Abstract
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 language | English |
|---|---|
| Pages (from-to) | 2077-2086 |
| Number of pages | 10 |
| Journal | Nucleic acids research |
| Volume | 31 |
| Issue number | 8 |
| DOIs | |
| Publication status | Published - Apr 15 2003 |
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All Science Journal Classification (ASJC) codes
- Genetics
Cite this
Structural basis of replication origin recognition by the DnaA protein. / Fujikawa, Norie; Kurumizaka, Hitoshi; Nureki, Osamu; Terada, Takaho; Shirouzu, Mikako; Katayama, Tsutomu; Yokoyama, Shigeyuki.
In: Nucleic acids research, Vol. 31, No. 8, 15.04.2003, p. 2077-2086.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Structural basis of replication origin recognition by the DnaA protein
AU - Fujikawa, Norie
AU - Kurumizaka, Hitoshi
AU - Nureki, Osamu
AU - Terada, Takaho
AU - Shirouzu, Mikako
AU - Katayama, Tsutomu
AU - Yokoyama, Shigeyuki
PY - 2003/4/15
Y1 - 2003/4/15
N2 - 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.
AB - 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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U2 - 10.1093/nar/gkg309
DO - 10.1093/nar/gkg309
M3 - Article
C2 - 12682358
AN - SCOPUS:0038476181
VL - 31
SP - 2077
EP - 2086
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 8
ER -