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The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: A novel homodimer assembling and the implication for effector‐binding mode

Among the transcription factors, the helix‐turn‐helix (HTH) GntR family comprised of FadR, HutC, MocR, YtrA, AraR, and PlmA subfamilies regulates the most varied biological processes. Generally, proteins belonging to this family contain an N‐terminal DNA‐binding domain and a C‐terminal effector‐binding/oligomerization domain. The members of the YtrA subfamily are much shorter than other members of this family, with chain lengths of 120–130 residues with about 50 residues located in the C‐terminal domain. Because of this length, the mode of dimerization and the ability to bind effectors by the C‐terminal domain are puzzling. Here, we first report the structure of the transcription factor CGL2947 from Corynebacterium glutamicum, which belongs to the YtrA family. The monomer is composed of a DNA‐binding domain containing a winged HTH motif in the N terminus and two helices (α4 and α5) with a fishhook‐shaped arrangement in the C terminus. Helices α4 and α5 of two monomers intertwine together to form a novel homodimer assembly. The effector‐accommodating pocket with 2‐methyl‐2,4‐pentanediol (MPD) docked was located, and it was suggested to represent a novel mode of effector binding. The structures in two crystal forms (MPD‐free and ‐bound in the proposed effector‐binding pocket) were solved. The structural variations have implications regarding how the effector‐induced conformational change modulates DNA affinity for YtrA family members.