Structural basis of replication origin recognition by the DnaA protein.
Fujikawa, Norie 1; Kurumizaka, Hitoshi 1,2; Nureki, Osamu 3; Terada, Takaho 1; Shirouzu, Mikako 1; Katayama, Tsutomu 4; Yokoyama, Shigeyuki 1,2,3,*
[Miscellaneous Article] Nucleic Acids Research. 31(8):2077-2086, April 15, 2003.

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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 A 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[degrees] 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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