Document Detail

Ligand access to the active site in Thermus thermophilus ba(3) and bovine heart aa(3) cytochrome oxidases.
MedLine Citation:
PMID:  23282175     Owner:  NLM     Status:  MEDLINE    
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.
William McDonald; Chie Funatogawa; Yang Li; Istvan Szundi; Ying Chen; James A Fee; C David Stout; Ólöf Einarsdóttir
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Publication Detail:
Type:  Journal Article; Research Support, American Recovery and Reinvestment Act; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, Non-P.H.S.     Date:  2013-01-18
Journal Detail:
Title:  Biochemistry     Volume:  52     ISSN:  1520-4995     ISO Abbreviation:  Biochemistry     Publication Date:  2013 Jan 
Date Detail:
Created Date:  2013-01-29     Completed Date:  2013-03-25     Revised Date:  2014-01-30    
Medline Journal Info:
Nlm Unique ID:  0370623     Medline TA:  Biochemistry     Country:  United States    
Other Details:
Languages:  eng     Pagination:  640-52     Citation Subset:  IM    
Data Bank Information
Bank Name/Acc. No.:
PDB/4GP4;  4GP5;  4GP8
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MeSH Terms
Amino Acid Motifs
Amino Acid Substitution
Bacterial Proteins / chemistry*,  genetics
Catalytic Domain
Copper / chemistry
Electron Transport Complex IV / chemistry*,  genetics
Molecular Dynamics Simulation
Mutagenesis, Site-Directed
Myocardium / enzymology*
Nitric Oxide / chemistry*
Oxygen / chemistry*
Protein Binding
Thermus thermophilus / enzymology*
Xenon / chemistry
Grant Support
Reg. No./Substance:
0/Bacterial Proteins; 0/Ligands; 31C4KY9ESH/Nitric Oxide; 3H3U766W84/Xenon; 789U1901C5/Copper; EC Transport Complex IV; S88TT14065/Oxygen

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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