7BCA

Crystal structure of the HTH DNA binding protein ArdK from R388 plasmid bound to a direct-repeat DNA element

Summary for 7BCA

• Entry DOI: 10.2210/pdb7bca/pdb
• Descriptor: KORA domain-containing protein, DNA (5'-D(*TP*GP*TP*CP*AP*AP*TP*AP*GP*GP*TP*GP*TP*CP*AP*AP*TP*AP*C)-3'), DNA (5'-D(*GP*TP*AP*TP*TP*GP*AP*CP*AP*CP*CP*TP*AP*TP*TP*GP*AP*CP*A)-3') (3 entities in total)
• Functional Keywords: dna binding protein, helix turn helix, direct repeat, plasmid conjugation
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 4
• Total formula weight: 34064.34

Authors

Fernandez-Lopez, R.,Boer, D.R.,Moncalian, G. (deposition date: 2020-12-18, release date: 2022-07-13, Last modification date: 2024-11-13)

Primary citation

Fernandez-Lopez, R.,Ruiz, R.,Del Campo, I.,Gonzalez-Montes, L.,Boer, D.R.,de la Cruz, F.,Moncalian, G.
Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors.
Nucleic Acids Res., 50:11938-11947, 2022

PubMed Abstract: Some transcription factors bind DNA motifs containing direct or inverted sequence repeats. Preference for each of these DNA topologies is dictated by structural constraints. Most prokaryotic regulators form symmetric oligomers, which require operators with a dyad structure. Binding to direct repeats requires breaking the internal symmetry, a property restricted to a few regulators, most of them from the AraC family. The KorA family of transcriptional repressors, involved in plasmid propagation and stability, includes members that form symmetric dimers and recognize inverted repeats. Our structural analyses show that ArdK, a member of this family, can form a symmetric dimer similar to that observed for KorA, yet it binds direct sequence repeats as a non-symmetric dimer. This is possible by the 180° rotation of one of the helix-turn-helix domains. We then probed and confirmed that ArdK shows affinity for an inverted repeat, which, surprisingly, is also recognized by a non-symmetrical dimer. Our results indicate that structural flexibility at different positions in the dimerization interface constrains transcription factors to bind DNA sequences with one of these two alternative DNA topologies.

PubMed: 36370103
DOI: 10.1093/nar/gkac1024

Experimental method

X-RAY DIFFRACTION (2.8 Å)