3DKY

Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), tetragonal form, to 3.6 Ang resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 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 ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replication protein repB
A, B, C, D, E, F
A, B, C, D, E, F
210Streptococcus agalactiaeMutation(s): 0 
Gene Names: repB
UniProt
Find proteins for P13921 (Streptococcus agalactiae)
Explore P13921 
Go to UniProtKB:  P13921
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13921
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.225 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.46α = 90
b = 91.46β = 90
c = 227.08γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
AMoREphasing
MOLREPphasing
PHENIXrefinement

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