Skip to main content
Article thumbnail
Location of Repository

Structure of the N-terminal oligomerization domain of DnaD reveals a unique tetramerization motif and provides insights into scaffold formation

By S. Schneider, Wenke Zhang, Panos Soultanas and Max Paoli


DnaD is a primosomal protein that remodels supercoiled plasmids. It binds to supercoiled forms and converts them to open forms without nicking. During this remodeling process, all the writhe is converted to twist and the plasmids are held around the periphery of large scaffolds made up of DnaD molecules. This DNA-remodeling function is the sum of a scaffold-forming activity on the N-terminal domain and a DNA-dependent oligomerization activity on the C-terminal domain. We have determined the crystal structure of the scaffold-forming N-terminal domain, which reveals a winged-helix architecture, with additional structural elements extending from both N- and C-termini. Four monomers form dimers that join into a tetramer. The N-terminal extension mediates dimerization and tetramerization, with extensive interactions and distinct interfaces. The wings and helices of the winged-helix domains remain exposed on the surface of the tetramer. Structure-guided mutagenesis and atomic force microscopy imaging indicate that these elements, together with the C-terminal extension, are involved in scaffold formation. Based upon our data, we propose a model for the DnaD-mediated scaffold formation

Year: 2008
OAI identifier:
Provided by: Nottingham ePrints

Suggested articles


  1. (2002). A functional interaction between the putative primosomal protein DnaI and the main replicative DNA helicase DnaB in Bacillus.
  2. (2004). A poxvirus protein forms a complex with left-handed Z-DNA: crystal structure of a Yatapoxvirus Zalpha bound to DNA.
  3. (2003). A two-protein strategy for the functional loading of a cellular replicative DNA helicase.
  4. (1993). Accommodating sequence changes in beta-hairpins in proteins.
  5. (2002). Bacillus subtilis and Its Closest Relatives; Chromosome replication and segregation.
  6. (1997). Complexes at the replication of B. subtilis with homologous and heterologous DnaA protein.
  7. (2004). Control of DNA replication initiation by recruitment of an essential initiation protein to the membrane of Bacillus subtilis.
  8. (2000). Control of initiation of sporulation by replication initiation genes in Bacillus subtilis.
  9. (2004). Coot: model-building tools for molecular graphics.
  10. (1999). Crystal structure of the Zalpha domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA.
  11. (2005). Crystal structures of the BlaI repressor from Staphylococcus aureus and its complex with DNA: insights into transcriptional regulation of the bla and mec operons.
  12. (2007). Crystallization and X-ray diffraction analysis of the DNA-remodelling protein DnaD from Bacillus subtilis. Acta Crystallographica Section F F63,
  13. (2006). DnaA: controlling the initiation of bacterial DNA replication and more.
  14. (2001). DnaB, DnaD and DnaI proteins are components of the Bacillus restart primosome.
  15. (2001). DnaD protein of Bacillus subtilis interacts with DnaA, the initiator protein of replication.
  16. (1999). Dynamic DNA contacts observed in the NMR structure of winged helix protein-DNA complex.
  17. (2001). Early steps of Bacillus subtilis primosome assembly.
  18. (2004). ESCRT-II, an endosome-associated complex required for protein sorting: crystal structure and interactions with ESCRT-III and membranes.
  19. (1998). Formation and stability of beta-hairpin structures in polypeptides.
  20. (2005). Functional interplay between the Bacillus subtilis DnaD and DnaB proteins essential for initiation and re-initiation of DNA replication.
  21. (1999). Functions of histone-like proteins in the initiation of DNA replication at oriC of E.
  22. (2006). Helicase binding to DnaI exposes a cryptic DNA-binding site during helicase loading Bacillus subtilis.
  23. (2004). Identification of temperature sensitive dnaD mutants in Staphylococcus aureus that are defective in chromosomal DNA replication.
  24. (1995). LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. doi
  25. (2007). Loading a ring: Structure of the Bacillus subtilis DnaB protein, a co-loader of the replicative helicase.
  26. (2003). Macromolecular TLS refinement in REFMAC at moderate resolutions.
  27. (2004). MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.
  28. (1987). Nucleotide sequence of Bacillus subtilis dnaB: a gene essential for DNA replication initiation and membrane attachment.
  29. (1995). Nucleotide sequence of the Bacillus subtilis dnaD gene.
  30. (1992). Opening of the replication origin of E. coli by DnaA protein with HU or IHF.
  31. (2006). Origin inactivation in bacterial DNA replication control.
  32. (1991). PCR-A practical approach.,
  33. (1995). Primosome assembly site in Bacillus subtilis.
  34. (1992). Prokaryotic DNA replication.
  35. (1996). PROMOTIF—a program to identify and analyze structural motifs in proteins.
  36. (1984). Protein HU in the enzymatic replication of the chromosomal origin of E. coli.
  37. (1993). Protein structure comparison by alignment of distance matrices.
  38. (2007). Proteins: Structure, Function, and Bioinformatics (in press) DnaD N-Domain native Se-Met peak Se-Met remote Data collection Spacegroup P 3121 P 3121 P 3121 Unit cell parameters (Å) a, b, c (Å)
  39. (1997). Refinement of macromolecular structures by the maximum-likelihood method.
  40. (2000). Role of PriA in replication fork reactivation in Escherichia coli.
  41. (2001). Roles of E. coli histone-like protein HU in DNA replication: HU suppresses the thermosensitivity of dnaA46ts.
  42. (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. doi
  43. (1990). Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three dimensional structure.
  44. (2000). Structure and function of hexameric helicases.
  45. (2004). Structure of the ESCRT-II endosomal trafficking complex.
  46. (2000). Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding.
  47. (2003). Structure validation by Calpha geometry and Cbeta deviation.
  48. (2002). Substructure solution with SHELXD.
  49. (2005). The Bacillus subtilis DnaD and DnaB proteins exhibit different DNA remodelling activities.
  50. (2004). The Bacillus subtilis DnaD protein: a putative link between DNA remodelling and initiation of DNA replication.
  51. (2006). The Bacillus subtilis primosomal protein DnaD untwists supercoiled DNA.
  52. (2006). The DNA-remodelling activity of DnaD is the sum of oligomerization and DNA-binding activities on separate domains.
  53. (1996). The nucleoid protein H-NS facilitates chromosome DNA replication in E. coli dnaA mutants.
  54. (2002). The PyMol molecular graphics system. DeLano Scientific,
  55. (2004). TOPS: an enhanced database of protein structural topology.

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.