1R71

Crystal Structure of the DNA binding domain of KorB in complex with the operator DNA

Summary for 1R71

• Entry DOI: 10.2210/pdb1r71/pdb
• Descriptor: 5'-D(*AP*(BRU)P*TP*TP*TP*AP*GP*CP*GP*GP*CP*TP*AP*AP*AP*AP*G)-3', 5'-D(*CP*(BRU)P*TP*TP*TP*AP*GP*CP*CP*GP*CP*TP*AP*AP*AP*AP*(BRU))-3', Transcriptional repressor protein korB, ... (4 entities in total)
• Functional Keywords: incp, plasmid partitioning, protein-dna complex, heilx-turn-helix motif, transcription factor, parb homologue, transcription-dna complex, transcription/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 12
• Total formula weight: 122225.47

Authors

Khare, D.,Ziegelin, G.,Lanka, E.,Heinemann, U. (deposition date: 2003-10-17, release date: 2004-06-01, Last modification date: 2024-02-14)

Primary citation

Khare, D.,Ziegelin, G.,Lanka, E.,Heinemann, U.
Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB.
Nat.Struct.Mol.Biol., 11:656-663, 2004

PubMed Abstract: The KorB protein of the broad-host-range plasmid RP4 acts as a multifunctional regulator of plasmid housekeeping genes, including those responsible for replication, maintenance and conjugation. Additionally, KorB functions as the ParB analog of the plasmid's partitioning system. The protein structure consists of eight helices, two of which belong to a predicted helix-turn-helix motif. Each half-site of the palindromic operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based mainly on two side chain interactions outside the helix-turn-helix motif with two bases next to the central base pair of the 13-base pair operator sequence. The surface of the KorB DNA-binding domain mirrors the overall acidity of KorB, whereas DNA binding occurs via a basic interaction surface. We present a model of KorB, including the structure of its dimerization domain, and discuss its interactions with the highly basic ParA homolog IncC.

PubMed: 15170177
DOI: 10.1038/nsmb773

Experimental method

X-RAY DIFFRACTION (2.2 Å)