1j1v

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Crystal structure of DnaA domainIV complexed with DnaAbox DNA

Structural highlights

1j1v is a 3 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.1Å
Ligands:MSE
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

DNAA_ECOLI Plays a key role in the initiation and regulation of chromosomal replication. Binds in an ATP-dependent fashion to the origin of replication (oriC) to initiate formation of the DNA replication initiation complex exactly once per cell cycle. Binds the DnaA box (consensus sequence 5'-TTATC[CA]A[CA]A-3'); subsequent binding of DNA polymerase III subunits leads to replisome formation. The DnaA-ATP form converts to DnaA-ADP; once converted to ADP the protein cannot initiate replication, ensuring only 1 round of replication per cell cycle. DnaA can inhibit its own gene expression as well as that of other genes such as dam, rpoH, ftsA and mioC.[1] [2] [3] Also required for replication of plasmid DNA; binds 4 dnaA boxes in the minimal plasmid RK2 replication origin (oriV).[4] [5] [6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

Structural basis of replication origin recognition by the DnaA protein.,Fujikawa N, Kurumizaka H, Nureki O, Terada T, Shirouzu M, Katayama T, Yokoyama S Nucleic Acids Res. 2003 Apr 15;31(8):2077-86. PMID:12682358[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
30 reviews cite this structure
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
Aravind et al. (2005)
29 more
94 other articles
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See Also

References

  1. ↑ Konieczny I, Doran KS, Helinski DR, Blasina A. Role of TrfA and DnaA proteins in origin opening during initiation of DNA replication of the broad host range plasmid RK2. J Biol Chem. 1997 Aug 8;272(32):20173-8. PMID:9242693
  2. ↑ Riber L, Lobner-Olesen A. Coordinated replication and sequestration of oriC and dnaA are required for maintaining controlled once-per-cell-cycle initiation in Escherichia coli. J Bacteriol. 2005 Aug;187(16):5605-13. PMID:16077105 doi:http://dx.doi.org/10.1128/JB.187.16.5605-5613.2005
  3. ↑ Keyamura K, Fujikawa N, Ishida T, Ozaki S, Su'etsugu M, Fujimitsu K, Kagawa W, Yokoyama S, Kurumizaka H, Katayama T. The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP DnaA-specific initiation complexes. Genes Dev. 2007 Aug 15;21(16):2083-99. PMID:17699754 doi:21/16/2083
  4. ↑ Konieczny I, Doran KS, Helinski DR, Blasina A. Role of TrfA and DnaA proteins in origin opening during initiation of DNA replication of the broad host range plasmid RK2. J Biol Chem. 1997 Aug 8;272(32):20173-8. PMID:9242693
  5. ↑ Riber L, Lobner-Olesen A. Coordinated replication and sequestration of oriC and dnaA are required for maintaining controlled once-per-cell-cycle initiation in Escherichia coli. J Bacteriol. 2005 Aug;187(16):5605-13. PMID:16077105 doi:http://dx.doi.org/10.1128/JB.187.16.5605-5613.2005
  6. ↑ Keyamura K, Fujikawa N, Ishida T, Ozaki S, Su'etsugu M, Fujimitsu K, Kagawa W, Yokoyama S, Kurumizaka H, Katayama T. The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP DnaA-specific initiation complexes. Genes Dev. 2007 Aug 15;21(16):2083-99. PMID:17699754 doi:21/16/2083
  7. ↑ 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. 2003 Apr 15;31(8):2077-86. PMID:12682358

Contents


PDB ID 1j1v

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