PDBsum entry 3hbx

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Lyase PDB id
Protein chains
(+ 0 more) 437 a.a.
Waters ×314

References listed in PDB file
Key reference
Title A common structural basis for ph- And calmodulin-Mediated regulation in plant glutamate decarboxylase.
Authors H.Gut, P.Dominici, S.Pilati, A.Astegno, M.V.Petoukhov, D.I.Svergun, M.G.Grütter, G.Capitani.
Ref. J Mol Biol, 2009, 392, 334-351. [DOI no: 10.1016/j.jmb.2009.06.080]
PubMed id 19580813
Glutamate decarboxylase (Gad) catalyzes glutamate to gamma-aminobutyrate conversion. Plant Gad is a approximately 340 kDa hexamer, involved in development and stress response, and regulated by pH and binding of Ca(2+)/calmodulin (CaM) to the C-terminal domain. We determined the crystal structure of Arabidopsis thaliana Gad1 in its CaM-free state, obtained a low-resolution structure of the calmodulin-activated Gad complex by small-angle X-ray scattering and identified the crucial residues, in the C-terminal domain, for regulation by pH and CaM binding. CaM activates Gad1 in a unique way by relieving two C-terminal autoinhibition domains of adjacent active sites, forming a 393 kDa Gad1-CaM complex with an unusual 1:3 stoichiometry. The complex is loosely packed: thanks to the flexible linkers connecting the enzyme core with the six C-terminal regulatory domains, the CaM molecules retain considerable positional and orientational freedom with respect to Gad1. The complex thus represents a prototype for a novel CaM-target interaction mode. Thanks to its two levels of regulation, both targeting the C-terminal domain, Gad can respond flexibly to different kinds of cellular stress occurring at different pH values.
Figure 1.
Fig. 1. Crystal structure of A. thaliana Gad1. (a and c) Surface representations of the Gad1 homohexamer. View along the 3-fold (a) and the 2-fold (c) non-crystallographic symmetry axes of the protein. (b) Cartoon representation of Gad1. The six subunits are depicted in different colours.
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 figures are reprinted by permission from Elsevier: J Mol Biol (2009, 392, 334-351) copyright 2009.
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