5UBD

Crystal structure of the N-terminal domain (domain 1) of RctB, RctB-1-124-L48M


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators.

Orlova, N.Gerding, M.Ivashkiv, O.Olinares, P.D.B.Chait, B.T.Waldor, M.K.Jeruzalmi, D.

(2017) Nucleic Acids Res. 45: 3724-3737

  • DOI: 10.1093/nar/gkw1288
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The conserved DnaA-oriC system is used to initiate replication of primary chromosomes throughout the bacterial kingdom; however, bacteria with multipartite genomes evolved distinct systems to initiate replication of secondary chromosomes. In the chol ...

    The conserved DnaA-oriC system is used to initiate replication of primary chromosomes throughout the bacterial kingdom; however, bacteria with multipartite genomes evolved distinct systems to initiate replication of secondary chromosomes. In the cholera pathogen, Vibrio cholerae, and in related species, secondary chromosome replication requires the RctB initiator protein. Here, we show that RctB consists of four domains. The structure of its central two domains resembles that of several plasmid replication initiators. RctB contains at least three DNA binding winged-helix-turn-helix motifs, and mutations within any of these severely compromise biological activity. In the structure, RctB adopts a head-to-head dimeric configuration that likely reflects the arrangement in solution. Therefore, major structural reorganization likely accompanies complex formation on the head-to-tail array of binding sites in oriCII. Our findings support the hypothesis that the second Vibrionaceae chromosome arose from an ancestral plasmid, and that RctB may have evolved additional regulatory features.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RctB replication initiator protein
A, B
130Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)Mutation(s): 1 
Find proteins for Q9KNG2 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KNG2
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.214 
  • Space Group: P 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/413 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 32.451α = 97.46
b = 38.167β = 91.49
c = 63.042γ = 98.43
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHENIXmodel building
HKL-2000data scaling
AutoSolphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM084162

Revision History 

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 1.1: 2017-05-03
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence