PMID:14523560

Citation	Yoshida, Y, Obita, T, Kokusho, Y, Ohmura, T, Katayama, T, Ueda, T and Imoto, T (2003) Identification of the region in Escherichia coli DnaA protein required for specific recognition of the DnaA box. Cell. Mol. Life Sci. 60:1998-2008
Abstract	DnaA protein binds specifically to a 9-base- pair motif called the DnaA box. Domain IV comprises 94 amino acid residues and is required for DNA binding. Using nuclear magnetic resonance analysis, we investigated the interaction between DnaA domain IV and both a DnaA box and a non-specific oligonucleotide that has a reduced affinity for DnaA. The 1H-15N HSQC spectrum of DnaA domain IV showed prominent chemical shift perturbations on six residues (Arg399, Ala404, Leu422, Asp433, Thr435 and Thr436) in the presence of the DnaA box. Through homology modeling, we located all of these residues on one side surface of the DnaA domain IV molecule. Moreover, we compared the chemical shift perturbation of the 1H-15N HSQC spectrum in the presence of the DnaA box with that in the presence of a non-specific oligonucleotide, and the results suggested that Leu422 imparts specificity in binding with the DnaA box.
Links	PubMed Online version:10.1007/s00018-003-3176-7
Keywords	Amino Acid Sequence; Bacterial Proteins/genetics; Bacterial Proteins/metabolism; Base Sequence; Binding Sites; DNA Replication; DNA-Binding Proteins/genetics; DNA-Binding Proteins/metabolism; Escherichia coli/metabolism; Models, Molecular; Protein Binding; Protein Structure, Tertiary
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