2DU9
crystal structure of the transcriptional factor from C.glutamicum
Summary for 2DU9
| Entry DOI | 10.2210/pdb2du9/pdb |
| Descriptor | Predicted transcriptional regulators, (4S)-2-METHYL-2,4-PENTANEDIOL (3 entities in total) |
| Functional Keywords | winged helix-turn-helix, transcription |
| Biological source | Corynebacterium glutamicum ATCC 13032 |
| Total number of polymer chains | 1 |
| Total formula weight | 14514.54 |
| Authors | Gao, Y.,Yao, M.,Tanaka, I. (deposition date: 2006-07-20, release date: 2007-07-24, Last modification date: 2024-11-20) |
| Primary citation | Gao, Y.,Yao, M.,Itou, H.,Zhou, Y.,Tanaka, I. The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: A novel homodimer assembling and the implication for effector-binding mode Protein Sci., 16:1878-1886, 2007 Cited by PubMed Abstract: 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. PubMed: 17766384DOI: 10.1110/ps.072976907 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.28 Å) |
Structure validation
Download full validation report
