NMR structure of the N-terminal domain of the replication initiator protein DnaA.
DnaA is an essential component in the initiation of bacterial chromosomal replication. DnaA binds to a series of 9 base pair repeats leading to oligomerization, recruitment of the DnaBC helicase, and the assembly of the replication fork machinery. The structure of the N-terminal domain (residues 1-100) of DnaA from Mycoplasma genitalium was determined by NMR spectroscopy. The backbone r.m.s.d. for the first 86 residues was 0.6 +/- 0.2 A based on 742 NOE, 50 hydrogen bond, 46 backbone angle, and 88 residual dipolar coupling restraints. Ultracentrifugation studies revealed that the domain is monomeric in solution. Features on the protein surface include a hydrophobic cleft flanked by several negative residues on one side, and positive residues on the other. A negatively charged ridge is present on the opposite face of the protein. These surfaces may be important sites of interaction with other proteins involved in the replication process. Together, the structure and NMR assignments should facilitate the design of new experiments to probe the protein-protein interactions essential for the initiation of DNA replication.
Lowery
Thomas J
TJ
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Pelton
Jeffrey G
JG
Chandonia
John-Marc
JM
Kim
Rosalind
R
Yokota
Hisao
H
Wemmer
David E
DE
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D002352:Carrier Proteins / Q000378:metabolism; D004261:DNA Replication; D004268:DNA-Binding Proteins / Q000737:chemistry*; D053488:DnaB Helicases / Q000378:metabolism; D004926:Escherichia coli / Q000378:metabolism; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008969:Molecular Sequence Data; D045704:Mycoplasma genitalium / Q000378:metabolism*; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013045:Species Specificity
D001426:Bacterial Proteins; D002352:Carrier Proteins; D004268:DNA-Binding Proteins; C523634:DiaA protein, E coli; C066312:DnaA protein, Bacteria; D053488:DnaB Helicases