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Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB

Item Type:Article
Title:Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB
Creators Name:Khare, D. and Ziegelin, G. and Lanka, E. and Heinemann, U.
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.
Keywords:Amino Acid Sequence, Amino Acid Sequence Homology, DNA, DNA-Binding Proteins, Helix-Turn-Helix Motifs, Molecular Models, Molecular Sequence Data, Plasmids, Protein Binding, Repressor Proteins, Site-Directed Mutagenesis
Source:Nature Structural & Molecular Biology
Publisher:Nature Publishing Group (U.S.A.)
Page Range:656-663
Date:1 January 2004
Official Publication:https://doi.org/10.1038/nsmb773
PubMed:View item in PubMed

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