7B23

DtxR-like iron-dependent regulator IdeR complexed with cobalt and the SACE_2689 promoter DNA-binding sequence

This is a non-PDB format compatible entry.

Summary for 7B23

• Entry DOI: 10.2210/pdb7b23/pdb
• Descriptor: DtxR family iron (Metal) dependent repressor, SACE_2689 promoter DNA-binding sequence, COBALT (II) ION, ... (5 entities in total)
• Functional Keywords: transcription, transcription regulation, repressor, regulator, transcription regulator, metal sensor, ider, iron-dependent regulator, dtxr, helix-turn-helix, metal ion, metal-binding protein, dna binding, protein-dna complex
• Biological source: Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338); More
• Total number of polymer chains: 8
• Total formula weight: 172974.57

Authors

Maurer, D.,Marcos-Torres, F.J.,Griese, J.J. (deposition date: 2020-11-26, release date: 2021-03-03, Last modification date: 2024-10-23)

Primary citation

Marcos-Torres, F.J.,Maurer, D.,Juniar, L.,Griese, J.J.
The bacterial iron sensor IdeR recognizes its DNA targets by indirect readout.
Nucleic Acids Res., 49:10120-10135, 2021

PubMed Abstract: The iron-dependent regulator IdeR is the main transcriptional regulator controlling iron homeostasis genes in Actinobacteria, including species from the Corynebacterium, Mycobacterium and Streptomyces genera, as well as the erythromycin-producing bacterium Saccharopolyspora erythraea. Despite being a well-studied transcription factor since the identification of the Diphtheria toxin repressor DtxR three decades ago, the details of how IdeR proteins recognize their highly conserved 19-bp DNA target remain to be elucidated. IdeR makes few direct contacts with DNA bases in its target sequence, and we show here that these contacts are not required for target recognition. The results of our structural and mutational studies support a model wherein IdeR mainly uses an indirect readout mechanism, identifying its targets via the sequence-dependent DNA backbone structure rather than through specific contacts with the DNA bases. Furthermore, we show that IdeR efficiently recognizes a shorter palindromic sequence corresponding to a half binding site as compared to the full 19-bp target previously reported, expanding the number of potential target genes controlled by IdeR proteins.

PubMed: 34417623
DOI: 10.1093/nar/gkab711

Experimental method

X-RAY DIFFRACTION (2.15 Å)