Sandbox Reserved 1600: Difference between revisions

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=Structure=

The focus of this page is to explain the structure and function of the [https://www.rcsb.org/structure/5DOQ ''~~Geobacillus~~ 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/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.

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. ''~~Geobacillus~~ thermodenitrificans'' was chosen because of the interest in the unique proton pathways, as described in the “Potential Proton Pathways” section.

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.

==Active Site==

[[Image:Hemes2.png|300 px|right|thumb|Figure 1. The active site of bd oxidase for ''~~Geobacillus~~ thermodenitrificans''. Heme B558 (pink; left), Heme B595 (pink; right), and Heme D (green). Important residues shown in blue. Measurements are shown in Å.]]

[[Image:Hemes2.png|300 px|right|thumb|Figure 1. The active site of bd oxidase for ''G. thermodenitrificans''. Heme B558 (pink; left), Heme B595 (pink; right), and Heme D (green). Important residues shown in blue. Measurements are shown in Å.]]

The active site for bd oxidase in ''G. thermodenitrificans'' is located in subunit Cyd A. The site consists of three iron hemes: <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> that are held together in a rigid triangular <scene name='83/838655/Hemes/8'>arrangement</scene> due to [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions].<ref name = ”Safarian” /> The <scene name='83/838655/Hemes_measurements/5'>length</scene> between each heme's central iron is relatively constant which serves to shuttle protons and electrons from one heme to another efficiently (Fig. 1). <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> is hypothesized to act as an electron acceptor, orientated toward the extracellular side by <scene name='83/838655/Bdoxidase_structure_heme/4'>His 186, Met 325, and Lys 252</scene> (Fig. 1).<ref name = ”Safarian” /> With <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> closest in proximity to the intracellular side, Heme B559 is likely the proton acceptor with two potential proton pathways. Both <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> and <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> then shuttle their respective ions directly to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> as this is the shortest pathway.

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@@ Line 10: / Line 10: @@
 =Structure=
-The focus of this page is to explain the structure and function of the [https://www.rcsb.org/structure/5DOQ ''Geobacillus 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/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.
-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. ''Geobacillus thermodenitrificans'' was chosen because of the interest in the unique proton pathways, as described in the “Potential Proton Pathways” section.
+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.
 ==Active Site==
-[[Image:Hemes2.png|300 px|right|thumb|Figure 1. The active site of bd oxidase for ''Geobacillus thermodenitrificans''. Heme B558 (pink; left), Heme B595 (pink; right), and Heme D (green). Important residues shown in blue. Measurements are shown in Å.]]
+[[Image:Hemes2.png|300 px|right|thumb|Figure 1. The active site of bd oxidase for ''G. thermodenitrificans''. Heme B558 (pink; left), Heme B595 (pink; right), and Heme D (green). Important residues shown in blue. Measurements are shown in Å.]]
 The active site for bd oxidase in ''G. thermodenitrificans'' is located in subunit Cyd A. The site consists of three iron hemes: <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>, <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene>, and <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> that are held together in a rigid triangular <scene name='83/838655/Hemes/8'>arrangement</scene> due to [https://en.wikipedia.org/wiki/Van_der_Waals_force Van der Waals interactions].<ref name = ”Safarian” /> The <scene name='83/838655/Hemes_measurements/5'>length</scene> between each heme's central iron is relatively constant which serves to shuttle protons and electrons from one heme to another efficiently (Fig. 1). <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene>  is hypothesized to act as an electron acceptor, orientated toward the extracellular side by <scene name='83/838655/Bdoxidase_structure_heme/4'>His 186, Met 325, and Lys 252</scene> (Fig. 1).<ref name = ”Safarian” /> With <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> closest in proximity to the intracellular side, Heme B559 is likely the proton acceptor with two potential proton pathways. Both <scene name='83/838655/Bd_oxidase_heme_558/3'>Heme B558</scene> and <scene name='83/838655/Bd_oxidase_heme_b_595/2'>Heme B595</scene> then shuttle their respective ions directly to <scene name='83/838655/Bd_oxidase_heme_d/2'>Heme D</scene> as this is the shortest pathway.