Figure 3.

P_II proteins and the ammonia channel. (A) The structure (PDB file 2NUU; Conroy et al., 2007) of the E. coli complex of GlnK (a P_II protein in charge of ammonia channel regulation) and the ammonia channel AmtB is shown to the right, whereas the zoom to the lower left shows only a part of the complex, to highlight the interaction of one T-loop with one channel. AmtB is in semi-transparent surface representation. GlnK is in the main figure in cartoon representation with each subunit colored differently, with the side-chain of the T-loop residue Arg47 shown in sticks representation. In the zoomed image GlnK is shown in surface representation in yellow with the T-loop residues highlighted in space-filling representation, illustrating the fact that the side-chain of Arg47 is the element getting deep into the channel and blocking it. (B) Super-imposition of the structures of Archeoglobus fulgidus GlnK3 (one of the three P_II proteins of the GlnK type in this archaeon; Maier et al., 2011) with ADP bound (green; PDB file code 3TA1) or with ATP and 2OG bound (yellow; PDB 3TA2) to illustrate how 2OG binding fixes the T-loops in an outwards-flexed position (relative to the positions without 2OG) that would be inappropriate for fitting the topography of the entry chambers to the three ammonia channels in trimeric Amt (the ammonia channel in this organism).