3VW4 | pdb_00003vw4

Crystal structure of the DNA-binding domain of ColE2-P9 Rep in complex with the replication origin

• PDB DOI: https://doi.org/10.2210/pdb3VW4/pdb
• NAKB: 3VW4

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-31 Released: 2013-07-31 
• Deposition Author(s): Itou, H., Yagura, M., Itoh, T., Shirakihara, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.262 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Structural Basis for Replication Origin Unwinding by An Initiator-Primase of Plasmid ColE2-P9: Duplex DNA Unwinding by A Single Protein

Itou, H., Yagura, M., Shirakihara, Y., Itoh, T.

(2015) J Biological Chem 290: 3601-3611

• PubMed: 25538245 
• DOI: https://doi.org/10.1074/jbc.M114.595645
• Primary Citation Related Structures: 
  3VW4


• PubMed Abstract: 
  

  Duplex DNA is generally unwound by protein oligomers prior to replication. The Rep protein of plasmid ColE2-P9 (34 kDa) is an essential initiator for plasmid DNA replication. This protein binds the replication origin (Ori) in a sequence-specific manner as a monomer and unwinds DNA. Here we present the crystal structure of the DNA-binding domain of Rep (E2Rep-DBD) in complex with Ori DNA. The structure unveils the basis for Ori-specific recognition by the E2Rep-DBD and also reveals that it unwinds DNA by the concerted actions of its three contiguous structural modules. The structure also shows that the functionally unknown PriCT domain, which forms a compact module, plays a central role in DNA unwinding. The conservation of the PriCT domain in the C termini of some archaeo-eukaryotic primases indicates that it probably plays a similar role in these proteins. Thus, this is the first report providing the structural basis for the functional importance of the conserved PriCT domain and also reveals a novel mechanism for DNA unwinding by a single protein.

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Organizational Affiliation: 
• From the Structural Biology Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan, [e-mail].
the Department of Cell Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan, and.
From the Structural Biology Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.
the Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.17 kDa 
• Atom Count: 3,689 
• Modeled Residue Count: 323 
• Deposited Residue Count: 348 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rep	A, B	128	Escherichia coli	Mutation(s): 0  Gene Names: rep
UniProt
Find proteins for Q06B24 (Escherichia coli) Explore Q06B24  Go to UniProtKB:  Q06B24

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*TP*GP*AP*GP*AP*CP*CP*AP*GP*AP*TP*AP*AP*GP*CP*CP*TP*TP*AP*TP*C)-3')	C, E	23	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*TP*AP*AP*GP*GP*CP*TP*TP*AP*TP*CP*TP*GP*GP*TP*CP*TP*CP*AP*TP*T)-3')	D, F	23	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.262 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.662	α = 90
b = 61.824	β = 90
c = 273.508	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-31 
Deposition Author(s): Itou, H., Yagura, M., Itoh, T., Shirakihara, Y.

Revision History  

• Version 1.0: 2013-07-31
  Type: Initial release
  
• Version 1.1: 2015-01-28
  Changes: Database references
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations