4gp5
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4gp5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ev3 4ev3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GP5 FirstGlance]. <br> | <table><tr><td colspan='2'>[[4gp5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4ev3 4ev3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GP5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GP5 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=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</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]] 2.7Å</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=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></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=4gp5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gp5 OCA], [https://pdbe.org/4gp5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gp5 RCSB], [https://www.ebi.ac.uk/pdbsum/4gp5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gp5 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=4gp5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gp5 OCA], [https://pdbe.org/4gp5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gp5 RCSB], [https://www.ebi.ac.uk/pdbsum/4gp5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gp5 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[https://www.uniprot.org/uniprot/COX1_THET8 COX1_THET8] | [https://www.uniprot.org/uniprot/COX1_THET8 COX1_THET8] | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Knowledge of the structure and dynamics of the ligand channel(s) in heme-copper oxidases is critical for understanding how the protein environment modulates their functions. Using photolabile NO and O2 carriers, we recently found that NO and O2 binding in Thermus thermophilus ba3 (Tt ba3) is ~10-times faster than in the bovine enzyme, indicating inherent structural differences that affect ligand access in these enzymes. Using x-ray crystallography, time-resolved optical absorption measurements, and theoretical calculations, we investigated ligand access in the Tt ba3 mutants Y133W, T231F, and Y133W&T231F, in which tyrosine and/or threonine in the O2-channel of Tt ba3 are replaced by the corresponding bulkier tryptophan and phenylalanine present in the aa3 enzymes. NO binding in Y133W and Y133W&T231F is 5-times slower than in wild-type ba3 and the T231F mutant, and the results show that the Tt ba3 Y133W mutation and the bovine W126 residue physically impede NO access to the binuclear center. In the bovine enzyme there is a hydrophobic "way-station," which may further slow ligand access to the active site. Classical simulations of Xe diffusion to the active sites in ba3 and bovine aa3 show conformational freedom of the bovine F238 and the F231 side chain of the Tt ba3 Y133W&T231F mutant, with both residues rotating out of the ligand channel, resulting in no effect on ligand access in either enzyme. | ||
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| - | Ligand Access to the Active Site in Thermus thermophilus ba3 and Bovine Heart aa3 Cytochrome Oxidases.,McDonald WJ, Funatogawa C, Li Y, Szundi I, Chen Y, Fee JA, Stout CD, Einarsdottir O Biochemistry. 2013 Jan 2. PMID:23282175<ref>PMID:23282175</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 4gp5" style="background-color:#fffaf0;"></div> | ||
==See Also== | ==See Also== | ||
*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]] | *[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]] | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Structure of Recombinant Cytochrome ba3 Oxidase mutant Y133W from Thermus thermophilus
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