Figure 2 - full size


Figure 2.
Fig. 2. Gad1, comparison with GadB and the active site structure. (a) C^α trace superposition of the subunits of Arabidopsis thaliana Gad1 (pale yellow) and Escherichia coli GadB at low pH (red, PDB code 1PMM). The active site loop (AL) of Gad1 is in orange. The PLP cofactor appears as ball-and-sticks (grey and atom colours). The position of the halide binding site S1 of GadB is denoted by a magenta sphere. For differences in the C-terminal region between Gad1 and GadB see b, depicting also the neutral-pH structure of GadB (2DGK). (b) Cartoon stereo view of the Gad1 active site cleft. Gad1 is in pale yellow with the C-terminal part of the small domain and the active site loop in orange. 2mF[o] – DF[c] electron density (0.8 σ) for the Gad1 loop is shown in blue. The last helix of the small domain and the active site loop of E. coli GadB are superimposed onto the Gad1 structure. GadB at neutral pH (2DGK, inactive conformation as 1PMO, in cyan) blocks its active site with the C-terminus and the active site loop. The His465 side chain forms a substituted aldamine with the cofactor and is in ball-and-stick mode (cyan). GadB at low pH (1PMM, active conformation; in red) has its C-terminus released and the active site loop shifted. (c) Stereo stick representation, in green and atom colours, of the active site. The cofactor is depicted in cyan and atom colours. Labels denote the cofactor and residues mentioned in Discussion.

The above figure is reprinted by permission from Elsevier: J Mol Biol (2009, 392, 334-351) copyright 2009.