2DU9: Crystal Structure Of The Transcriptional Factor From C.Glutamicum

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 (alpha4 and alpha5) with a fishhook-shaped arrangement in the C terminus. Helices alpha4 and alpha5 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.
PDB ID: 2DU9Download
MMDB ID: 52969
PDB Deposition Date: 2006/7/20
Updated in MMDB: 2012/10
Experimental Method:
x-ray diffraction
Resolution: 2.28  Å
Source Organism:
Similar Structures:
Biological Unit for 2DU9: dimeric; determined by author and by software (PISA,PQS)
Molecular Components in 2DU9
Label Count Molecule
Proteins (2 molecules)
Predicted Transcriptional Regulators
Molecule annotation
Chemicals (2 molecules)
* Click molecule labels to explore molecular sequence information.

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