1J1V | pdb_00001j1v

Crystal structure of DnaA domainIV complexed with DnaAbox DNA

• PDB DOI: https://doi.org/10.2210/pdb1J1V/pdb
• NAKB: 1J1V

• Classification: replication/DNA
• Organism(s): Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-12-18 Released: 2003-04-22 
• Deposition Author(s): Fujikawa, N., Kurumizaka, H., Nureki, O., Terada, T., Shirouzu, M., Katayama, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Literature

Structural basis of replication origin recognition by the DnaA protein

Fujikawa, N., Kurumizaka, H., Nureki, O., Terada, T., Shirouzu, M., Katayama, T., Yokoyama, S.

(2003) Nucleic Acids Res 31: 2077-2086

• PubMed: 12682358 
• DOI: https://doi.org/10.1093/nar/gkg309
• Primary Citation Related Structures: 
  1J1V


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 
• RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.78 kDa 
• Atom Count: 1,422 
• Modeled Residue Count: 120 
• Deposited Residue Count: 120 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromosomal replication initiator protein dnaA	C [auth A]	94	Escherichia coli	Mutation(s): 2  Gene Names: DnaA EC: 3.6.4
UniProt
Find proteins for P03004 (Escherichia coli (strain K12)) Explore P03004  Go to UniProtKB:  P03004

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*TP*TP*AP*TP*CP*CP*AP*CP*AP*GP*G)-3'	A [auth B]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*TP*GP*TP*GP*GP*AP*TP*AP*AP*CP*A)-3'	B [auth C]	13	N/A

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	C [auth A]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.385	α = 90
b = 50.385	β = 90
c = 158.83	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SHARP	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-22 
Deposition Author(s): Fujikawa, N., Kurumizaka, H., Nureki, O., Terada, T., Shirouzu, M., Katayama, T., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2003-04-22
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-10-30
  Changes: Structure summary