6GYG

X-ray structure of the apo form of the establishement gene regulator Reg576 of the G+ plasmid p576


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Novel regulatory mechanism of establishment genes of conjugative plasmids.

Val-Calvo, J.Luque-Ortega, J.R.Crespo, I.Miguel-Arribas, A.Abia, D.Sanchez-Hevia, D.L.Serrano, E.Gago-Cordoba, C.Ares, S.Alfonso, C.Rojo, F.Wu, L.J.Boer, D.R.Meijer, W.J.J.

(2018) Nucleic Acids Res 46: 11910-11926

  • DOI: https://doi.org/10.1093/nar/gky996
  • Primary Citation of Related Structures:  
    6GYG

  • PubMed Abstract: 

    The principal route for dissemination of antibiotic resistance genes is conjugation by which a conjugative DNA element is transferred from a donor to a recipient cell. Conjugative elements contain genes that are important for their establishment in the new host, for instance by counteracting the host defense mechanisms acting against incoming foreign DNA. Little is known about these establishment genes and how they are regulated. Here, we deciphered the regulation mechanism of possible establishment genes of plasmid p576 from the Gram-positive bacterium Bacillus pumilus. Unlike the ssDNA promoters described for some conjugative plasmids, the four promoters of these p576 genes are repressed by a repressor protein, which we named Reg576. Reg576 also regulates its own expression. After transfer of the DNA, these genes are de-repressed for a period of time until sufficient Reg576 is synthesized to repress the promoters again. Complementary in vivo and in vitro analyses showed that different operator configurations in the promoter regions of these genes lead to different responses to Reg576. Each operator is bound with extreme cooperativity by two Reg576-dimers. The X-ray structure revealed that Reg576 has a Ribbon-Helix-Helix core and provided important insights into the high cooperativity of DNA recognition.


  • Organizational Affiliation

    Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription regulator Reg576
A, B
70Bacillus altitudinisMutation(s): 0 
Gene Names: ABW03_19300
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.278α = 90
b = 44.278β = 90
c = 141.166γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
AutoPROCdata scaling
Arcimboldophasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-77883-C2-2-P

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-11-28
    Changes: Data collection, Database references
  • Version 1.2: 2018-12-26
    Changes: Data collection, Database references
  • Version 1.3: 2019-07-10
    Changes: Data collection, Structure summary
  • Version 1.4: 2019-10-16
    Changes: Data collection, Structure summary