PDBsum entry 2z4r

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protein ligands metals Protein-protein interface(s) links
DNA binding protein PDB id
Protein chains
240 a.a. *
ADP ×3
_MG ×3
Waters ×4
* Residue conservation analysis
PDB id:
Name: DNA binding protein
Title: Crystal structure of domain iii from the thermotoga maritima replication initiation protein dnaa
Structure: Chromosomal replication initiator protein dnaa. Chain: a, b, c. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: dnaa. Expressed in: escherichia coli. Expression_system_taxid: 562.
3.05Å     R-factor:   0.231     R-free:   0.264
Authors: N.Fujikawa,S.Ozaki,W.Kagawa,S.-Y.Park,T.Katayama, H.Kurumizaka,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
S.Ozaki et al. (2008). A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin. J Biol Chem, 283, 8351-8362. PubMed id: 18216012 DOI: 10.1074/jbc.M708684200
25-Jun-07     Release date:   19-Feb-08    
Go to PROCHECK summary

Protein chains
No UniProt id for this chain
Struc: 240 a.a.
Key:    Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     regulation of DNA replication   3 terms 
  Biochemical function     nucleotide binding     6 terms  


DOI no: 10.1074/jbc.M708684200 J Biol Chem 283:8351-8362 (2008)
PubMed id: 18216012  
A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin.
S.Ozaki, H.Kawakami, K.Nakamura, N.Fujikawa, W.Kagawa, S.Y.Park, S.Yokoyama, H.Kurumizaka, T.Katayama.
Initiation of chromosomal replication and its cell cycle-coordinated regulation bear crucial and fundamental mechanisms in most cellular organisms. Escherichia coli DnaA protein forms a homomultimeric complex with the replication origin (oriC). ATP-DnaA multimers unwind the duplex within the oriC unwinding element (DUE). In this study, structural analyses suggested that several residues exposed in the central pore of the putative structure of DnaA multimers could be important for unwinding. Using mutation analyses, we found that, of these candidate residues, DnaA Val-211 and Arg-245 are prerequisites for initiation in vivo and in vitro. Whereas DnaA V211A and R245A proteins retained normal affinities for ATP/ADP and DNA and activity for the ATP-specific conformational change of the initiation complex in vitro, oriC complexes of these mutant proteins were inactive in DUE unwinding and in binding to the single-stranded DUE. Unlike oriC complexes including ADP-DnaA or the mutant DnaA, ATP-DnaA-oriC complexes specifically bound the upper strand of single-stranded DUE. Specific T-rich sequences within the strand were required for binding. The corresponding conserved residues of the DnaA ortholog in Thermotoga maritima, an ancient eubacterium, were also required for DUE unwinding, consistent with the idea that the mechanism and regulation for DUE unwinding can be evolutionarily conserved. These findings provide novel insights into mechanisms for pore-mediated origin unwinding, ATP/ADP-dependent regulation, and helicase loading of the initiation complex.
  Selected figure(s)  
Figure 1.
FIGURE 1. Structural models of DnaA oligomers and tmaDnaA mutants. A, crystal structure of tmaDnaA AAA^+ domain. The crystal structure of tmaDnaA AAA^+ domain bound to ADP was solved by molecular replacement. The A. aeolicus DnaA AAA^+ domain structure (22) was used as a search model. The subdomains IIIa and IIIb within AAA^+ domain are depicted as a ribbon model in different colors. B, structure comparison. Structures of AAA^+ domain of tmaDnaA and A. aeolicus DnaA, colored purple and cyan, respectively, were superimposed for subdomain IIIa. Structures are shown in a frame model. C, a ring model structure of tmaDnaA. A hexameric ring model was constructed using the determined structure of tmaDnaA AAA^+ domain. Each protomer is colored differently. The amino acid residues of Val-176, Met-179, Lys-180, Lys-209, and Gly-211 are exposed on the pore surface of the ring and are colored in red. For i–vi, see panel F. D, a spiral filament model structure of tmaDnaA. A spiral filament model was constructed using the structure of tmaDnaA AAA^+ domain, based on the spiral filament structure of the A. aeolicus DnaA AAA^+ domain (37). The model filament is shown viewed down the helical axis (top), as well as perpendicularly to the axis (bottom). Each protomer is colored differently. The amino acid residues described above are also exposed on the pore surface of the spiral filament and are colored red. E, the pore surfaces of the tmaDnaA ring and spiral filament. Three consecutive molecules of tmaDnaA within the ring (C) and spiral (D) models are shown. The amino acid residues described above and analyzed in this study are colored red and indicated. F, amino acid sequences, including the putative pore region of representative DnaA orthologs. i–vi correspond to E. coli DnaA residues of Val-211, Leu-214, Gln-215, Lys-223, Lys-243, and Arg-245, respectively. Residues corresponding to these are highlighted in yellow for hydrophobic residues or in purple for basic residues. The secondary structures of A. aeolicus DnaA (helix 3- 6) are also shown (22). Ecoli, Escherichia coli; Thema, Thermotoga maritima; Aquae, Aquifex aeolicus; Helph, Helicobacter pylori; Bacsu, Bacillus subtilis; Myctu, Mycobacterium tuberculosis; Chlmu, and Chlamydia muridarum. G, tma-oriC unwinding assay. The indicated amounts of wild-type (WT) or mutant tmaDnaA proteins were incubated at 48 °C for 10 min in the presence of pOZ14 (200 fmol), which bears the tma-oriC, followed by digestion with P1 nuclease and AlwNI.
Figure 10.
FIGURE 10. A model for open complex formation. A, a model of DnaA complexes and ATP-dependent conformational change. Light blue, ADP; light pink, ATP; yellow, H-motif; blue, B-motif; and red, arginine finger. B, possible mixed complexes. The initiation activity of the mixed complexes is indicated by ± (moderate) or + (active). Mixed complexes of wild-type DnaA with mutant DnaA of the B-motif (i), H-motif (ii), or arginine finger (iii) are shown. Light gray color indicates mutant DnaA protomers.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 8351-8362) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21227921 E.C.Dueber, A.Costa, J.E.Corn, S.D.Bell, and J.M.Berger (2011).
Molecular determinants of origin discrimination by Orc1 initiators in archaea.
  Nucleic Acids Res, 39, 3621-3631.  
21299647 G.Charbon, L.Riber, M.Cohen, O.Skovgaard, K.Fujimitsu, T.Katayama, and A.Løbner-Olesen (2011).
Suppressors of DnaA(ATP) imposed overinitiation in Escherichia coli.
  Mol Microbiol, 79, 914-928.  
21964332 K.E.Duderstadt, K.Chuang, and J.M.Berger (2011).
DNA stretching by bacterial initiators promotes replication origin opening.
  Nature, 478, 209-213.
PDB code: 3r8f
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.  
20511501 B.Koch, X.Ma, and A.Løbner-Olesen (2010).
Replication of Vibrio cholerae chromosome I in Escherichia coli: dependence on dam methylation.
  J Bacteriol, 192, 3903-3914.  
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.  
20017116 R.L.Rich, and D.G.Myszka (2010).
Grading the commercial optical biosensor literature-Class of 2008: 'The Mighty Binders'.
  J Mol Recognit, 23, 1.  
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.  
19833870 D.T.Miller, J.E.Grimwade, T.Betteridge, T.Rozgaja, J.J.Torgue, and A.C.Leonard (2009).
Bacterial origin recognition complexes direct assembly of higher-order DnaA oligomeric structures.
  Proc Natl Acad Sci U S A, 106, 18479-18484.  
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
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.  
19841480 K.Kurokawa, H.Mizumura, T.Takaki, Y.Ishii, N.Ichihashi, B.L.Lee, and K.Sekimizu (2009).
Rapid exchange of bound ADP on the Staphylococcus aureus replication initiation protein DnaA.
  J Biol Chem, 284, 34201-34210.  
19007419 L.Riber, K.Fujimitsu, T.Katayama, and A.Løbner-Olesen (2009).
Loss of Hda activity stimulates replication initiation from I-box, but not R4 mutant origins in Escherichia coli.
  Mol Microbiol, 71, 107-122.  
19089981 Q.Xu, C.L.Rife, D.Carlton, M.D.Miller, S.S.Krishna, M.A.Elsliger, P.Abdubek, T.Astakhova, H.J.Chiu, T.Clayton, L.Duan, J.Feuerhelm, S.K.Grzechnik, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, A.Kumar, D.McMullan, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, R.Reyes, H.van den Bedem, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
Crystal structure of a novel archaeal AAA+ ATPase SSO1545 from Sulfolobus solfataricus.
  Proteins, 74, 1041-1049.
PDB code: 2fna
19000695 Q.Xu, D.McMullan, P.Abdubek, T.Astakhova, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, M.A.Elsliger, J.Feuerhelm, J.Hale, G.W.Han, L.Jaroszewski, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, S.Sri Krishna, A.Kumar, D.Marciano, M.D.Miller, A.T.Morse, E.Nigoghossian, A.Nopakun, L.Okach, S.Oommachen, J.Paulsen, C.Puckett, R.Reyes, C.L.Rife, N.Sefcovic, C.Trame, H.van den Bedem, D.Weekes, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2009).
A structural basis for the regulatory inactivation of DnaA.
  J Mol Biol, 385, 368-380.
PDB code: 3bos
18974771 la Cueva-Mendez, and K.Labib (2008).
New insights into the chromosome cycle. Conference on the Replication & Segregation of Chromosomes.
  EMBO Rep, 9, 1177-1181.  
19013274 M.L.Mott, J.P.Erzberger, M.M.Coons, and J.M.Berger (2008).
Structural synergy and molecular crosstalk between bacterial helicase loaders and replication initiators.
  Cell, 135, 623-634.
PDB codes: 3ec2 3ecc
18685104 M.Rajewska, L.Kowalczyk, G.Konopa, and I.Konieczny (2008).
Specific mutations within the AT-rich region of a plasmid replication origin affect either origin opening or helicase loading.
  Proc Natl Acad Sci U S A, 105, 11134-11139.  
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.