PDBsum entry 3bos

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protein ligands metals Protein-protein interface(s) links
Hydrolase regulator,DNA binding protein PDB id
Protein chains
230 a.a. *
CDP ×2
EDO ×14
_MG ×2
Waters ×554
* Residue conservation analysis
PDB id:
Name: Hydrolase regulator,DNA binding protein
Title: Crystal structure of a putative DNA replication regulator hd (sama_1916) from shewanella amazonensis sb2b at 1.75 a reso
Structure: Putative DNA replication factor. Chain: a, b. Engineered: yes
Source: Shewanella amazonensis. Organism_taxid: 326297. Strain: sb2b. Atcc: baa-1098. Gene: yp_927791.1, sama_1916. Expressed in: escherichia coli. Expression_system_taxid: 562.
1.75Å     R-factor:   0.168     R-free:   0.201
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
Q.Xu et al. (2009). A structural basis for the regulatory inactivation of DnaA. J Mol Biol, 385, 368-380. PubMed id: 19000695 DOI: 10.1016/j.jmb.2008.10.059
17-Dec-07     Release date:   15-Jan-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
A1S6W5  (A1S6W5_SHEAM) -  Regulatory inactivation of DnaA Hda protein
241 a.a.
230 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA replication   2 terms 
  Biochemical function     nucleotide binding     1 term  


DOI no: 10.1016/j.jmb.2008.10.059 J Mol Biol 385:368-380 (2009)
PubMed id: 19000695  
A structural basis for the regulatory inactivation of DnaA.
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, I.A.Wilson.
Regulatory inactivation of DnaA is dependent on Hda (homologous to DnaA), a protein homologous to the AAA+ (ATPases associated with diverse cellular activities) ATPase region of the replication initiator DnaA. When bound to the sliding clamp loaded onto duplex DNA, Hda can stimulate the transformation of active DnaA-ATP into inactive DnaA-ADP. The crystal structure of Hda from Shewanella amazonensis SB2B at 1.75 A resolution reveals that Hda resembles typical AAA+ ATPases. The arrangement of the two subdomains in Hda (residues 1-174 and 175-241) differs dramatically from that of DnaA. A CDP molecule anchors the Hda domains in a conformation that promotes dimer formation. The Hda dimer adopts a novel oligomeric assembly for AAA+ proteins in which the arginine finger, crucial for ATP hydrolysis, is fully exposed and available to hydrolyze DnaA-ATP through a typical AAA+ type of mechanism. The sliding clamp binding motifs at the N-terminus of each Hda monomer are partially buried and combine to form an antiparallel beta-sheet at the dimer interface. The inaccessibility of the clamp binding motifs in the CDP-bound structure of Hda suggests that conformational changes are required for Hda to form a functional complex with the clamp. Thus, the CDP-bound Hda dimer likely represents an inactive form of Hda.
  Selected figure(s)  
Figure 2.
Fig. 2. The Hda dimer. (a) The two monomers are shown in orange and green. The residues that are involved in dimer formation are shown in blue in one monomer. The two arginine fingers (Arg161) in the dimer are shown as red sticks. The bound nucleotides and magnesium ions are shown in sticks and spheres, respectively. (b) The surface representation shows the opposite side of the dimer in (a) (left). The right panel shows the Hda dimer colored by sequence conservation. The most conserved residues are shown in magenta, while the least conserved residues are in cyan.
Figure 8.
Fig. 8. Hypothetical models for DnaA–Hda interaction. (a) Putative interaction between the base domain of Hda (shown in ribbon representation) and DnaA. Domains III, IIIb, and IV of DnaA are shown as surfaces and in gray, magenta, and cyan, respectively. (b) The bipartite active site for ATP hydrolysis is formed by the conserved residues in the DnaA–Hda (white/green) heterodimeric complex shown in (a).
  The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2009, 385, 368-380) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20944226 A.E.Speers, and B.F.Cravatt (2010).
Ligands in crystal structures that aid in functional characterization.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1306-1308.  
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.  
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