Paper Citing NAMD - Abstract
Sharma, Vivek; Wikstroem, Marten; Laakkonen, Liisa
Modeling the active-site structure of the cbb(3)-type oxidase from Rhodobacter sphaeroides
BIOCHEMISTRY, 47:4221-4227, APR 8 2008
The active site of the heme-copper oxidases comprises a redox-active high-spin heme and a tris-histidine copper center CUB. Two amino acids in the close vicinity of the metals, a tyrosine and a tryptophan from helix 6, have been shown to be absolutely required for the catalytic function and should be considered part of the active site. Additionally, amino acid residues from interhelical loops strongly modify the activity. In a separate subfamily of heme-copper oxidases, the cbb(3)-type oxidases, the metal centers are identical, the tyrosine is found in helix 7, but nothing is known of the corresponding tryptophan or of the involvement of the loop residues. We have observed a conserved aromatic cluster in the known oxidase structures, including the essential tryptophan and loop residues, and refined our earlier model of the cbb(3)-type oxidase from Rhodobacter sphaeroides to test the feasibility of a similar structure. In the refined model, the interactions around the A-propionate of the high-spin heme resemble closely those seen in crystal structures of other terminal oxidases. Two alternative models (G- and C-models) that differ for the positioning of conserved tryptophans in helix 6, are presented. Molecular dynamics simulations on the catalytic subunit of the cbb(3)-type oxidase model result in a conformational change of the activesite tyrosine, which may be related to different ligand-binding properties of the cbb(3)-type oxidases. The relationship between sequence and functional data for defining the subfamily is discussed.
