4GP5

Structure of Recombinant Cytochrome ba3 Oxidase mutant Y133W from Thermus thermophilus

Replaces:  4EV3

Summary for 4GP5

• Entry DOI: 10.2210/pdb4gp5/pdb
• Related: 4G70 4G71 4G72 4G7Q 4G7R 4G7S 4GP4 4GP8
• Descriptor: Cytochrome c oxidase subunit 1, Cytochrome c oxidase subunit 2, Cytochrome c oxidase polypeptide 2A, ... (10 entities in total)
• Functional Keywords: oxidoreductase, proton pump
• Biological source: Thermus thermophilus; More
• Cellular location: Cell membrane; Multi-pass membrane protein: Q5SJ79; Cell membrane; Single-pass membrane protein: Q5SJ80 P82543
• Total number of polymer chains: 3
• Total formula weight: 93240.64

Authors

Li, Y.,Chen, Y.,Stout, C.D. (deposition date: 2012-08-20, release date: 2013-01-16, Last modification date: 2024-02-28)

Primary citation

McDonald, W.,Funatogawa, C.,Li, Y.,Szundi, I.,Chen, Y.,Fee, J.A.,Stout, C.D.,Einarsdottir, O.
Ligand Access to the Active Site in Thermus thermophilusba(3) and Bovine Heart aa(3) Cytochrome Oxidases.
Biochemistry, 52:640-652, 2013

PubMed Abstract: Knowledge of the structure and dynamics of the ligand channel(s) in heme-copper oxidases is critical for understanding how the protein environment modulates the functions of these enzymes. Using photolabile NO and O(2) carriers, we recently found that NO and O(2) binding in Thermus thermophilus (Tt) ba(3) is ~10 times faster than in the bovine enzyme, indicating that inherent structural differences affect ligand access in these enzymes. Using X-ray crystallography, time-resolved optical absorption measurements, and theoretical calculations, we investigated ligand access in wild-type Tt ba(3) and the mutants, Y133W, T231F, and Y133W/T231F, in which tyrosine and threonine in the O(2) channel of Tt ba(3) are replaced by the corresponding bulkier tryptophan and phenylalanine, respectively, present in the aa(3) enzymes. NO binding in Y133W and Y133W/T231F was found to be 5 times slower than in wild-type ba(3) and the T231F mutant. The results show that the Tt ba(3) 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 diffusion of Xe to the active sites in ba(3) and bovine aa(3) show conformational freedom of the bovine F238 and the F231 side chain of the Tt ba(3) Y133W/T231F mutant, with both residues rotating out of the ligand channel, resulting in no effect on ligand access in either enzyme.

PubMed: 23282175
DOI: 10.1021/bi301358a

Experimental method

X-RAY DIFFRACTION (2.7 Å)