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 

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This is version 1.1 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: 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 ...

    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

    the Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto 390-8621, Japan.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RepA, B128Escherichia coliMutation(s): 0 
Gene Names: repBvCmsNSP006_05755
Find proteins for Q06B24 (Escherichia coli)
Explore Q06B24 
Go to UniProtKB:  Q06B24
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganismImage
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, E23N/A
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
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, F23N/A
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

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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