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Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB
- Source :
- Nature Structural & Molecular Biology. 11:656-663
- Publication Year :
- 2004
- Publisher :
- Springer Science and Business Media LLC, 2004.
-
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.
- Subjects :
- Models, Molecular
Base pair
Stereochemistry
Molecular Sequence Data
Helix-turn-helix
Plasma protein binding
Biology
chemistry.chemical_compound
Plasmid
Protein structure
Structural Biology
Sequence-specific DNA binding
Amino Acid Sequence
Molecular Biology
Peptide sequence
Helix-Turn-Helix Motifs
Genetics
Sequence Homology, Amino Acid
DNA
DNA-Binding Proteins
Repressor Proteins
chemistry
Mutagenesis, Site-Directed
Plasmids
Protein Binding
Subjects
Details
- ISSN :
- 15459985 and 15459993
- Volume :
- 11
- Database :
- OpenAIRE
- Journal :
- Nature Structural & Molecular Biology
- Accession number :
- edsair.doi.dedup.....6fd7e09f984eb835cf9759cd48ee3b8d