9VVU
Crystal structure of the LysR-type transcriptional regulator CutR from mycobacterium sp. strain JC1
Summary for 9VVU
| Entry DOI | 10.2210/pdb9vvu/pdb |
| Descriptor | LysR family transcriptional regulator, 1,2-ETHANEDIOL, GLYCEROL, ... (4 entities in total) |
| Functional Keywords | lysr family transcriptional regulator, transcription |
| Biological source | Mycobacterium sp. DSM 3803 |
| Total number of polymer chains | 2 |
| Total formula weight | 68651.12 |
| Authors | |
| Primary citation | Cho, H.J.,Lee, K.Y.,Lee, H.S.,Kang, B.S. Symmetric Dimeric Structure and Ligand Recognition of CutR, a LysR-Type Transcriptional Regulator from Mycobacterium sp. Strain JC1. Int J Mol Sci, 26:-, 2025 Cited by PubMed Abstract: Mycobacteria possess carbon monoxide dehydrogenase (CO-DH) to utilize CO as an energy source and to resist host defense mechanisms. The expression of the CO-DH gene is regulated by CutR, a LysR-type transcriptional regulator (LTTR) that exhibits unique characteristics, suggesting that it functions as a dimer rather than the typical tetramer. Size-exclusion chromatography revealed that CutR forms a stable dimer. Electrophoretic mobility shift assays demonstrated that dimeric CutR specifically binds to an inverted repeat sequence (IR1) containing T-n12-A motifs located upstream of the gene, which encodes the medium subunit of CO-DH. Crystal structure determination at 1.8 Å resolution revealed that CutR consists of an N-terminal DNA-binding domain with a winged helix-turn-helix motif and a C-terminal ligand-binding domain comprising two regulatory subdomains (RD1 and RD2), forming a unique two-fold symmetrical homodimer. This dimer is stabilized through four interfaces, including an extensive 12-stranded antiparallel β-sheet formed between RD1 subdomains via intertwining C-terminal β11 strands. This represents the first symmetric dimeric LTTR structure with tightly associated ligand-binding domains. The recognition helices are spaced closer together than they are in typical DNA-bound LTTRs, despite binding longer T-n12-A sequences, suggesting that a conformational change is required to enhance DNA-binding affinity. A putative ligand-binding site was identified between the RD1 and RD2 subdomains, where glycerol binding induced local conformational changes. Comparative genomic analysis revealed conservation of CutR and the IR1 sequence across species, supporting the dimeric regulatory mechanism and providing new insights into LTTR diversity. PubMed: 41226566DOI: 10.3390/ijms262110533 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.8 Å) |
Structure validation
Download full validation report
