Paper Citing NAMD - Abstract
Sharma, V.; Puustinen, A.; Wikstrom, M.; Laakkonen, L.
Sequence analysis of the cbb(3) oxidases and an atomic model for the Rhodobacter sphaeroides enzyme
BIOCHEMISTRY, 45:5754-5765, MAY 9 2006
The cbb(3)-type oxidases are members of the heme-copper oxidase superfamily, distant by sequence comparisons, but sharing common functional characteristics. To understand the minimal common properties of the superfamily, and to learn about cbb(3)-type oxidases specifically, we have analyzed a wide set of heme-copper oxidase sequences and built a homology model of the catalytic subunit of the cbb(3) oxidase from Rhodobacter sphaeroides. We conclude that with regard to the active site surroundings, the cbb(3) oxidases greatly resemble the structurally known oxidases, while major differences are found in three segments: the additional N-terminal stretch of ca. 60 amino acids, the segment following helix 3 to the end of helix 5, and the C-terminus from helix I I onward. The conserved core contains the active site tyrosine and also an analogue of the K-channel of proton transfer, but centered on a well-conserved histidine in the lower part of helix 7. Modeling the variant parts of the enzyme suggests that two periplasmic loops (between helices 3 and 4 and between helices I I and 12) could interact with each other as a part of the active site structure and might have an important role in proton pumping. An analogue of the D-channel is not found, but an alternative channel might form around helix 9. A preliminary packing model of the trimeric enzyme is also presented.
