Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), trigonal form, to 2.7 Ang resolution

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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Plasmid replication initiator RepB forms a hexamer reminiscent of ring helicases and has mobile nuclease domains

Boer, D.R.Ruiz-Maso, J.A.Lopez-Blanco, J.R.Blanco, A.G.Vives-Llacer, M.Chacon, P.Uson, I.Gomis-Ruth, F.X.Espinosa, M.Llorca, O.del Solar, G.Coll, M.

(2009) EMBO J 28: 1666-1678

  • DOI: https://doi.org/10.1038/emboj.2009.125
  • Primary Citation of Related Structures:  
    3DKX, 3DKY

  • PubMed Abstract: 

    RepB initiates plasmid rolling-circle replication by binding to a triple 11-bp direct repeat (bind locus) and cleaving the DNA at a specific distant site located in a hairpin loop within the nic locus of the origin. The structure of native full-length RepB reveals a hexameric ring molecule, where each protomer has two domains. The origin-binding and catalytic domains show a three-layer alpha-beta-alpha sandwich fold. The active site is positioned at one of the faces of the beta-sheet and coordinates a Mn2+ ion at short distance from the essential nucleophilic Y99. The oligomerization domains (ODs), each consisting of four alpha-helices, together define a compact ring with a central channel, a feature found in ring helicases. The toroidal arrangement of RepB suggests that, similar to ring helicases, it encircles one of the DNA strands during replication to confer processivity to the replisome complex. The catalytic domains appear to be highly mobile with respect to ODs. This mobility may account for the adaptation of the protein to two distinct DNA recognition sites.

  • Organizational Affiliation

    Institute for Research in Biomedicine, Barcelona Science Park, Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Replication protein repB
A, B, C
210Streptococcus agalactiaeMutation(s): 0 
Gene Names: repB
Find proteins for P13921 (Streptococcus agalactiae)
Explore P13921 
Go to UniProtKB:  P13921
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13921
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.611α = 90
b = 85.611β = 90
c = 245.53γ = 120
Software Package:
Software NamePurpose
ProDCdata collection
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description