1J1V

Crystal structure of DnaA domainIV complexed with DnaAbox DNA

Summary for 1J1V

• Entry DOI: 10.2210/pdb1j1v/pdb
• Descriptor: 5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3', 5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3', Chromosomal replication initiator protein dnaA, ... (4 entities in total)
• Functional Keywords: protein-dna complex, replication, riken structural genomics/proteomics initiative, rsgi, structural genomics, replication-dna complex, replication/dna
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P03004
• Total number of polymer chains: 3
• Total formula weight: 18776.28

Authors

Fujikawa, N.,Kurumizaka, H.,Nureki, O.,Terada, T.,Shirouzu, M.,Katayama, T.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2002-12-18, release date: 2003-04-22, Last modification date: 2024-10-30)

Primary citation

Fujikawa, N.,Kurumizaka, H.,Nureki, O.,Terada, T.,Shirouzu, M.,Katayama, T.,Yokoyama, S.
Structural basis of replication origin recognition by the DnaA protein
NUCLEIC ACIDS RES., 31:2077-2086, 2003

PubMed 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 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 approximately 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.

PubMed: 12682358
DOI: 10.1093/nar/gkg309

Experimental method

X-RAY DIFFRACTION (2.1 Å)