Denitrifying bacteria are important agents in managing waste, as well as being a source of nitric oxide in the atmosphere. One of the electron transfer pathways in which nitrates are converted eventually to N2 via NO2 and NO, utilizes, for the particularly potent denitrifying bacteria Alcaligenes faecalis, Strain S-6, a copper containing nitrite reductase, and a blue protein which which while normally acting as the agent which transfers an electron to the nitrite reductase, can also act as an inhibitor in the presence of O2. The organism """"""""Achromobacter cycloclastes"""""""" also contains a similar pair of molecules in its denitrification pathway. We have determined the chemical sequence and the protein folding of the blue protein (cupredoxin) from A. faecalis, and plan to continue to elucidate the structural details at high resolution of the differences between the two oxidation states of the molecule. The structure is such that a plausible hypothesis for the origin of the specificity between the blue protein and its nitrite reductase resides in a C-terminal helix of the blue protein, which also looks as if could be easily removed proteolytically. This hypothesis will be tested by carrying out the cleavage and testing for remaining specificity of interaction. That these blue copper protein are specifically designed for binding just copper has been demonstrated by McMillin and Engeseth, by doing heat capacity measurements on the related blue copper protein, azurin, with metals other than copper bound, and without any metal. We plan to examine the structure of azurin without a copper, by X-ray diffraction methods, in order to gain insight into the role the metal plays in the protein integrity. Finally, in order to provide information on the partner of cupredoxin 1, we plan to determine the structure of the copper containing nitrite reductase from """"""""Achromobacter cycloclastes"""""""". This will reveal the structure of a new kind of copper protein as well as allow us to examine the details of the interaction of it and its cupredoxin (a homolog of the A. faecalis one), two partners in a specific electron transfer chain.
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