Structural basis of replication origin recognition by the DnaA protein

Norie Fujikawa, Hitoshi Kurumizaka, Osamu Nureki, Takaho Terada, Mikako Shirouzu, Tsutomu Katayama, Shigeyuki Yokoyama*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

155 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)2077-2086
Number of pages10
JournalNucleic Acids Research
Issue number8
Publication statusPublished - 2003 Apr 15
Externally publishedYes

ASJC Scopus subject areas

  • Genetics


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