scene name='83/838655/Bdoxidase_only_helicies/2'> 19 transmembrane helices</scene> that are arranged in a nearly oval shape.<ref name = ”Safarian” /> The protein contains two structurally similar subunits, <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA</scene>, seen in blue, and <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB</scene>, seen in red, each containing nine helices, and one smaller subunit, <scene name='83/838655/Bdoxidase_cydx_subunit/2'>CydX</scene>, in teal, with one transmembrane helix. These subunits interact using hydrophobic residues and symmetry at the interfaces. The CydX subunit, whose function is not currently known, is positioned in the same way as CydS, a separate subunit that is found in the bd oxidase homologue from [https://www.rcsb.org/structure/6RKO ''E. coli'' bd oxidase], but is not found in ''G. thermodenitrificans''. Due to its similar structure and position to CydS, CydX has been hypothesized to potentially stabilize <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> during potential structural rearrangements of the Q loop upon binding and oxidation of ubiquinone (Fig. 1), the function of CydS in ''E. coli.''<ref name = ”Safarian” /> The <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene> is a hydrophilic region above Cyd A. The lack of [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] in this hydrophobic protein allows the protein to be flexible and go through a large conformational change for reduction of dioxygen. <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> is mostly involved in the proton pathway, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> is involved with the oxygen pathway.

The focus of this page is to explain the structure and function of the [https://www.rcsb.org/structure/5DOQ ''G. thermodenitrificans’'' bd oxidase]. The <scene name='83/838655/Bdoxidase_structure_full/4'>overall structure</scene> contains <scene name='83/838655/Bdoxidase_only_helicies/2'> 19 transmembrane helices</scene> that are arranged in a nearly oval shape.<ref name = ”Safarian” /> The protein contains two structurally similar subunits, <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA</scene>, seen in blue, and <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB</scene>, seen in red, each containing nine helices, and one smaller subunit, <scene name='83/838655/Bdoxidase_cydx_subunit/2'>CydX</scene>, in teal, with one transmembrane helix. These subunits interact using hydrophobic residues and symmetry at the interfaces. The CydX subunit, whose function is not currently known, is positioned in the same way as CydS, a separate subunit that is found in the bd oxidase homologue from [https://www.rcsb.org/structure/6RKO ''E. coli'' bd oxidase], but is not found in ''G. thermodenitrificans''. Due to its similar structure and position to CydS, CydX has been hypothesized to potentially stabilize <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> during potential structural rearrangements of the Q loop upon binding and oxidation of ubiquinone (Fig. 1), the function of CydS in ''E. coli.''<ref name = ”Safarian” /> The <scene name='83/838655/Bdoxidase_q_loop/3'>Q loop</scene> is a hydrophilic region above Cyd A. The lack of [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] in this hydrophobic protein allows the protein to be flexible and go through a large conformational change for reduction of dioxygen. <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> is mostly involved in the proton pathway, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> is involved with the oxygen pathway.

Other structures of bd oxidase exist that contain a variety of potential routes for the different reactants of the reduction of oxygen. For example, the bd oxidase of ''E. coli'' contains a different orientation of the Hemes and many different mechanisms of proton shuttling. ''G. thermodenitrificans'' was chosen because of the interest in the unique proton pathways, as described in the “Potential Proton Pathways” section.

Line 24:

==Electron Source==

An electron source is needed in order for the redox reaction of O₂ to occur. Cytochrome bd oxidase uses the quinol molecule [https://en.wikipedia.org/wiki/Coenzyme_Q10 ubiquinone] as an electron donor (Figure 2). [[Image:Ubiquinone.jpg|200 px|right|thumb|Figure 2. Chemical structure of ubiquinone.]] As shown in the <scene name='83/838655/Bdoxidase_structure_full/4'>overall structure</scene>, the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene> is on the extracellular surface and provides a binding site for ubiquinone.<ref name = ”Safarian” /> Heme <scene name='83/838655/Bdoxidase_qloop_zoom/3'>B558 is closest in proximity to the Q loop</scene> and thus is the suggested [https://en.wikipedia.org/wiki/Electron_acceptor electron acceptor]. This suggestion is further supported by the <scene name='83/838655/Bdoxidase_trp/2'>conservation of Trp374</scene> often found as intermediate electron receptors in biological [https://en.wikipedia.org/wiki/Electron_transport_chain electron transfer chains].<ref name =”Safarian” />

An electron source is needed in order for the redox reaction of O₂ to occur. Cytochrome bd oxidase uses the quinol molecule [https://en.wikipedia.org/wiki/Coenzyme_Q10 ubiquinone] as an electron donor (Figure 2). [[Image:Ubiquinone.jpg|200 px|right|thumb|Figure 2. Chemical structure of ubiquinone.]] As shown in the <scene name='83/838655/Bdoxidase_structure_full/4'>overall structure</scene>, the <scene name='83/838655/Bdoxidase_q_loop/3'>Q loop</scene> is on the extracellular surface and provides a binding site for ubiquinone.<ref name = ”Safarian” /> Heme <scene name='83/838655/Bdoxidase_qloop_zoom/3'>B558 is closest in proximity to the Q loop</scene> and thus is the suggested [https://en.wikipedia.org/wiki/Electron_acceptor electron acceptor]. This suggestion is further supported by the <scene name='83/838655/Bdoxidase_trp/2'>conservation of Trp374</scene> often found as intermediate electron receptors in biological [https://en.wikipedia.org/wiki/Electron_transport_chain electron transfer chains].<ref name =”Safarian” />

==Potential Proton Pathways==

Line 38:

As mentioned above, the purpose of the bd oxidase is to reduce O₂ to 2H₂O using quinol as the reducing substrate, yielding the overall reaction of O₂ + 4H+ + 4e- → 2H₂O. The oxygen comes from the extracellular side of the protein, and enters through the oxygen entry site to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene>. This pathway is depicted in orange in Figure 4.

The electrons required for the reduction mechanism come from a ubiquinol molecule (Fig. 2) that simultaneously binds to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene> and gets oxidized giving 4e- to <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>. Once at <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, the 4e- will be shuttled directly to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> to be used in the reaction. The electron pathway is depicted in blue in Figure 4.

The electrons required for the reduction mechanism come from a ubiquinol molecule (Fig. 2) that simultaneously binds to the <scene name='83/838655/Bdoxidase_q_loop/3'>Q loop</scene> and gets oxidized giving 4e- to <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>. Once at <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, the 4e- will be shuttled directly to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> to be used in the reaction. The electron pathway is depicted in blue in Figure 4.

The protons that are required in the pathway are not provided by a pump, but rather via intracellular water. The <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene> utilize amino acids with properties that help shuttle the protons from the intracellular side of the protein to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> in the active site. The <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene> passes through the <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA subunit</scene>, shown in purple in Figure 4. The <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene> proceeds through the <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB subunit</scene>, shown in green in Figure 4.

Sandbox Reserved 1600: Difference between revisions

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 6: / Line 6: @@
 There are two main types of respiratory cytochrome oxidases: the heme/copper oxidases and the heme-only cytochrome bd quinol oxidase, which is what bd oxidase falls under.<ref name=”Das”>PMID:15743950</ref> Heme-only cytochrome bd quinol oxidases are associated with microaerobic dioxygen respiration, and they have a high affinity for oxygen.
-The [https://www.uniprot.org/proteomes/UP000001578 ''G. thermodenitrificans''] is a facultative aerobic thermophilic bacterium that utilizes the bd oxidase mechanism. The oxygen enters the enzyme through the selective <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen entry site</scene> that funnels the extracellular oxygen to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> in the active site. The electrons for the reaction are provided by ubiquinone molecule bound to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene>. The protons for the reaction are provided by one of two <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene>, either the <scene name='83/838655/Bdoxidase_cyda_pathway/6'>CydA pathway</scene>or <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. Both of the proton pathways utilize the intracellular water molecules for the proton source, and shuttle them to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>.
+The [https://www.uniprot.org/proteomes/UP000001578 ''G. thermodenitrificans''] is a facultative aerobic thermophilic bacterium that utilizes the bd oxidase mechanism. The oxygen enters the enzyme through the selective <scene name='83/832926/Potential_oxygen_entry_site/1'>oxygen entry site</scene> that funnels the extracellular oxygen to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> in the active site. The electrons for the reaction are provided by ubiquinone molecule bound to the <scene name='83/838655/Bdoxidase_q_loop/3'>Q loop</scene>. The protons for the reaction are provided by one of two <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene>, either the <scene name='83/838655/Bdoxidase_cyda_pathway/6'>CydA pathway</scene>or <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene>. Both of the proton pathways utilize the intracellular water molecules for the proton source, and shuttle them to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>.
 <StructureSection  load='5DOQ'  size='350'  frame='true' side='right' caption='bd oxidase (PDB: [[5doq]])' scene='83/838655/Bdoxidase_structure_full/3'>
 =Structure=
-The focus of this page is to explain the structure and function of the [https://www.rcsb.org/structure/5DOQ ''G. thermodenitrificans’'' bd oxidase]. The <scene name='83/838655/Bdoxidase_structure_full/4'>overall structure</scene> contains <scene name='83/838655/Bdoxidase_only_helicies/2'> 19 transmembrane helices</scene> that are arranged in a nearly oval shape.<ref name = ”Safarian” /> The protein contains two structurally similar subunits, <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA</scene>, seen in <font color='blue'><b>blue</b></font>, and <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB</scene>, seen in <font color='red'><b>red</b></font>, each containing nine helices, and one smaller subunit, <scene name='83/838655/Bdoxidase_cydx_subunit/2'>CydX</scene>, in <font color='teal'><b>teal</b></font>, with one transmembrane helix. These subunits interact using hydrophobic residues and symmetry at the interfaces. The CydX subunit, whose function is not currently known, is positioned in the same way as CydS, a separate subunit that is found in the bd oxidase homologue from [https://www.rcsb.org/structure/6RKO ''E. coli'' bd oxidase], but is not found in ''G. thermodenitrificans''. Due to its similar structure and position to CydS, CydX has been hypothesized to potentially stabilize <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> during potential structural rearrangements of the Q loop upon binding and oxidation of ubiquinone (Fig. 1), the function of CydS in ''E. coli.''<ref name = ”Safarian” /> The <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene> is a hydrophilic region above Cyd A. The lack of [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] in this hydrophobic protein allows the protein to be flexible and go through a large conformational change for reduction of dioxygen. <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> is mostly involved in the proton pathway, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> is involved with the oxygen pathway.
+The focus of this page is to explain the structure and function of the [https://www.rcsb.org/structure/5DOQ ''G. thermodenitrificans’'' bd oxidase]. The <scene name='83/838655/Bdoxidase_structure_full/4'>overall structure</scene> contains <scene name='83/838655/Bdoxidase_only_helicies/2'> 19 transmembrane helices</scene> that are arranged in a nearly oval shape.<ref name = ”Safarian” /> The protein contains two structurally similar subunits, <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA</scene>, seen in <font color='blue'><b>blue</b></font>, and <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB</scene>, seen in <font color='red'><b>red</b></font>, each containing nine helices, and one smaller subunit, <scene name='83/838655/Bdoxidase_cydx_subunit/2'>CydX</scene>, in <font color='teal'><b>teal</b></font>, with one transmembrane helix. These subunits interact using hydrophobic residues and symmetry at the interfaces. The CydX subunit, whose function is not currently known, is positioned in the same way as CydS, a separate subunit that is found in the bd oxidase homologue from [https://www.rcsb.org/structure/6RKO ''E. coli'' bd oxidase], but is not found in ''G. thermodenitrificans''. Due to its similar structure and position to CydS, CydX has been hypothesized to potentially stabilize <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> during potential structural rearrangements of the Q loop upon binding and oxidation of ubiquinone (Fig. 1), the function of CydS in ''E. coli.''<ref name = ”Safarian” /> The <scene name='83/838655/Bdoxidase_q_loop/3'>Q loop</scene> is a hydrophilic region above Cyd A. The lack of [https://en.wikipedia.org/wiki/Hydrogen_bond hydrogen bonding] in this hydrophobic protein allows the protein to be flexible and go through a large conformational change for reduction of dioxygen. <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> is mostly involved in the proton pathway, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> is involved with the oxygen pathway.
 Other structures of bd oxidase exist that contain a variety of potential routes for the different reactants of the reduction of oxygen. For example, the bd oxidase of ''E. coli'' contains a different orientation of the Hemes and many different mechanisms of proton shuttling. ''G. thermodenitrificans'' was chosen because of the interest in the unique proton pathways, as described in the “Potential Proton Pathways” section.
@@ Line 24: / Line 24: @@
 ==Electron Source==
-An electron source is needed in order for the redox reaction of O₂ to occur. Cytochrome bd oxidase uses the quinol molecule [https://en.wikipedia.org/wiki/Coenzyme_Q10 ubiquinone] as an electron donor (Figure 2). [[Image:Ubiquinone.jpg|200 px|right|thumb|Figure 2. Chemical structure of ubiquinone.]] As shown in the <scene name='83/838655/Bdoxidase_structure_full/4'>overall structure</scene>, the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene> is on the extracellular surface and provides a binding site for ubiquinone.<ref name = ”Safarian” /> Heme <scene name='83/838655/Bdoxidase_qloop_zoom/3'>B558 is closest in proximity to the Q loop</scene> and thus is the suggested [https://en.wikipedia.org/wiki/Electron_acceptor electron acceptor]. This suggestion is further supported by the <scene name='83/838655/Bdoxidase_trp/2'>conservation of Trp374</scene> often found as intermediate electron receptors in biological [https://en.wikipedia.org/wiki/Electron_transport_chain electron transfer chains].<ref name =”Safarian” />
+An electron source is needed in order for the redox reaction of O₂ to occur. Cytochrome bd oxidase uses the quinol molecule [https://en.wikipedia.org/wiki/Coenzyme_Q10 ubiquinone] as an electron donor (Figure 2). [[Image:Ubiquinone.jpg|200 px|right|thumb|Figure 2. Chemical structure of ubiquinone.]] As shown in the <scene name='83/838655/Bdoxidase_structure_full/4'>overall structure</scene>, the <scene name='83/838655/Bdoxidase_q_loop/3'>Q loop</scene> is on the extracellular surface and provides a binding site for ubiquinone.<ref name = ”Safarian” /> Heme <scene name='83/838655/Bdoxidase_qloop_zoom/3'>B558 is closest in proximity to the Q loop</scene> and thus is the suggested [https://en.wikipedia.org/wiki/Electron_acceptor electron acceptor]. This suggestion is further supported by the <scene name='83/838655/Bdoxidase_trp/2'>conservation of Trp374</scene> often found as intermediate electron receptors in biological [https://en.wikipedia.org/wiki/Electron_transport_chain electron transfer chains].<ref name =”Safarian” />
 ==Potential Proton Pathways==
@@ Line 38: / Line 38: @@
 As mentioned above, the purpose of the bd oxidase is to reduce O₂ to 2H₂O using quinol as the reducing substrate, yielding the overall reaction of O₂ + 4H<sup>+</sup> + 4e<sup>-</sup> → 2H₂O. The oxygen comes from the extracellular side of the protein, and enters through the oxygen entry site to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene>. This pathway is depicted in <font color='orange'><b>orange</b></font> in Figure 4.
-The electrons required for the reduction mechanism come from a ubiquinol molecule (Fig. 2) that simultaneously binds to the <scene name='83/838655/Bdoxidase_q_loop/2'>Q loop</scene> and gets oxidized giving 4e<sup>-</sup> to <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>. Once at <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, the 4e<sup>-</sup> will be shuttled directly to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> to be used in the reaction. The electron pathway is depicted in <font color='blue'><b>blue</b></font> in Figure 4.
+The electrons required for the reduction mechanism come from a ubiquinol molecule (Fig. 2) that simultaneously binds to the <scene name='83/838655/Bdoxidase_q_loop/3'>Q loop</scene> and gets oxidized giving 4e<sup>-</sup> to <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>. Once at <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, the 4e<sup>-</sup> will be shuttled directly to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> to be used in the reaction. The electron pathway is depicted in <font color='blue'><b>blue</b></font> in Figure 4.
 The protons that are required in the pathway are not provided by a pump, but rather via intracellular water. The <scene name='83/838655/Bdoxidase_proton_pathways/1'>potential proton pathways</scene> utilize amino acids with properties that help shuttle the protons from the intracellular side of the protein to <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> in the active site. The <scene name='83/838655/Bdoxidase_cyda_pathway_glu108/1'>CydA pathway</scene> passes through the <scene name='83/838655/Bdoxidase_cyda_subunit/2'>CydA subunit</scene>, shown in <font color='purple'><b>purple</b></font> in Figure 4. The <scene name='83/838655/Bdoxidase_cydb_pathway/3'>CydB pathway</scene> proceeds through the <scene name='83/838655/Bdoxidase_cydb_subunit/2'>CydB subunit</scene>, shown in <font color='green'><b>green</b></font> in Figure 4.