7bbq

Crystal structure of the HTH DNA binding protein ArdK from R388 plasmid. Apo form.

spinqualitylabelsall models 7bbq, resolution 3.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7bbq is a 1 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3Å Ligands: MSE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q6I6B7_ECOLX Publication Abstract from PubMed 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 degrees 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. Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors.,Fernandez-Lopez R, Ruiz R, Del Campo I, Gonzalez-Montes L, Boer DR, de la Cruz F, Moncalian G Nucleic Acids Res. 2022 Nov 11;50(20):11938-11947. doi: 10.1093/nar/gkac1024. PMID:36370103 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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