Identification of the region in Escherichia coli DnaA protein required for specific recognition of the DnaA box

Y. Yoshida, T. Obita, Y. Kokusho, T. Ohmura, Tsutomu Katayama, Tadashi Ueda, T. Imoto

Research output: Contribution to journalArticle

9 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)1998-2008
Number of pages11
JournalCellular and Molecular Life Sciences
Volume60
Issue number9
DOIs
Publication statusPublished - Sep 1 2003

Fingerprint

Escherichia coli Proteins
Chemical shift
Oligonucleotides
Escherichia coli
Base Pairing
Proteins
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Amino Acids
Molecules
DNA

All Science Journal Classification (ASJC) codes

  • Molecular Medicine
  • Molecular Biology
  • Pharmacology
  • Cellular and Molecular Neuroscience
  • Cell Biology

Cite this

Identification of the region in Escherichia coli DnaA protein required for specific recognition of the DnaA box. / Yoshida, Y.; Obita, T.; Kokusho, Y.; Ohmura, T.; Katayama, Tsutomu; Ueda, Tadashi; Imoto, T.

In: Cellular and Molecular Life Sciences, Vol. 60, No. 9, 01.09.2003, p. 1998-2008.

Research output: Contribution to journalArticle

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AU - Katayama, Tsutomu

AU - Ueda, Tadashi

AU - Imoto, T.

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AB - 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.

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