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
N1 - Funding Information:
We thank Dr M. Kawamoto (JASRI) for help with collecting diffraction data at SPring-8, Ms N. Obayashi for the cell-free protein production and Ms T. Nakayama for the manuscript preparation. This work was supported by the Bioarchitect Research Program (RIKEN) and by the Ministry of Education, Sports, Culture, Science and Technology of Japan.
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.
UR - http://www.scopus.com/inward/record.url?scp=0038476181&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=0038476181&partnerID=8YFLogxK
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 -