3VW4

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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 Biol Chem 290: 3601-3611

  • DOI: https://doi.org/10.1074/jbc.M114.595645
  • Primary Citation of 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.

    • Organizational Affiliation: 

    From the Structural Biology Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan, hitou@nig.ac.jp.


Macromolecules

Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rep
A, B
128Escherichia coliMutation(s): 0 
Gene Names: rep
UniProt
Find proteins for Q06B24 (Escherichia coli)
Explore Q06B24 
Go to UniProtKB:  Q06B24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06B24
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
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
23N/A
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 3
MoleculeChains LengthOrganismImage
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
23N/A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.662α = 90
b = 61.824β = 90
c = 273.508γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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