Similarities in the structure of the transcriptional repressor AmtR in two different space groups suggest a model for the interaction with GlnK

Abstract

AmtR belongs to the TetR family of transcription regulators and is a global nitrogen regulator that is induced under nitrogen-starvation conditions in Corynebacterium glutamicum. AmtR regulates the expression of transporters and enzymes for the assimilation of ammonium and alternative nitrogen sources, for example urea, amino acids etc. The recognition of operator DNA by homodimeric AmtR is not regulated by small-molecule effectors as in other TetR-family members but by a trimeric adenylylated P_II-type signal transduction protein named GlnK. The crystal structure of ligand-free AmtR (AmtR_orth) has been solved at a resolution of 2.1 Å in space group P2₁2₁2. Comparison of its quaternary assembly with the previously solved native AmtR structure (PDB entry 5dy1) in a trigonal crystal system (AmtR_tri) not only shows how a solvent-content reduction triggers a space-group switch but also suggests a model for how dimeric AmtR might stoichiometrically interact with trimeric adenylylated GlnK.

Keywords: AmtR adenylylated GlnK complex stoichiometry; Corynebacterium glutamicum; crystal-packing comparison; nitrogen regulation; transcription regulator effector complex.

Figure 1

(a) AmtR dimer, with the DBD shown in green and the dimerization helices in blue. The helices are labelled from H1 to H10. Helix H10 is coloured yellow and loop L8–9 is shown in red. (b) Hexameric assembly formed by a trimer of dimers in the asymmetric unit. (c) Schematic representation of the topology of the hexameric AmtR assembly. The three dimers are shown as segments of a circle in different shades of grey.

Figure 2

(a) Superposition of the three AmtR dimers present in AmtR_orth on top of each other (in different shades of blue) and of the AmtR_tri dimer (shown in green). (b) Superposition of the AmtR_orth hexamer (the colour coding is similar to that in Fig. 1 ▸) and the crystallographic AmtR_tri hexamer (grey).

Figure 3

(a) Schematic representation of the topology of the (AmtR₂)₃ pseudohexamer. The three dimers are shown as segments of a circle in different shades of grey. (b) Schematic representation of the theoretical (AmtR₂)₃ hexamer following compaction along the former 3₁ screw axis, which has now morphed into a threefold rotation axis. (c) Schematic representation of the topology of a proposed (AmtR₂)₃–(GlnK₃)₂ complex. (d) Ribbon representation of the pseudo-hexameric AmtR dimers, in which each dimer of AmtR is shown in a different colour. Distances between the TetR-type repressor effector-binding sites are marked with black lines. (e, f) The distances between the GlnK T-loops are marked as seen in the crystal structures of GlnK with (e) oxaloacetic acid in the binding pocket (PDB entry 3ta2, 1.9 Å resolution; Maier et al., 2011 ▸) and (f) in complex with E. coli AmtB (PDB entry 2ns1, 1.96 Å resolution; Gruswitz et al., 2007 ▸).