Symmetric Dimeric Structure and Ligand Recognition of CutR, a LysR-Type Transcriptional Regulator from Mycobacterium sp. Strain JC1

TL;DR

This paper reveals the dimeric structure of CutR, a protein that regulates CO-DH gene expression in Mycobacterium, and how it binds to DNA.

Contribution

The study presents the first symmetric dimeric structure of a LysR-type regulator with detailed ligand-binding and DNA recognition features.

Findings

CutR forms a stable dimer and binds to a specific DNA sequence upstream of the CO-DH gene.

The crystal structure of CutR shows a unique symmetrical dimer with a conserved ligand-binding site.

Comparative genomics supports the dimeric regulatory mechanism across Mycobacterium species.

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 cutB 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 Mycobacterium species, supporting the dimeric regulatory mechanism and providing new insights into LTTR diversity.

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