|
|
| Line 3: |
Line 3: |
| | <StructureSection load='3bvd' size='340' side='right'caption='[[3bvd]], [[Resolution|resolution]] 3.37Å' scene=''> | | <StructureSection load='3bvd' size='340' side='right'caption='[[3bvd]], [[Resolution|resolution]] 3.37Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3bvd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BVD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3bvd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3BVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3BVD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.37Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2qpd|2qpd]]</div></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=HAS:HEME-AS'>HAS</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=XE:XENON'>XE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cbaA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaB, ctaC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]), cbaD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])</td></tr>
| + | |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=3bvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvd OCA], [https://pdbe.org/3bvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bvd RCSB], [https://www.ebi.ac.uk/pdbsum/3bvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bvd ProSAT]</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=3bvd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bvd OCA], [https://pdbe.org/3bvd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3bvd RCSB], [https://www.ebi.ac.uk/pdbsum/3bvd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3bvd ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/COX2_THET8 COX2_THET8]] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).
| + | [https://www.uniprot.org/uniprot/COX1_THET8 COX1_THET8] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| Line 38: |
Line 36: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Cytochrome-c oxidase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Thermus thermophilus]] | + | [[Category: Thermus thermophilus HB8]] |
| - | [[Category: Chen, Y]] | + | [[Category: Chen Y]] |
| - | [[Category: Fee, J A]] | + | [[Category: Fee JA]] |
| - | [[Category: Luna, V M]] | + | [[Category: Luna VM]] |
| - | [[Category: Stout, C D]] | + | [[Category: Stout CD]] |
| - | [[Category: Copper]]
| + | |
| - | [[Category: Cytochrome ba3 oxidase]]
| + | |
| - | [[Category: Electron transport]]
| + | |
| - | [[Category: Formylation]]
| + | |
| - | [[Category: Heme]]
| + | |
| - | [[Category: Hydrogen ion transport]]
| + | |
| - | [[Category: Integral membrane protein]]
| + | |
| - | [[Category: Ion transport]]
| + | |
| - | [[Category: Iron]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Respiratory chain]]
| + | |
| - | [[Category: Transmembrane]]
| + | |
| - | [[Category: Transport]]
| + | |
| - | [[Category: Xenon]]
| + | |
| Structural highlights
3bvd is a 3 chain structure with sequence from Thermus thermophilus HB8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 3.37Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
COX1_THET8
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Cytochrome ba 3 is a cytochrome c oxidase from the plasma membrane of Thermus thermophilus and is the preferred terminal enzyme of cellular respiration at low dioxygen tensions. Using cytochrome ba 3 crystals pressurized at varying conditions under Xe or Kr gas, and X-ray data for six crystals, we identify the relative affinities of Xe and Kr atoms for as many as seven distinct binding sites. These sites track a continuous, Y-shaped channel, 18-20 A in length, lined by hydrophobic residues, which leads from the surface of the protein where two entrance holes, representing the top of the Y, connect the bilayer to the a 3-Cu B center at the base of the Y. Considering the increased affinity of O 2 for hydrophobic environments, the hydrophobic nature of the channel, its orientation within the bilayer, its connection to the active site, its uniform diameter, its virtually complete occupation by Xe, and its isomorphous presence in the native enzyme, we infer that the channel is a diffusion pathway for O 2 into the dinuclear center of cytochrome ba 3. These observations provide a basis for analyzing similar channels in other oxidases of known structure, and these structures are discussed in terms of mechanisms of O 2 transport in biological systems, details of CO binding to and egress from the dinuclear center, the bifurcation of the oxygen-in and water-out pathways, and the possible role of the oxygen channel in aerobic thermophily.
Crystallographic Studies of Xe and Kr Binding within the Large Internal Cavity of Cytochrome ba3 from Thermus thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases(,).,Luna VM, Chen Y, Fee JA, Stout CD Biochemistry. 2008 Apr 22;47(16):4657-65. Epub 2008 Apr 1. PMID:18376849[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Luna VM, Chen Y, Fee JA, Stout CD. Crystallographic Studies of Xe and Kr Binding within the Large Internal Cavity of Cytochrome ba3 from Thermus thermophilus: Structural Analysis and Role of Oxygen Transport Channels in the Heme-Cu Oxidases(,). Biochemistry. 2008 Apr 22;47(16):4657-65. Epub 2008 Apr 1. PMID:18376849 doi:10.1021/bi800045y
|
