4U87

Crystal structure of the Ba-soaked C2 crystal form of pMV158 replication initiator RepB (P3221 space group)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158.

Boer, D.R.Ruiz-Maso, J.A.Rueda, M.Petoukhov, M.V.Machon, C.Svergun, D.I.Orozco, M.Del Solar, G.Coll, M.

(2016) Sci Rep 6: 20915-20915

  • DOI: 10.1038/srep20915

  • PubMed Abstract: 
  • DNA replication initiation is a vital and tightly regulated step in all replicons and requires an initiator factor that specifically recognizes the DNA replication origin and starts replication. RepB from the promiscuous streptococcal plasmid pMV158 ...

    DNA replication initiation is a vital and tightly regulated step in all replicons and requires an initiator factor that specifically recognizes the DNA replication origin and starts replication. RepB from the promiscuous streptococcal plasmid pMV158 is a hexameric ring protein evolutionary related to viral initiators. Here we explore the conformational plasticity of the RepB hexamer by i) SAXS, ii) sedimentation experiments, iii) molecular simulations and iv) X-ray crystallography. Combining these techniques, we derive an estimate of the conformational ensemble in solution showing that the C-terminal oligomerisation domains of the protein form a rigid cylindrical scaffold to which the N-terminal DNA-binding/catalytic domains are attached as highly flexible appendages, featuring multiple orientations. In addition, we show that the hinge region connecting both domains plays a pivotal role in the observed plasticity. Sequence comparisons and a literature survey show that this hinge region could exists in other initiators, suggesting that it is a common, crucial structural element for DNA binding and manipulation.


    Organizational Affiliation

    Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Replication protein RepB
A, B, C
210Streptococcus agalactiaeMutation(s): 0 
Gene Names: repB
Find proteins for P13921 (Streptococcus agalactiae)
Go to UniProtKB:  P13921
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BA
Query on BA

Download SDF File 
Download CCD File 
B, C
BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.800α = 90.00
b = 85.800β = 90.00
c = 246.160γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministerio de Ciencia e InnovacionSpainBFU2008-02372/BMC
Ministerio de Ciencia e InnovacionSpainBFU2011-22588
Generalitat de CatalunyaSpainSGR2009-1309
European UnionSILVER, No. 260644

Revision History 

  • Version 1.0: 2015-08-26
    Type: Initial release
  • Version 1.1: 2016-02-24
    Type: Database references