PDBsum entry 2e0g

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protein links
Replication PDB id
Protein chain
107 a.a. *
* Residue conservation analysis
PDB id:
Name: Replication
Title: Dnaa n-terminal domain
Structure: Chromosomal replication initiator protein dnaa. Chain: a. Fragment: n-terminal domain. Engineered: yes
Source: Escherichia coli k12. Organism_taxid: 83333. Strain: k-12. Gene: dnaa. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
NMR struc: 25 models
Authors: Y.Abe,T.Katayama,T.Ueda,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
Y.Abe et al. (2007). Structure and function of DnaA N-terminal domains: specific sites and mechanisms in inter-DnaA interaction and in DnaB helicase loading on oriC. J Biol Chem, 282, 17816-17827. PubMed id: 17420252 DOI: 10.1074/jbc.M701841200
07-Oct-06     Release date:   01-May-07    
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Protein chain
Pfam   ArchSchema ?
P03004  (DNAA_ECOLI) -  Chromosomal replication initiator protein DnaA
467 a.a.
107 a.a.
Key:    PfamA domain  Secondary structure  CATH domain


DOI no: 10.1074/jbc.M701841200 J Biol Chem 282:17816-17827 (2007)
PubMed id: 17420252  
Structure and function of DnaA N-terminal domains: specific sites and mechanisms in inter-DnaA interaction and in DnaB helicase loading on oriC.
Y.Abe, T.Jo, Y.Matsuda, C.Matsunaga, T.Katayama, T.Ueda.
DnaA forms a homomultimeric complex with the origin of chromosomal replication (oriC) to unwind duplex DNA. The interaction of the DnaA N terminus with the DnaB helicase is crucial for the loading of DnaB onto the unwound region. Here, we determined the DnaA N terminus structure using NMR. This region (residues 1-108) consists of a rigid region (domain I) and a flexible region (domain II). Domain I has an alpha-alpha-beta-beta-alpha-beta motif, similar to that of the K homology (KH) domain, and has weak affinity for oriC single-stranded DNA, consistent with KH domain function. A hydrophobic surface carrying Trp-6 most likely forms the interface for domain I dimerization. Glu-21 is located on the opposite surface of domain I from the Trp-6 site and is crucial for DnaB helicase loading. These findings suggest a model for DnaA homomultimer formation and DnaB helicase loading on oriC.
  Selected figure(s)  
Figure 5.
FIGURE 5. The surface of the DnaA N terminus and the residues analyzed. The structure of the DnaA N terminus is shown as a space-filling model on which amino acids at sites of mutations are plotted. The color scheme for the mutants is as follows: red, acidic residues; blue, basic residues; green, hydrophobic residues; magenta, polar residues.
Figure 8.
FIGURE 8. Model of the mechanism of DnaA multimerization and interaction with DnaB. A, schematic presentation of DnaA. DnaA domains I–IV, Glu-21, the hydrophobic patch (HP) including Trp-6, and the second DnaB-binding site on the N terminus of domain III are indicated. B, schematic presentation of the structure of a DnaA multimer on oriC and interaction with DnaB. DnaA domain III forms a head-to-tail multimer. Domain I forms a head-to-head dimers, which causes rotation of the domain to expose Glu-21 on the surface of the DnaA multimer. Thus, a series of DnaB interaction sites form a DnaB entry gate. The unwound ssDNA region may be localized near the DnaB entry site.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 17816-17827) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21035377 A.C.Leonard, and J.E.Grimwade (2010).
Regulating DnaA complex assembly: it is time to fill the gaps.
  Curr Opin Microbiol, 13, 766-772.  
20130679 H.Kawakami, and T.Katayama (2010).
DnaA, ORC, and Cdc6: similarity beyond the domains of life and diversity.
  Biochem Cell Biol, 88, 49-62.  
20157337 T.Katayama, S.Ozaki, K.Keyamura, and K.Fujimitsu (2010).
Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC.
  Nat Rev Microbiol, 8, 163-170.  
19940251 G.Natrajan, M.F.Noirot-Gros, A.Zawilak-Pawlik, U.Kapp, and L.Terradot (2009).
The structure of a DnaA/HobA complex from Helicobacter pylori provides insight into regulation of DNA replication in bacteria.
  Proc Natl Acad Sci U S A, 106, 21115-21120.
PDB code: 2wp0
19170875 I.Flåtten, Morigen, and K.Skarstad (2009).
DnaA protein interacts with RNA polymerase and partially protects it from the effect of rifampicin.
  Mol Microbiol, 71, 1018-1030.  
19400775 K.Boeneman, S.Fossum, Y.Yang, N.Fingland, K.Skarstad, and E.Crooke (2009).
Escherichia coli DnaA forms helical structures along the longitudinal cell axis distinct from MreB filaments.
  Mol Microbiol, 72, 645-657.  
19401329 K.Fujimitsu, T.Senriuchi, and T.Katayama (2009).
Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA.
  Genes Dev, 23, 1221-1233.  
19632993 K.Keyamura, Y.Abe, M.Higashi, T.Ueda, and T.Katayama (2009).
DiaA dynamics are coupled with changes in initial origin complexes leading to helicase loading.
  J Biol Chem, 284, 25038-25050.  
19546317 K.L.Molt, V.A.Sutera, K.K.Moore, and S.T.Lovett (2009).
A role for nonessential domain II of initiator protein, DnaA, in replication control.
  Genetics, 183, 39-49.  
18502852 K.Fujimitsu, M.Su'etsugu, Y.Yamaguchi, K.Mazda, N.Fu, H.Kawakami, and T.Katayama (2008).
Modes of overinitiation, dnaA gene expression, and inhibition of cell division in a novel cold-sensitive hda mutant of Escherichia coli.
  J Bacteriol, 190, 5368-5381.  
18957591 S.Nozaki, and T.Ogawa (2008).
Determination of the minimum domain II size of Escherichia coli DnaA protein essential for cell viability.
  Microbiology, 154, 3379-3384.  
17699754 K.Keyamura, N.Fujikawa, T.Ishida, S.Ozaki, M.Su'etsugu, K.Fujimitsu, W.Kagawa, S.Yokoyama, H.Kurumizaka, and T.Katayama (2007).
The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP DnaA-specific initiation complexes.
  Genes Dev, 21, 2083-2099.
PDB code: 2yva
17680349 T.J.Lowery, J.G.Pelton, J.M.Chandonia, R.Kim, H.Yokota, and D.E.Wemmer (2007).
NMR structure of the N-terminal domain of the replication initiator protein DnaA.
  J Struct Funct Genomics, 8, 11-17.
PDB code: 2jmp
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.