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Nucleic Acids Research, 2003, Vol. 31, No. 8 2077-2086
© 2003 Oxford University Press

Structural basis of replication origin recognition by the DnaA protein

Norie Fujikawa1, Hitoshi Kurumizaka1,2, Osamu Nureki3, Takaho Terada1, Mikako Shirouzu1, Tsutomu Katayama4 and Shigeyuki Yokoyama1,2,3

1 RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan, 2 Cellular Signaling Laboratory, RIKEN Harima Institute at SPring8, 1-1-1 Kohto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan, 3 Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan and 4 Department of Molecular Biology, Kyushu University Graduate School of Pharmaceutical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan

The authors wish it to be known that, in their opinion, the first three authors should be regarded as joint First Authors

Escherichia coli DnaA binds to 9 bp sequences (DnaA boxes) in the replication origin, oriC, to form a complex initiating chromosomal DNA replication. In the present study, we determined the crystal structure of its DNA-binding domain (domain IV) complexed with a DnaA box at 2.1 Å resolution. DnaA domain IV contains a helix–turn–helix motif for DNA binding. One helix and a loop of the helix– turn–helix motif are inserted into the major groove and 5 bp (3' two-thirds of the DnaA box sequence) are recognized through base-specific hydrogen bonds and van der Waals contacts with the C5-methyl groups of thymines. In the minor groove, Arg399, located in the loop adjacent to the motif, recognizes three more base pairs (5' one-third of the DnaA box sequence) by base-specific hydrogen bonds. DNA bending by ~28° was also observed in the complex. These base-specific interactions explain how DnaA exhibits higher affinity for the strong DnaA boxes (R1, R2 and R4) than the weak DnaA boxes (R3 and M) in the replication origin.


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