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| | ==THE STRUCTURE OF BD OXIDASE FROM ESCHERICHIA COLI== | | ==THE STRUCTURE OF BD OXIDASE FROM ESCHERICHIA COLI== |
| - | <StructureSection load='6rx4' size='340' side='right'caption='[[6rx4]], [[Resolution|resolution]] 3.30Å' scene=''> | + | <SX load='6rx4' size='340' side='right' viewer='molstar' caption='[[6rx4]], [[Resolution|resolution]] 3.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6rx4]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_(strain_k12) Escherichia coli (strain k12)] and [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RX4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RX4 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6rx4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RX4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RX4 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</scene>, <scene name='pdbligand=HEB:HEME+B/C'>HEB</scene>, <scene name='pdbligand=PEE:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=UQ8:UBIQUINONE-8'>UQ8</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.3Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</scene>, <scene name='pdbligand=HEB:HEME+B/C'>HEB</scene>, <scene name='pdbligand=PEE:1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE'>PEE</scene>, <scene name='pdbligand=UQ8:UBIQUINONE-8'>UQ8</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ubiquinol_oxidase_(electrogenic,_proton-motive_force_generating) Ubiquinol oxidase (electrogenic, proton-motive force generating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=7.1.1.7 7.1.1.7] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6rx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rx4 OCA], [https://pdbe.org/6rx4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rx4 RCSB], [https://www.ebi.ac.uk/pdbsum/6rx4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rx4 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6rx4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rx4 OCA], [http://pdbe.org/6rx4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rx4 RCSB], [http://www.ebi.ac.uk/pdbsum/6rx4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rx4 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CYDA_ECOLI CYDA_ECOLI]] A terminal oxidase that produces a proton motive force by the vectorial transfer of protons across the inner membrane. It is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at low aeration. Generates a proton motive force using protons and electrons from opposite sides of the membrane to generate H(2)O, transferring 1 proton/electron.<ref>PMID:19542282</ref> <ref>PMID:21987791</ref> <ref>PMID:2656671</ref> <ref>PMID:6307994</ref> <ref>PMID:7577938</ref> [[http://www.uniprot.org/uniprot/CYDX_ECOLI CYDX_ECOLI]] Required for correct functioning of cytochrome bd-I oxidase. This protein and AppX may have some functional overlap. [[http://www.uniprot.org/uniprot/CYDB_ECOLI CYDB_ECOLI]] A terminal oxidase that produces a proton motive force by the vectorial transfer of protons across the inner membrane. It is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at low aeration. Generates a proton motive force using protons and electrons from opposite sides of the membrane to generate H(2)O, transferring 1 proton/electron.<ref>PMID:19542282</ref> <ref>PMID:21987791</ref> <ref>PMID:6307994</ref> | + | [https://www.uniprot.org/uniprot/CYDA_ECOLI CYDA_ECOLI] A terminal oxidase that produces a proton motive force by the vectorial transfer of protons across the inner membrane. It is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at low aeration. Generates a proton motive force using protons and electrons from opposite sides of the membrane to generate H(2)O, transferring 1 proton/electron.<ref>PMID:19542282</ref> <ref>PMID:21987791</ref> <ref>PMID:2656671</ref> <ref>PMID:6307994</ref> <ref>PMID:7577938</ref> |
| | + | <div style="background-color:#fffaf0;"> |
| | + | == Publication Abstract from PubMed == |
| | + | Cytochrome bd oxidases are terminal reductases of bacterial and archaeal respiratory chains. The enzyme couples the oxidation of ubiquinol or menaquinol with the reduction of dioxygen to water, thus contributing to the generation of the protonmotive force. Here, we determine the structure of the Escherichia coli bd oxidase treated with the specific inhibitor aurachin by cryo-electron microscopy (cryo-EM). The major subunits CydA and CydB are related by a pseudo two fold symmetry. The heme b and d cofactors are found in CydA, while ubiquinone-8 is bound at the homologous positions in CydB to stabilize its structure. The architecture of the E. coli enzyme is highly similar to that of Geobacillus thermodenitrificans, however, the positions of heme b595 and d are interchanged, and a common oxygen channel is blocked by a fourth subunit and substituted by a more narrow, alternative channel. Thus, with the same overall fold, the homologous enzymes exhibit a different mechanism. |
| | + | |
| | + | Homologous bd oxidases share the same architecture but differ in mechanism.,Thesseling A, Rasmussen T, Burschel S, Wohlwend D, Kagi J, Muller R, Bottcher B, Friedrich T Nat Commun. 2019 Nov 13;10(1):5138. doi: 10.1038/s41467-019-13122-4. PMID:31723136<ref>PMID:31723136</ref> |
| | + | |
| | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | + | </div> |
| | + | <div class="pdbe-citations 6rx4" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Cytochrome bd oxidase|Cytochrome bd oxidase]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| - | </StructureSection> | + | </SX> |
| - | [[Category: Escherichia coli k-12]] | + | [[Category: Escherichia coli K-12]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Boettcher, B]] | + | [[Category: Boettcher B]] |
| - | [[Category: Friedrich, T]] | + | [[Category: Friedrich T]] |
| - | [[Category: Rasmussen, T]] | + | [[Category: Rasmussen T]] |
| - | [[Category: Thesseling, A]] | + | [[Category: Thesseling A]] |
| - | [[Category: Bd oxidase]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Terminal oxidase]]
| + | |
| Structural highlights
Function
CYDA_ECOLI A terminal oxidase that produces a proton motive force by the vectorial transfer of protons across the inner membrane. It is the component of the aerobic respiratory chain of E.coli that predominates when cells are grown at low aeration. Generates a proton motive force using protons and electrons from opposite sides of the membrane to generate H(2)O, transferring 1 proton/electron.[1] [2] [3] [4] [5]
Publication Abstract from PubMed
Cytochrome bd oxidases are terminal reductases of bacterial and archaeal respiratory chains. The enzyme couples the oxidation of ubiquinol or menaquinol with the reduction of dioxygen to water, thus contributing to the generation of the protonmotive force. Here, we determine the structure of the Escherichia coli bd oxidase treated with the specific inhibitor aurachin by cryo-electron microscopy (cryo-EM). The major subunits CydA and CydB are related by a pseudo two fold symmetry. The heme b and d cofactors are found in CydA, while ubiquinone-8 is bound at the homologous positions in CydB to stabilize its structure. The architecture of the E. coli enzyme is highly similar to that of Geobacillus thermodenitrificans, however, the positions of heme b595 and d are interchanged, and a common oxygen channel is blocked by a fourth subunit and substituted by a more narrow, alternative channel. Thus, with the same overall fold, the homologous enzymes exhibit a different mechanism.
Homologous bd oxidases share the same architecture but differ in mechanism.,Thesseling A, Rasmussen T, Burschel S, Wohlwend D, Kagi J, Muller R, Bottcher B, Friedrich T Nat Commun. 2019 Nov 13;10(1):5138. doi: 10.1038/s41467-019-13122-4. PMID:31723136[6]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Bekker M, de Vries S, Ter Beek A, Hellingwerf KJ, de Mattos MJ. Respiration of Escherichia coli can be fully uncoupled via the nonelectrogenic terminal cytochrome bd-II oxidase. J Bacteriol. 2009 Sep;191(17):5510-7. doi: 10.1128/JB.00562-09. Epub 2009 Jun 19. PMID:19542282 doi:http://dx.doi.org/10.1128/JB.00562-09
- ↑ Borisov VB, Murali R, Verkhovskaya ML, Bloch DA, Han H, Gennis RB, Verkhovsky MI. Aerobic respiratory chain of Escherichia coli is not allowed to work in fully uncoupled mode. Proc Natl Acad Sci U S A. 2011 Oct 18;108(42):17320-4. doi:, 10.1073/pnas.1108217108. Epub 2011 Oct 10. PMID:21987791 doi:http://dx.doi.org/10.1073/pnas.1108217108
- ↑ Fang H, Lin RJ, Gennis RB. Location of heme axial ligands in the cytochrome d terminal oxidase complex of Escherichia coli determined by site-directed mutagenesis. J Biol Chem. 1989 May 15;264(14):8026-32. PMID:2656671
- ↑ Miller MJ, Gennis RB. The purification and characterization of the cytochrome d terminal oxidase complex of the Escherichia coli aerobic respiratory chain. J Biol Chem. 1983 Aug 10;258(15):9159-65. PMID:6307994
- ↑ Kaysser TM, Ghaim JB, Georgiou C, Gennis RB. Methionine-393 is an axial ligand of the heme b558 component of the cytochrome bd ubiquinol oxidase from Escherichia coli. Biochemistry. 1995 Oct 17;34(41):13491-501. doi: 10.1021/bi00041a029. PMID:7577938 doi:http://dx.doi.org/10.1021/bi00041a029
- ↑ Thesseling A, Rasmussen T, Burschel S, Wohlwend D, Kagi J, Muller R, Bottcher B, Friedrich T. Homologous bd oxidases share the same architecture but differ in mechanism. Nat Commun. 2019 Nov 13;10(1):5138. doi: 10.1038/s41467-019-13122-4. PMID:31723136 doi:http://dx.doi.org/10.1038/s41467-019-13122-4
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